From d880265afb222bd9ac0449b1584020b97ddd5418 Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Mon, 10 Feb 2020 10:50:30 +0000 Subject: [PATCH 01/11] fix URLs --- .Rbuildignore | 2 +- README.Rmd | 7 ++- README.md | 126 +++++++++++++++++++++++++------------------------- 3 files changed, 66 insertions(+), 69 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index a658b72..57a8f49 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,4 +8,4 @@ ^\.travis\.yml$ ^appveyor\.yml$ ^codecov\.yml$ - +^docs$ diff --git a/README.Rmd b/README.Rmd index 7c681ad..b165e83 100644 --- a/README.Rmd +++ b/README.Rmd @@ -44,7 +44,7 @@ There are four MSF outbreak dictionaries available in {epidict}: - Measles/Rubella ("measles") - Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("ajs") -> You can read more about the outbreak dictionaries at +> You can read more about the outbreak dictionaries at The dictionary can be obtained via the `msf_dict()` function, which specifies a dictionary that describes recorded variables (`data_element_shortname`) in rows @@ -64,7 +64,7 @@ In addition, there are three MSF survey dictionaries available: - Malnutrition ("nutrition") - Vaccination Coverage ("vaccination") -> You can read more about the survey dictionaries at +> You can read more about the survey dictionaries at These are accessible via `msf_dict_survey()` where the variables are in `column_name` and are often labeled by question number. @@ -88,10 +88,9 @@ gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") ## Cleaning data with the dictionaries -You can use the dictionaries to clean the data via the [{matchmaker}](https://repidemicsconsortium.org/matchmaker) package (currently on GitHub): +You can use the dictionaries to clean the data via the [{matchmaker}](https://www.repidemicsconsortium.org/matchmaker) package: ```{r lookup, message = FALSE} -# remotes::install_github("reconhub/matchmaker@*release") library("matchmaker") library("dplyr") diff --git a/README.md b/README.md index c8e90ab..91ef081 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ There are four MSF outbreak dictionaries available in {epidict}: - Acute Jaundice Syndrome (often suspected to be Hepatitis E) (“ajs”) > You can read more about the outbreak dictionaries at -> +> The dictionary can be obtained via the `msf_dict()` function, which specifies a dictionary that describes recorded variables @@ -131,7 +131,7 @@ In addition, there are three MSF survey dictionaries available: - Vaccination Coverage (“vaccination”) > You can read more about the survey dictionaries at -> +> These are accessible via `msf_dict_survey()` where the variables are in `column_name` and are often labeled by question number. @@ -196,16 +196,16 @@ gen_data("Measles", varnames = "data_element_shortname", numcases = 100, org = " #> # A tibble: 100 x 52 #> seizure_episodes trimester croup dehydration_lev… residential_sta… #> -#> 1 1 0 SO 5 -#> 2 0 1 UN 2 -#> 3 1 1 SO 3 -#> 4 1 1 SE 4 -#> 5 1 0 SE 3 -#> 6 1 1 SO 2 -#> 7 0 1 UN 2 -#> 8 0 1 0 UN 4 -#> 9 1 1 UN 5 -#> 10 1 0 SO 5 +#> 1 0 0 UN 3 +#> 2 1 0 NO 4 +#> 3 1 1 SO 1 +#> 4 0 1 SE 1 +#> 5 1 3 1 NO 5 +#> 6 1 1 UN 4 +#> 7 0 0 SO 1 +#> 8 0 1 SO 5 +#> 9 1 0 SE 1 +#> 10 0 0 NO 3 #> # … with 90 more rows, and 47 more variables: #> # previously_vaccinated , patient_origin_free_text , #> # age_days , msf_involvement , @@ -232,16 +232,16 @@ gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") #> # A tibble: 100 x 41 #> q77_what_is_the… health_district village q14_hh_no q15_home #> -#> 1 3 District B Villag… 5 No -#> 2 1 District A Villag… 4 Yes -#> 3 2 District A Villag… 6 Yes -#> 4 3 District B Villag… 4 No -#> 5 3 District B Villag… 3 Yes -#> 6 2 District A Villag… 2 No -#> 7 2 District A Villag… 4 Yes +#> 1 1 District A Villag… 6 Yes +#> 2 3 District B Villag… 2 No +#> 3 2 District A Villag… 1 No +#> 4 2 District A Villag… 1 No +#> 5 3 District B Villag… 2 No +#> 6 4 District B Villag… 4 No +#> 7 4 District B Villag… 4 No #> 8 1 District A Villag… 3 Yes -#> 9 4 District B Villag… 3 Yes -#> 10 4 District B Villag… 5 No +#> 9 4 District B Villag… 1 No +#> 10 4 District B Villag… 2 Yes #> # … with 90 more rows, and 36 more variables: q16_occupant_age , #> # q58_consent , q75_caretaker , q76_caretaker_other , #> # q65_consent_no_reason , q66_consent_no_reason_other , @@ -264,11 +264,9 @@ gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") ## Cleaning data with the dictionaries You can use the dictionaries to clean the data via the -[{matchmaker}](https://repidemicsconsortium.org/matchmaker) package -(currently on GitHub): +[{matchmaker}](https://www.repidemicsconsortium.org/matchmaker) package: ``` r -# remotes::install_github("reconhub/matchmaker@*release") library("matchmaker") library("dplyr") @@ -281,26 +279,26 @@ print(dat) #> # A tibble: 20 x 45 #> trimester exit_status treatment_facil… dehydration_lev… #> -#> 1 DH NA SE -#> 2 TR NA SE -#> 3 DH NA NO -#> 4 DD NA UN -#> 5 TR NA NO -#> 6 TR NA NO -#> 7 DOA NA NO -#> 8 AD NA SO -#> 9 AD NA NO -#> 10 LA NA SO -#> 11 TR NA NO -#> 12 AD NA UN -#> 13 DD NA SO -#> 14 DOA NA UN -#> 15 LA NA UN -#> 16 DD NA SO -#> 17 DD NA SE -#> 18 DD NA UN -#> 19 AD NA SE -#> 20 1 LA NA SO +#> 1 AD NA NO +#> 2 DOA NA SO +#> 3 DOA NA SO +#> 4 AD NA UN +#> 5 DOA NA SO +#> 6 AD NA SE +#> 7 DD NA UN +#> 8 DH NA UN +#> 9 DH NA SE +#> 10 DH NA SE +#> 11 DH NA NO +#> 12 DOA NA SO +#> 13 DOA NA NO +#> 14 DH NA SE +#> 15 DOA NA NO +#> 16 DOA NA NO +#> 17 TR NA SE +#> 18 LA NA UN +#> 19 TR NA SO +#> 20 DOA NA SE #> # … with 41 more variables: comments_on_lab_results , #> # fluids_treatment_plan , time_to_death , #> # malaria_rdt_at_admission , previously_vaccinated , @@ -367,26 +365,26 @@ print(dat_clean) #> # A tibble: 20 x 45 #> trimester exit_status treatment_facil… dehydration_lev… #> -#> 1 Discharged… NA Severe -#> 2 Transferre… NA Severe -#> 3 Discharged… NA None -#> 4 Dead in fa… NA Unknown -#> 5 Transferre… NA None -#> 6 Transferre… NA None -#> 7 Dead on ar… NA None -#> 8 Transferre… NA Some -#> 9 Transferre… NA None -#> 10 Left again… NA Some -#> 11 Transferre… NA None -#> 12 Transferre… NA Unknown -#> 13 Dead in fa… NA Some -#> 14 Dead on ar… NA Unknown -#> 15 Left again… NA Unknown -#> 16 Dead in fa… NA Some -#> 17 Dead in fa… NA Severe -#> 18 Dead in fa… NA Unknown -#> 19 Transferre… NA Severe -#> 20 1st trim… Left again… NA Some +#> 1 Transferre… NA None +#> 2 Dead on ar… NA Some +#> 3 Dead on ar… NA Some +#> 4 Transferre… NA Unknown +#> 5 Dead on ar… NA Some +#> 6 Transferre… NA Severe +#> 7 Dead in fa… NA Unknown +#> 8 Discharged… NA Unknown +#> 9 Discharged… NA Severe +#> 10 Discharged… NA Severe +#> 11 Discharged… NA None +#> 12 Dead on ar… NA Some +#> 13 Dead on ar… NA None +#> 14 Discharged… NA Severe +#> 15 Dead on ar… NA None +#> 16 Dead on ar… NA None +#> 17 Transferre… NA Severe +#> 18 Left again… NA Unknown +#> 19 Transferre… NA Some +#> 20 Dead on ar… NA Severe #> # … with 41 more variables: comments_on_lab_results , #> # fluids_treatment_plan , time_to_death , #> # malaria_rdt_at_admission , previously_vaccinated , From a063d337100239b402ab83ca24ee2251ee6b6fbb Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Mon, 10 Feb 2020 10:57:30 +0000 Subject: [PATCH 02/11] add github URL --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 305e88a..dffdc17 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,7 @@ Description: The 'R4EPIs' project seeks to provide Measles, Meningitis) and three surveys (Retrospective mortality and access to care, Malnutrition, and Vaccination coverage). In addition, a data generator from these dictionaries is provided. -URL: https://r4epis.netlify.com, https://github.com/R4EPI/epidict +URL: https://r4epis.netlify.com, https://github.com/R4EPI/epidict, https://r4epi.github.io/epidict License: GPL-3 Imports: tibble, From 76bb2f01682b476a760c41f08a357849bb4d68be Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Mon, 10 Feb 2020 11:30:32 +0000 Subject: [PATCH 03/11] Increment version number --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index dffdc17..c49e588 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: epidict Title: Standardized Data Dictionaries for the 'R4EPIs' Project -Version: 0.0.0.9000 +Version: 0.1.0 Authors@R: c( person(given = "Zhian N.", family = "Kamvar", diff --git a/NEWS.md b/NEWS.md index cef8d05..e329d62 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# epidict 0.1.0 + +* Fix broken URLs in README +* Release to CRAN + # epidict 0.0.0.9000 * Added a `NEWS.md` file to track changes to the package. From 41aea3548b6078e5eda2013fff00075bfd58a823 Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Mon, 10 Feb 2020 17:07:46 +0000 Subject: [PATCH 04/11] begin on vignette idea... may not work out --- .gitignore | 1 + DESCRIPTION | 6 +- README.Rmd | 103 +------------------------- man/epidict-package.Rd | 1 + man/rmdhunks/introduction.Rmd | 132 ++++++++++++++++++++++++++++++++++ vignettes/.gitignore | 2 + vignettes/Measles.Rmd | 42 +++++++++++ vignettes/intro.Rmd | 19 +++++ 8 files changed, 203 insertions(+), 103 deletions(-) create mode 100644 man/rmdhunks/introduction.Rmd create mode 100644 vignettes/.gitignore create mode 100644 vignettes/Measles.Rmd create mode 100644 vignettes/intro.Rmd diff --git a/.gitignore b/.gitignore index f6dd9ad..63d237c 100644 --- a/.gitignore +++ b/.gitignore @@ -40,3 +40,4 @@ vignettes/*.pdf # README html preview README.html +inst/doc diff --git a/DESCRIPTION b/DESCRIPTION index c49e588..fc3722f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,8 +36,12 @@ Imports: Suggests: testthat (>= 2.1.0), matchmaker, - covr + covr, + knitr, + rmarkdown, + DT Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.0.2 +VignetteBuilder: knitr diff --git a/README.Rmd b/README.Rmd index b165e83..9755d3a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,108 +22,7 @@ knitr::opts_chunk$set( [![Codecov test coverage](https://codecov.io/gh/R4EPI/epidict/branch/master/graph/badge.svg)](https://codecov.io/gh/R4EPI/epidict?branch=master) -The goal of {epidict} is to provide standardized data dictionaries for the MSF -R4EPIs project. -## Installation - -To install a stable version of {epidict}, please use the R4epis repository: - -```r -# install.packages("drat") -drat::addRepo("R4EPI") -install.packages("epidict") -``` - -## Accessing dictionaries - -There are four MSF outbreak dictionaries available in {epidict}: - - - Cholera/Acute watery diarrhea ("cholera") - - Meningitis - - Measles/Rubella ("measles") - - Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("ajs") - -> You can read more about the outbreak dictionaries at - -The dictionary can be obtained via the `msf_dict()` function, which specifies a -dictionary that describes recorded variables (`data_element_shortname`) in rows -and their possible options (if categorical): - -```{r outbreak} -library("epidict") -msf_dict("Measles", compact = FALSE) -msf_dict("AJS", compact = FALSE) -msf_dict("Cholera", compact = FALSE) -msf_dict("Meningitis", compact = FALSE) -``` - -In addition, there are three MSF survey dictionaries available: - - - Retrospective mortality and access to care ("mortality") - - Malnutrition ("nutrition") - - Vaccination Coverage ("vaccination") - -> You can read more about the survey dictionaries at - -These are accessible via `msf_dict_survey()` where the variables are in -`column_name` and are often labeled by question number. - -```{r survey} -msf_dict_survey("Mortality", compact = FALSE) -msf_dict_survey("Nutrition", compact = FALSE) -msf_dict_survey("Vaccination", compact = FALSE) -``` - -## Generating data - -The {epidict} package has a function for generating data that's called -`gen_data()`, which takes three arguments: The dictionary, which column -describes the variable names, and how many rows are needed in the output. - -```{r gendata} -gen_data("Measles", varnames = "data_element_shortname", numcases = 100, org = "MSF") -gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") -``` - -## Cleaning data with the dictionaries - -You can use the dictionaries to clean the data via the [{matchmaker}](https://www.repidemicsconsortium.org/matchmaker) package: - -```{r lookup, message = FALSE} -library("matchmaker") -library("dplyr") - -dat <- gen_data(dictionary = "Cholera", - varnames = "data_element_shortname", - numcases = 20, - org = "MSF" -) -print(dat) - -# We want the expanded dictionary, so we will select `compact = FALSE` -dict <- msf_dict(disease = "Cholera", - long = TRUE, - compact = FALSE, - tibble = TRUE -) -print(dict) - -# We can use linelist's clean_variable_spelling to translate the codes. First, -# we want to reorder the columns of the dictionary like so: -# -# - 1st column: option codes -# - 2nd column: translations -# - 3rd column: data column name -# - 4th column: order of options - -# Now we can use linelist to filter the data: -dat_clean <- matchmaker::match_df(dat, dict, - from = "option_code", - to = "option_name", - by = "data_element_shortname", - order = "option_order_in_set" -) -print(dat_clean) +```{r intro-hunk, child="man/rmdhunks/introduction.Rmd"} ``` diff --git a/man/epidict-package.Rd b/man/epidict-package.Rd index 95078b2..6e2d981 100644 --- a/man/epidict-package.Rd +++ b/man/epidict-package.Rd @@ -19,6 +19,7 @@ Useful links: \itemize{ \item \url{https://r4epis.netlify.com} \item \url{https://github.com/R4EPI/epidict} + \item \url{https://r4epi.github.io/epidict} } } diff --git a/man/rmdhunks/introduction.Rmd b/man/rmdhunks/introduction.Rmd new file mode 100644 index 0000000..8910c32 --- /dev/null +++ b/man/rmdhunks/introduction.Rmd @@ -0,0 +1,132 @@ +The goal of {epidict} is to provide standardized data dictionaries for the MSF +R4EPIs project. Learn more about R4EPIs at + +## Installation + +You can install {epidict} from CRAN: + +``` r +install.packages("epidict") +``` + +
+ +Click here for alternative installation options +If there is a bugfix or feature that is not yet on CRAN, you can install it via +the {drat} package: + + +You can install {epidict} from the R4EPI repository: + +```{r eval = FALSE} +# install.packages("drat") +drat::addRepo("R4EPI") +install.packages("epidict") +``` + +You can also install the in-development version from GitHub using the {remotes} +package (but there's no guarantee that it will be stable): + +```{r eval = FALSE} +# install.packages("remotes") +remotes::install_github("R4EPI/epidict") +``` + + + + +## Accessing dictionaries + +There are four MSF outbreak dictionaries available in {epidict}: + + - Cholera/Acute watery diarrhea ("cholera") + - Meningitis + - Measles/Rubella ("measles") + - Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("ajs") + +> You can read more about the outbreak dictionaries at + +The dictionary can be obtained via the `msf_dict()` function, which specifies a +dictionary that describes recorded variables (`data_element_shortname`) in rows +and their possible options (if categorical): + +```{r outbreak} +library("epidict") +msf_dict("Measles", compact = FALSE) +msf_dict("AJS", compact = FALSE) +msf_dict("Cholera", compact = FALSE) +msf_dict("Meningitis", compact = FALSE) +``` + +In addition, there are three MSF survey dictionaries available: + + - Retrospective mortality and access to care ("mortality") + - Malnutrition ("nutrition") + - Vaccination Coverage ("vaccination") + +> You can read more about the survey dictionaries at + +These are accessible via `msf_dict_survey()` where the variables are in +`column_name` and are often labeled by question number. + +```{r survey} +msf_dict_survey("Mortality", compact = FALSE) +msf_dict_survey("Nutrition", compact = FALSE) +msf_dict_survey("Vaccination", compact = FALSE) +``` + +## Generating data + +The {epidict} package has a function for generating data that's called +`gen_data()`, which takes three arguments: The dictionary, which column +describes the variable names, and how many rows are needed in the output. + +```{r gendata} +gen_data("Measles", varnames = "data_element_shortname", numcases = 100, org = "MSF") +gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") +``` + +## Cleaning data with the dictionaries + +You can use the dictionaries to clean the data via the [{matchmaker}](https://www.repidemicsconsortium.org/matchmaker) package: + +```{r lookup, message = FALSE} +library("matchmaker") +library("dplyr") + +dat <- gen_data(dictionary = "Cholera", + varnames = "data_element_shortname", + numcases = 20, + org = "MSF" +) +print(dat) + +# We want the expanded dictionary, so we will select `compact = FALSE` +dict <- msf_dict(disease = "Cholera", + long = TRUE, + compact = FALSE, + tibble = TRUE +) +print(dict) + +# We can use linelist's clean_variable_spelling to translate the codes. First, +# we want to reorder the columns of the dictionary like so: +# +# - 1st column: option codes +# - 2nd column: translations +# - 3rd column: data column name +# - 4th column: order of options + +# Now we can use linelist to filter the data: +dat_clean <- matchmaker::match_df(dat, dict, + from = "option_code", + to = "option_name", + by = "data_element_shortname", + order = "option_order_in_set" +) +print(dat_clean) +``` + diff --git a/vignettes/.gitignore b/vignettes/.gitignore new file mode 100644 index 0000000..097b241 --- /dev/null +++ b/vignettes/.gitignore @@ -0,0 +1,2 @@ +*.html +*.R diff --git a/vignettes/Measles.Rmd b/vignettes/Measles.Rmd new file mode 100644 index 0000000..72a8193 --- /dev/null +++ b/vignettes/Measles.Rmd @@ -0,0 +1,42 @@ +--- +title: "Measles dictionary" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Measles dictionary} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + echo = FALSE +) +``` + +# Variables in the dictionary + +The Measles dictionary contains definitions for `r nrow(epidict::msf_dict("Measles"))` variables: + +```{r measles, results="asis"} +library(epidict) +measles <- msf_dict("Measles") +names_desc <- measles[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +# Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r measles_values, results = "asis"} +meas <- tidyr::unnest(measles, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(meas) +``` + +# Exploring the data set + +You can explore the original data set with `browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict"))`, but treat it as read-only. + diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd new file mode 100644 index 0000000..6ea319f --- /dev/null +++ b/vignettes/intro.Rmd @@ -0,0 +1,19 @@ +--- +title: "Introduction to epidict" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Introduction to epidict} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +```{r intro-hunk, child="../man/rmdhunks/introduction.Rmd"} +``` + From 9a5eeba7f6f6f4f6fac311f4706655dba4cea40e Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Tue, 11 Feb 2020 10:40:07 +0000 Subject: [PATCH 05/11] update vignettes --- README.md | 259 ++++++++++++++++++---------------- man/rmdhunks/introduction.Rmd | 14 +- vignettes/Measles.Rmd | 42 ------ vignettes/Outbreaks.Rmd | 126 +++++++++++++++++ vignettes/Surveys.Rmd | 101 +++++++++++++ 5 files changed, 375 insertions(+), 167 deletions(-) delete mode 100644 vignettes/Measles.Rmd create mode 100644 vignettes/Outbreaks.Rmd create mode 100644 vignettes/Surveys.Rmd diff --git a/README.md b/README.md index 91ef081..8815a6c 100644 --- a/README.md +++ b/README.md @@ -18,12 +18,29 @@ coverage](https://codecov.io/gh/R4EPI/epidict/branch/master/graph/badge.svg)](ht The goal of {epidict} is to provide standardized data dictionaries for -the MSF R4EPIs project. +the MSF R4EPIs project. Learn more about R4EPIs at + ## Installation -To install a stable version of {epidict}, please use the R4epis -repository: +You can install {epidict} from CRAN: + +``` r +install.packages("epidict") +``` + +
+ + + +Click here for alternative +installation options If there is a bugfix or feature that is +not yet on CRAN, you can install it via the {drat} package: + +You can install {epidict} from the R4EPI repository: ``` r # install.packages("drat") @@ -31,6 +48,16 @@ drat::addRepo("R4EPI") install.packages("epidict") ``` +You can also install the in-development version from GitHub using the +{remotes} package (but there’s no guarantee that it will be stable): + +``` r +# install.packages("remotes") +remotes::install_github("R4EPI/epidict") +``` + + + ## Accessing dictionaries There are four MSF outbreak dictionaries available in {epidict}: @@ -50,78 +77,74 @@ categorical): ``` r library("epidict") -msf_dict("Measles", compact = FALSE) -#> # A tibble: 176 x 11 +msf_dict("Measles") +#> # A tibble: 52 x 8 #> data_element_uid data_element_na… data_element_sh… data_element_de… #> #> 1 DE_ESYM_012 esym_012_seizur… seizure_episodes Complication (S… -#> 2 DE_ESYM_012 esym_012_seizur… seizure_episodes Complication (S… -#> 3 DE_EGEN_013 egen_013_pregna… trimester If pregnant, tr… -#> 4 DE_EGEN_013 egen_013_pregna… trimester If pregnant, tr… -#> 5 DE_EGEN_013 egen_013_pregna… trimester If pregnant, tr… -#> 6 DE_ESYM_014 esym_014_croup croup Complication (C… -#> 7 DE_ESYM_014 esym_014_croup croup Complication (C… -#> 8 DE_ESYM_002 esym_002_dehydr… dehydration_lev… Dehydration bas… -#> 9 DE_ESYM_002 esym_002_dehydr… dehydration_lev… Dehydration bas… -#> 10 DE_ESYM_002 esym_002_dehydr… dehydration_lev… Dehydration bas… -#> # … with 166 more rows, and 7 more variables: +#> 2 DE_EGEN_013 egen_013_pregna… trimester If pregnant, tr… +#> 3 DE_ESYM_014 esym_014_croup croup Complication (C… +#> 4 DE_ESYM_002 esym_002_dehydr… dehydration_lev… Dehydration bas… +#> 5 DE_EGEN_030 egen_030_reside… residential_sta… Whether the pat… +#> 6 DE_EGEN_020 egen_020_previo… previously_vacc… Has the patient… +#> 7 DE_EGEN_062 egen_062_patien… patient_origin_… Name of village… +#> 8 DE_EGEN_010 egen_010_age_da… age_days Age of patient … +#> 9 DE_EGEN_029 egen_029_msf_in… msf_involvement How extensive i… +#> 10 DE_EGEN_053 egen_053_nutrit… nutrition_statu… What is the nut… +#> # … with 42 more rows, and 4 more variables: #> # data_element_valuetype , data_element_formname , -#> # used_optionset_uid , option_code , option_name , -#> # option_uid , option_order_in_set -msf_dict("AJS", compact = FALSE) -#> # A tibble: 215 x 11 +#> # used_optionset_uid , options +msf_dict("AJS") +#> # A tibble: 68 x 8 #> data_element_uid data_element_na… data_element_sh… data_element_de… #> #> 1 NA egen_044_event_… event_file_type Is the event fi… -#> 2 NA egen_044_event_… event_file_type Is the event fi… -#> 3 NA egen_044_event_… event_file_type Is the event fi… -#> 4 NA egen_001_patien… case_number Anonymised pati… -#> 5 NA egen_004_date_o… date_of_consult… Date patient pr… -#> 6 NA egen_022_detect… detected_by How patient was… -#> 7 NA egen_022_detect… detected_by How patient was… -#> 8 NA egen_022_detect… detected_by How patient was… -#> 9 NA egen_022_detect… detected_by How patient was… -#> 10 NA egen_005_patien… patient_facilit… Patient is pres… -#> # … with 205 more rows, and 7 more variables: +#> 2 NA egen_001_patien… case_number Anonymised pati… +#> 3 NA egen_004_date_o… date_of_consult… Date patient pr… +#> 4 NA egen_022_detect… detected_by How patient was… +#> 5 NA egen_005_patien… patient_facilit… Patient is pres… +#> 6 NA egen_029_msf_in… msf_involvement How extensive i… +#> 7 NA egen_008_age_ye… age_years Age of patient … +#> 8 NA egen_009_age_mo… age_months Age of patient … +#> 9 NA egen_010_age_da… age_days Age of patient … +#> 10 NA egen_011_sex sex Sex of patient … +#> # … with 58 more rows, and 4 more variables: #> # data_element_valuetype , data_element_formname , -#> # used_optionset_uid , option_code , option_name , -#> # option_uid , option_order_in_set -msf_dict("Cholera", compact = FALSE) -#> # A tibble: 182 x 11 +#> # used_optionset_uid , options +msf_dict("Cholera") +#> # A tibble: 45 x 8 #> data_element_uid data_element_na… data_element_sh… data_element_de… #> #> 1 FF7d81Zy0yQ egen_013_pregna… trimester If pregnant, tr… -#> 2 FF7d81Zy0yQ egen_013_pregna… trimester If pregnant, tr… -#> 3 FF7d81Zy0yQ egen_013_pregna… trimester If pregnant, tr… -#> 4 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 5 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 6 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 7 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 8 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 9 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… -#> 10 wjCDTwXmtix egen_064_treatm… treatment_facil… Name of facilit… -#> # … with 172 more rows, and 7 more variables: +#> 2 ADfNqpCL5kf egen_015_exit_s… exit_status Final status of… +#> 3 wjCDTwXmtix egen_064_treatm… treatment_facil… Name of facilit… +#> 4 UUVnMdaBY5T esym_002_dehydr… dehydration_lev… Dehydration bas… +#> 5 BTZdJKpS3S5 egen_059_commen… comments_on_lab… Any additional … +#> 6 bpT8T341oQG egen_054_fluids… fluids_treatmen… What was the fl… +#> 7 FqPqIr5m0AQ egen_017_time_b… time_to_death Hours between p… +#> 8 epbKb1GczaS esym_003_malari… malaria_rdt_at_… Malaria rapid d… +#> 9 F04TM58HHsd egen_020_previo… previously_vacc… Has the patient… +#> 10 CfRNuWWuTr5 egen_058_choler… cholera_pcr_res… Was a PCR test … +#> # … with 35 more rows, and 4 more variables: #> # data_element_valuetype , data_element_formname , -#> # used_optionset_uid , option_code , option_name , -#> # option_uid , option_order_in_set -msf_dict("Meningitis", compact = FALSE) -#> # A tibble: 173 x 11 +#> # used_optionset_uid , options +msf_dict("Meningitis") +#> # A tibble: 53 x 8 #> data_element_uid data_element_na… data_element_sh… data_element_de… #> #> 1 Ow8ss6T1tT5 esym_028_seizur… seizures_at_adm… Presenting symp… -#> 2 Ow8ss6T1tT5 esym_028_seizur… seizures_at_adm… Presenting symp… -#> 3 CEEr9lcwKVG esym_036_kernig… kernigs_brudzin… Presenting symp… -#> 4 CEEr9lcwKVG esym_036_kernig… kernigs_brudzin… Presenting symp… -#> 5 tIe59Htd2Ba esym_012_seizur… seizure_episodes Complication (S… -#> 6 tIe59Htd2Ba esym_012_seizur… seizure_episodes Complication (S… -#> 7 Sjms36Aj6bT esym_023_febril… febrile_coma Complication (F… -#> 8 Sjms36Aj6bT esym_023_febril… febrile_coma Complication (F… -#> 9 BTZdJKpS3S5 egen_059_commen… comments_on_lab… Any additional … -#> 10 wHnNEMRrS5A esym_025_chills… chills Presenting symp… -#> # … with 163 more rows, and 7 more variables: +#> 2 CEEr9lcwKVG esym_036_kernig… kernigs_brudzin… Presenting symp… +#> 3 tIe59Htd2Ba esym_012_seizur… seizure_episodes Complication (S… +#> 4 Sjms36Aj6bT esym_023_febril… febrile_coma Complication (F… +#> 5 BTZdJKpS3S5 egen_059_commen… comments_on_lab… Any additional … +#> 6 wHnNEMRrS5A esym_025_chills… chills Presenting symp… +#> 7 T3Gn8mTYu0c esym_026_stiff_… stiff_neck Presenting symp… +#> 8 JCexRYsmjmS eobr_006_ti_sam… ti_result_organ… TI sample resul… +#> 9 myL5BYzy6zW esym_034_coma_a… coma Presenting symp… +#> 10 AhllpMovCeu egen_062_patien… patient_origin_… Name of village… +#> # … with 43 more rows, and 4 more variables: #> # data_element_valuetype , data_element_formname , -#> # used_optionset_uid , option_code , option_name , -#> # option_uid , option_order_in_set +#> # used_optionset_uid , options ``` In addition, there are three MSF survey dictionaries available: @@ -137,7 +160,7 @@ These are accessible via `msf_dict_survey()` where the variables are in `column_name` and are often labeled by question number. ``` r -msf_dict_survey("Mortality", compact = FALSE) +msf_dict_survey("Mortality") #> # A tibble: 128 x 7 #> level column_name description data_element_va… option_code option_name #> @@ -152,7 +175,7 @@ msf_dict_survey("Mortality", compact = FALSE) #> 9 0 q45_cq2 Head of Ho… TEXT 1 No #> 10 0 q49_cq3 Head of Ho… TEXT 0 Yes #> # … with 118 more rows, and 1 more variable: option_order_in_set -msf_dict_survey("Nutrition", compact = FALSE) +msf_dict_survey("Nutrition") #> # A tibble: 29 x 7 #> level column_name description data_element_va… option_code option_name #> @@ -167,7 +190,7 @@ msf_dict_survey("Nutrition", compact = FALSE) #> 9 0 q49_cq3 Head of Ho… TEXT 0 Yes #> 10 0 q49_cq3 Head of Ho… TEXT 1 No #> # … with 19 more rows, and 1 more variable: option_order_in_set -msf_dict_survey("Vaccination", compact = FALSE) +msf_dict_survey("Vaccination") #> # A tibble: 113 x 7 #> level column_name description data_element_va… option_code option_name #> @@ -196,16 +219,16 @@ gen_data("Measles", varnames = "data_element_shortname", numcases = 100, org = " #> # A tibble: 100 x 52 #> seizure_episodes trimester croup dehydration_lev… residential_sta… #> -#> 1 0 0 UN 3 -#> 2 1 0 NO 4 -#> 3 1 1 SO 1 -#> 4 0 1 SE 1 -#> 5 1 3 1 NO 5 -#> 6 1 1 UN 4 -#> 7 0 0 SO 1 -#> 8 0 1 SO 5 -#> 9 1 0 SE 1 -#> 10 0 0 NO 3 +#> 1 1 2 0 SO 2 +#> 2 0 1 NO 5 +#> 3 1 0 UN 3 +#> 4 1 0 UN 3 +#> 5 0 1 UN 3 +#> 6 1 0 SE 1 +#> 7 1 0 UN 5 +#> 8 1 0 NO 3 +#> 9 1 1 SO 3 +#> 10 0 3 1 SE 2 #> # … with 90 more rows, and 47 more variables: #> # previously_vaccinated , patient_origin_free_text , #> # age_days , msf_involvement , @@ -232,16 +255,16 @@ gen_data("Vaccination", varnames = "column_name", numcases = 100, org = "MSF") #> # A tibble: 100 x 41 #> q77_what_is_the… health_district village q14_hh_no q15_home #> -#> 1 1 District A Villag… 6 Yes -#> 2 3 District B Villag… 2 No -#> 3 2 District A Villag… 1 No -#> 4 2 District A Villag… 1 No -#> 5 3 District B Villag… 2 No -#> 6 4 District B Villag… 4 No -#> 7 4 District B Villag… 4 No -#> 8 1 District A Villag… 3 Yes -#> 9 4 District B Villag… 1 No -#> 10 4 District B Villag… 2 Yes +#> 1 4 District B Villag… 7 No +#> 2 4 District B Villag… 4 Yes +#> 3 4 District B Villag… 4 Yes +#> 4 4 District B Villag… 1 Yes +#> 5 1 District A Villag… 7 No +#> 6 1 District A Villag… 3 Yes +#> 7 2 District A Villag… 3 No +#> 8 1 District A Villag… 6 No +#> 9 4 District B Villag… 4 No +#> 10 2 District A Villag… 1 Yes #> # … with 90 more rows, and 36 more variables: q16_occupant_age , #> # q58_consent , q75_caretaker , q76_caretaker_other , #> # q65_consent_no_reason , q66_consent_no_reason_other , @@ -279,26 +302,26 @@ print(dat) #> # A tibble: 20 x 45 #> trimester exit_status treatment_facil… dehydration_lev… #> -#> 1 AD NA NO -#> 2 DOA NA SO +#> 1 DD NA SO +#> 2 DD NA UN #> 3 DOA NA SO -#> 4 AD NA UN -#> 5 DOA NA SO -#> 6 AD NA SE -#> 7 DD NA UN -#> 8 DH NA UN -#> 9 DH NA SE +#> 4 DH NA NO +#> 5 DD NA UN +#> 6 DOA NA SE +#> 7 LA NA SO +#> 8 DD NA SO +#> 9 DH NA UN #> 10 DH NA SE -#> 11 DH NA NO -#> 12 DOA NA SO -#> 13 DOA NA NO -#> 14 DH NA SE -#> 15 DOA NA NO -#> 16 DOA NA NO -#> 17 TR NA SE -#> 18 LA NA UN -#> 19 TR NA SO -#> 20 DOA NA SE +#> 11 DH NA SO +#> 12 DD NA SO +#> 13 DOA NA SO +#> 14 DD NA SO +#> 15 TR NA UN +#> 16 TR NA UN +#> 17 TR NA NO +#> 18 DH NA SO +#> 19 DH NA SO +#> 20 AD NA SE #> # … with 41 more variables: comments_on_lab_results , #> # fluids_treatment_plan , time_to_death , #> # malaria_rdt_at_admission , previously_vaccinated , @@ -365,26 +388,26 @@ print(dat_clean) #> # A tibble: 20 x 45 #> trimester exit_status treatment_facil… dehydration_lev… #> -#> 1 Transferre… NA None -#> 2 Dead on ar… NA Some +#> 1 Dead in fa… NA Some +#> 2 Dead in fa… NA Unknown #> 3 Dead on ar… NA Some -#> 4 Transferre… NA Unknown -#> 5 Dead on ar… NA Some -#> 6 Transferre… NA Severe -#> 7 Dead in fa… NA Unknown -#> 8 Discharged… NA Unknown -#> 9 Discharged… NA Severe +#> 4 Discharged… NA None +#> 5 Dead in fa… NA Unknown +#> 6 Dead on ar… NA Severe +#> 7 Left again… NA Some +#> 8 Dead in fa… NA Some +#> 9 Discharged… NA Unknown #> 10 Discharged… NA Severe -#> 11 Discharged… NA None -#> 12 Dead on ar… NA Some -#> 13 Dead on ar… NA None -#> 14 Discharged… NA Severe -#> 15 Dead on ar… NA None -#> 16 Dead on ar… NA None -#> 17 Transferre… NA Severe -#> 18 Left again… NA Unknown -#> 19 Transferre… NA Some -#> 20 Dead on ar… NA Severe +#> 11 Discharged… NA Some +#> 12 Dead in fa… NA Some +#> 13 Dead on ar… NA Some +#> 14 Dead in fa… NA Some +#> 15 Transferre… NA Unknown +#> 16 Transferre… NA Unknown +#> 17 Transferre… NA None +#> 18 Discharged… NA Some +#> 19 Discharged… NA Some +#> 20 Transferre… NA Severe #> # … with 41 more variables: comments_on_lab_results , #> # fluids_treatment_plan , time_to_death , #> # malaria_rdt_at_admission , previously_vaccinated , diff --git a/man/rmdhunks/introduction.Rmd b/man/rmdhunks/introduction.Rmd index 8910c32..727e6fe 100644 --- a/man/rmdhunks/introduction.Rmd +++ b/man/rmdhunks/introduction.Rmd @@ -55,10 +55,10 @@ and their possible options (if categorical): ```{r outbreak} library("epidict") -msf_dict("Measles", compact = FALSE) -msf_dict("AJS", compact = FALSE) -msf_dict("Cholera", compact = FALSE) -msf_dict("Meningitis", compact = FALSE) +msf_dict("Measles") +msf_dict("AJS") +msf_dict("Cholera") +msf_dict("Meningitis") ``` In addition, there are three MSF survey dictionaries available: @@ -73,9 +73,9 @@ These are accessible via `msf_dict_survey()` where the variables are in `column_name` and are often labeled by question number. ```{r survey} -msf_dict_survey("Mortality", compact = FALSE) -msf_dict_survey("Nutrition", compact = FALSE) -msf_dict_survey("Vaccination", compact = FALSE) +msf_dict_survey("Mortality") +msf_dict_survey("Nutrition") +msf_dict_survey("Vaccination") ``` ## Generating data diff --git a/vignettes/Measles.Rmd b/vignettes/Measles.Rmd deleted file mode 100644 index 72a8193..0000000 --- a/vignettes/Measles.Rmd +++ /dev/null @@ -1,42 +0,0 @@ ---- -title: "Measles dictionary" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Measles dictionary} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -```{r, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>", - echo = FALSE -) -``` - -# Variables in the dictionary - -The Measles dictionary contains definitions for `r nrow(epidict::msf_dict("Measles"))` variables: - -```{r measles, results="asis"} -library(epidict) -measles <- msf_dict("Measles") -names_desc <- measles[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] -DT::datatable(names_desc) -``` - -# Option codes - -The dictionaries are exported using option codes that can be translated to -human-readable format. This table shows how they are translated. - -```{r measles_values, results = "asis"} -meas <- tidyr::unnest(measles, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] -DT::datatable(meas) -``` - -# Exploring the data set - -You can explore the original data set with `browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict"))`, but treat it as read-only. - diff --git a/vignettes/Outbreaks.Rmd b/vignettes/Outbreaks.Rmd new file mode 100644 index 0000000..97cee1a --- /dev/null +++ b/vignettes/Outbreaks.Rmd @@ -0,0 +1,126 @@ +--- +title: "MSF Outbreak Dictionaries" +output: + rmarkdown::html_vignette: + toc: true +vignette: > + %\VignetteIndexEntry{MSF outbreak dictionaries} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + echo = FALSE +) +``` + +There are four MSF outbreak dictionaries available: + + - Cholera/Acute watery diarrhea ("cholera") + - Meningitis + - Measles/Rubella ("measles") + - Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("ajs") + +> You can read more about the outbreak dictionaries at + +# Acute Jaundice Syndrome (AJS) + +## Variables in the dictionary + +The AJS dictionary contains definitions for `r nrow(epidict::msf_dict("AJS"))` variables: + +```{r ajs, results="asis"} +library(epidict) +ajs <- msf_dict("AJS") +names_desc <- ajs[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r ajs_values, results = "asis"} +ajs_codes <- tidyr::unnest(ajs, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(ajs_codes) +``` + +# Cholera + +## Variables in the dictionary + +The Cholera dictionary contains definitions for `r nrow(epidict::msf_dict("Cholera"))` variables: + +```{r cholera, results="asis"} +library(epidict) +cholera <- msf_dict("Cholera") +names_desc <- cholera[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r cholera_values, results = "asis"} +cholera_codes <- tidyr::unnest(cholera, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(cholera_codes) +``` + + +# Measles + +## Variables in the dictionary + +The Measles dictionary contains definitions for `r nrow(epidict::msf_dict("Measles"))` variables: + +```{r measles, results="asis"} +library(epidict) +measles <- msf_dict("Measles") +names_desc <- measles[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r measles_values, results = "asis"} +measles_codes <- tidyr::unnest(measles, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(measles_codes) +``` + +# Meningitis + +## Variables in the dictionary + +The Meningitis dictionary contains definitions for `r nrow(epidict::msf_dict("Meningitis"))` variables: + +```{r meningitis, results="asis"} +library(epidict) +meningitis <- msf_dict("Meningitis") +names_desc <- meningitis[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r meningitis_values, results = "asis"} +meningitis_codes <- tidyr::unnest(meningitis, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(meningitis_codes) +``` + + +# Exploring the dictionaries + +You can explore the excel-formatted dictionaries with `browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict"))`, but treat it as read-only. + diff --git a/vignettes/Surveys.Rmd b/vignettes/Surveys.Rmd new file mode 100644 index 0000000..66b2d25 --- /dev/null +++ b/vignettes/Surveys.Rmd @@ -0,0 +1,101 @@ +--- +title: "MSF Survey Dictionaries" +output: + rmarkdown::html_vignette: + toc: true +vignette: > + %\VignetteIndexEntry{MSF Survey Dictionaries} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + echo = FALSE +) +``` + +There are three MSF survey dictionaries available: + + - Retrospective mortality and access to care ("mortality") + - Malnutrition ("nutrition") + - Vaccination Coverage ("vaccination") + +> You can read more about the survey dictionaries at + +# Retrospective mortality and access to care ("mortality") + +## Variables in the dictionary + +The Mortality dictionary contains definitions for `r nrow(epidict::msf_dict_survey("Mortality"))` variables: + +```{r mortality, results="asis"} +library(epidict) +mortality <- msf_dict_survey("Mortality", compact = TRUE) +names_desc <- mortality[c("column_name", "description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r mortality_values, results = "asis"} +mortality_codes <- tidyr::unnest(mortality, cols = options)[c("column_name", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(mortality_codes) +``` + +# Malnutrition ("nutrition") + +## Variables in the dictionary + +The Nutrition dictionary contains definitions for `r nrow(epidict::msf_dict_survey("Nutrition"))` variables: + +```{r nutrition, results="asis"} +library(epidict) +nutrition <- msf_dict_survey("Nutrition", compact = TRUE) +names_desc <- nutrition[c("column_name", "description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r nutrition_values, results = "asis"} +nutrition_codes <- tidyr::unnest(nutrition, cols = options)[c("column_name", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(nutrition_codes) +``` + +# Vaccination Coverage ("vaccination") + +## Variables in the dictionary + +The Vaccination dictionary contains definitions for `r nrow(epidict::msf_dict_survey("Vaccination"))` variables: + +```{r vaccination, results="asis"} +library(epidict) +vaccination <- msf_dict_survey("Vaccination", compact = TRUE) +names_desc <- vaccination[c("column_name", "description", "data_element_valuetype")] +DT::datatable(names_desc) +``` + +## Option codes + +The dictionaries are exported using option codes that can be translated to +human-readable format. This table shows how they are translated. + +```{r vaccination_values, results = "asis"} +vaccination_codes <- tidyr::unnest(vaccination, cols = options)[c("column_name", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")] +DT::datatable(vaccination_codes) +``` + + +# Exploring the dictionaries + +You can explore the excel-formatted dictionaries with `browseURL(system.file("extdata", "MSF-survey-dict.xlsx", package = "epidict"))`, but treat it as read-only. + From 83a8d64737aa2616d7384bd68dc7beb4f29e4c57 Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Tue, 11 Feb 2020 10:41:49 +0000 Subject: [PATCH 06/11] update site --- docs/404.html | 20 +- docs/CODE_OF_CONDUCT.html | 20 +- docs/CONTRIBUTING.html | 20 +- docs/ISSUE_TEMPLATE.html | 20 +- docs/LICENSE.html | 20 +- docs/SUPPORT.html | 20 +- docs/articles/Outbreaks.html | 248 +++ .../crosstalk-1.0.0/css/crosstalk.css | 27 + .../crosstalk-1.0.0/js/crosstalk.js | 1471 +++++++++++++++++ .../crosstalk-1.0.0/js/crosstalk.js.map | 37 + .../crosstalk-1.0.0/js/crosstalk.min.js | 2 + .../crosstalk-1.0.0/js/crosstalk.min.js.map | 1 + .../datatables-binding-0.12/datatables.js | 1323 +++++++++++++++ .../datatables-crosstalk.css | 7 + .../css/jquery.dataTables.extra.css | 8 + .../css/jquery.dataTables.min.css | 1 + .../js/jquery.dataTables.min.js | 180 ++ .../htmlwidgets-1.5.1/htmlwidgets.js | 903 ++++++++++ .../Outbreaks_files/jquery-1.12.4/LICENSE.txt | 37 + .../jquery-1.12.4/jquery.min.js | 5 + docs/articles/Surveys.html | 223 +++ .../crosstalk-1.0.0/css/crosstalk.css | 27 + .../crosstalk-1.0.0/js/crosstalk.js | 1471 +++++++++++++++++ .../crosstalk-1.0.0/js/crosstalk.js.map | 37 + .../crosstalk-1.0.0/js/crosstalk.min.js | 2 + .../crosstalk-1.0.0/js/crosstalk.min.js.map | 1 + .../datatables-binding-0.12/datatables.js | 1323 +++++++++++++++ .../datatables-crosstalk.css | 7 + .../css/jquery.dataTables.extra.css | 8 + .../css/jquery.dataTables.min.css | 1 + .../js/jquery.dataTables.min.js | 180 ++ .../htmlwidgets-1.5.1/htmlwidgets.js | 903 ++++++++++ .../Surveys_files/jquery-1.12.4/LICENSE.txt | 37 + .../Surveys_files/jquery-1.12.4/jquery.min.js | 5 + docs/articles/index.html | 162 ++ docs/articles/intro.html | 496 ++++++ docs/authors.html | 20 +- docs/index.html | 692 ++++---- docs/news/index.html | 29 +- docs/pkgdown.yml | 5 +- docs/reference/epidict-package.html | 21 +- docs/reference/gen_data.html | 20 +- docs/reference/index.html | 20 +- docs/reference/msf_dict.html | 20 +- 44 files changed, 9733 insertions(+), 347 deletions(-) create mode 100644 docs/articles/Outbreaks.html create mode 100644 docs/articles/Outbreaks_files/crosstalk-1.0.0/css/crosstalk.css create mode 100644 docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js create mode 100644 docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js.map create mode 100644 docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.min.js create mode 100644 docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.min.js.map create mode 100644 docs/articles/Outbreaks_files/datatables-binding-0.12/datatables.js create mode 100644 docs/articles/Outbreaks_files/datatables-css-0.0.0/datatables-crosstalk.css create mode 100644 docs/articles/Outbreaks_files/dt-core-1.10.20/css/jquery.dataTables.extra.css create mode 100644 docs/articles/Outbreaks_files/dt-core-1.10.20/css/jquery.dataTables.min.css create mode 100644 docs/articles/Outbreaks_files/dt-core-1.10.20/js/jquery.dataTables.min.js create mode 100644 docs/articles/Outbreaks_files/htmlwidgets-1.5.1/htmlwidgets.js create mode 100644 docs/articles/Outbreaks_files/jquery-1.12.4/LICENSE.txt create mode 100644 docs/articles/Outbreaks_files/jquery-1.12.4/jquery.min.js create mode 100644 docs/articles/Surveys.html create mode 100644 docs/articles/Surveys_files/crosstalk-1.0.0/css/crosstalk.css create mode 100644 docs/articles/Surveys_files/crosstalk-1.0.0/js/crosstalk.js create mode 100644 docs/articles/Surveys_files/crosstalk-1.0.0/js/crosstalk.js.map create mode 100644 docs/articles/Surveys_files/crosstalk-1.0.0/js/crosstalk.min.js create mode 100644 docs/articles/Surveys_files/crosstalk-1.0.0/js/crosstalk.min.js.map create mode 100644 docs/articles/Surveys_files/datatables-binding-0.12/datatables.js create mode 100644 docs/articles/Surveys_files/datatables-css-0.0.0/datatables-crosstalk.css create mode 100644 docs/articles/Surveys_files/dt-core-1.10.20/css/jquery.dataTables.extra.css create mode 100644 docs/articles/Surveys_files/dt-core-1.10.20/css/jquery.dataTables.min.css create mode 100644 docs/articles/Surveys_files/dt-core-1.10.20/js/jquery.dataTables.min.js create mode 100644 docs/articles/Surveys_files/htmlwidgets-1.5.1/htmlwidgets.js create mode 100644 docs/articles/Surveys_files/jquery-1.12.4/LICENSE.txt create mode 100644 docs/articles/Surveys_files/jquery-1.12.4/jquery.min.js create mode 100644 docs/articles/index.html create mode 100644 docs/articles/intro.html diff --git a/docs/404.html b/docs/404.html index c95cc28..880af51 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
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  • Changelog
    • diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 961295c..8e5d763 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
  • + + +
  • Changelog
    • diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index e975b7d..694bc26 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
  • + + +
  • Changelog
    • diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index 98ae129..4387efa 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
  • + + +
  • Changelog
    • diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 8cfa046..74956f2 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
  • + + +
  • Changelog
    • diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html index 4b9cbaa..05b4710 100644 --- a/docs/SUPPORT.html +++ b/docs/SUPPORT.html @@ -67,7 +67,7 @@ epidict - 0.0.0.9000 + 0.1.0 @@ -82,6 +82,24 @@
  • Reference
    • +
  • + + +
  • Changelog
    • diff --git a/docs/articles/Outbreaks.html b/docs/articles/Outbreaks.html new file mode 100644 index 0000000..b132434 --- /dev/null +++ b/docs/articles/Outbreaks.html @@ -0,0 +1,248 @@ + + + + + + + +MSF Outbreak Dictionaries • epidict + + + + + + + + + + +
    +
    + + + + +
    + + + +
    +
    +
    +

    MSF Outbreak Dictionaries

    + + + Source: vignettes/Outbreaks.Rmd + + +
    + + + +

    There are four MSF outbreak dictionaries available:

    +
      +
    • Cholera/Acute watery diarrhea (“cholera”)
      • +
    • Meningitis
      • +
    • Measles/Rubella (“measles”)
      • +
    • Acute Jaundice Syndrome (often suspected to be Hepatitis E) (“ajs”)
      • +
    +
    +

    You can read more about the outbreak dictionaries at https://r4epis.netlify.com/outbreaks

    +
    +
    +

    +Acute Jaundice Syndrome (AJS)

    +
    +

    +Variables in the dictionary

    +

    The AJS dictionary contains definitions for 68 variables:

    +
    + +
    +
    +

    +Option codes

    +

    The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

    +
    + +
    +
    +
    +

    +Cholera

    +
    +

    +Variables in the dictionary

    +

    The Cholera dictionary contains definitions for 45 variables:

    +
    + +
    +
    +

    +Option codes

    +

    The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

    +
    + +
    +
    +
    +

    +Measles

    +
    +

    +Variables in the dictionary

    +

    The Measles dictionary contains definitions for 52 variables:

    +
    + +
    +
    +

    +Option codes

    +

    The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

    +
    + +
    +
    +
    +

    +Meningitis

    +
    +

    +Variables in the dictionary

    +

    The Meningitis dictionary contains definitions for 53 variables:

    +
    + +
    +
    +

    +Option codes

    +

    The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

    +
    + +
    +
    +
    +

    +Exploring the dictionaries

    +

    You can explore the excel-formatted dictionaries with browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict")), but treat it as read-only.

    +
    +
    + + + +
    + + + +
    +

    Developed by Zhian N. Kamvar, Alex Spina, Lukas Richter, Patrick Keating.

    +
    + +
    +

    Site built with pkgdown 1.4.1.

    +
    + +
    +
    + + + + + + diff --git a/docs/articles/Outbreaks_files/crosstalk-1.0.0/css/crosstalk.css b/docs/articles/Outbreaks_files/crosstalk-1.0.0/css/crosstalk.css new file mode 100644 index 0000000..46befd2 --- /dev/null +++ b/docs/articles/Outbreaks_files/crosstalk-1.0.0/css/crosstalk.css @@ -0,0 +1,27 @@ +/* Adjust margins outwards, so column contents line up with the edges of the + parent of container-fluid. */ +.container-fluid.crosstalk-bscols { + margin-left: -30px; + margin-right: -30px; + white-space: normal; +} + +/* But don't adjust the margins outwards if we're directly under the body, + i.e. we were the top-level of something at the console. */ +body > .container-fluid.crosstalk-bscols { + margin-left: auto; + margin-right: auto; +} + +.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: inline-block; + padding-right: 12px; + vertical-align: top; +} + +@media only screen and (max-width:480px) { + .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: block; + padding-right: inherit; + } +} diff --git a/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js new file mode 100644 index 0000000..8e6ee30 --- /dev/null +++ b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js @@ -0,0 +1,1471 @@ +(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o b) { + return 1; + } +} + +/** + * @private + */ + +var FilterSet = function () { + function FilterSet() { + _classCallCheck(this, FilterSet); + + this.reset(); + } + + _createClass(FilterSet, [{ + key: "reset", + value: function reset() { + // Key: handle ID, Value: array of selected keys, or null + this._handles = {}; + // Key: key string, Value: count of handles that include it + this._keys = {}; + this._value = null; + this._activeHandles = 0; + } + }, { + key: "update", + value: function update(handleId, keys) { + if (keys !== null) { + keys = keys.slice(0); // clone before sorting + keys.sort(naturalComparator); + } + + var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys), + added = _diffSortedLists.added, + removed = _diffSortedLists.removed; + + this._handles[handleId] = keys; + + for (var i = 0; i < added.length; i++) { + this._keys[added[i]] = (this._keys[added[i]] || 0) + 1; + } + for (var _i = 0; _i < removed.length; _i++) { + this._keys[removed[_i]]--; + } + + this._updateValue(keys); + } + + /** + * @param {string[]} keys Sorted array of strings that indicate + * a superset of possible keys. + * @private + */ + + }, { + key: "_updateValue", + value: function _updateValue() { + var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys; + + var handleCount = Object.keys(this._handles).length; + if (handleCount === 0) { + this._value = null; + } else { + this._value = []; + for (var i = 0; i < keys.length; i++) { + var count = this._keys[keys[i]]; + if (count === handleCount) { + this._value.push(keys[i]); + } + } + } + } + }, { + key: "clear", + value: function clear(handleId) { + if (typeof this._handles[handleId] === "undefined") { + return; + } + + var keys = this._handles[handleId]; + if (!keys) { + keys = []; + } + + for (var i = 0; i < keys.length; i++) { + this._keys[keys[i]]--; + } + delete this._handles[handleId]; + + this._updateValue(); + } + }, { + key: "value", + get: function get() { + return this._value; + } + }, { + key: "_allKeys", + get: function get() { + var allKeys = Object.keys(this._keys); + allKeys.sort(naturalComparator); + return allKeys; + } + }]); + + return FilterSet; +}(); + +exports.default = FilterSet; + +},{"./util":11}],4:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.default = group; + +var _var2 = require("./var"); + +var _var3 = _interopRequireDefault(_var2); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +// Use a global so that multiple copies of crosstalk.js can be loaded and still +// have groups behave as singletons across all copies. +global.__crosstalk_groups = global.__crosstalk_groups || {}; +var groups = global.__crosstalk_groups; + +function group(groupName) { + if (groupName && typeof groupName === "string") { + if (!groups.hasOwnProperty(groupName)) { + groups[groupName] = new Group(groupName); + } + return groups[groupName]; + } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) { + // Appears to already be a group object + return groupName; + } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") { + return group(groupName[0]); + } else { + throw new Error("Invalid groupName argument"); + } +} + +var Group = function () { + function Group(name) { + _classCallCheck(this, Group); + + this.name = name; + this._vars = {}; + } + + _createClass(Group, [{ + key: "var", + value: function _var(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name); + return this._vars[name]; + } + }, { + key: "has", + value: function has(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + return this._vars.hasOwnProperty(name); + } + }]); + + return Group; +}(); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./var":12}],5:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _selection = require("./selection"); + +var _filter = require("./filter"); + +require("./input"); + +require("./input_selectize"); + +require("./input_checkboxgroup"); + +require("./input_slider"); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +var defaultGroup = (0, _group2.default)("default"); + +function var_(name) { + return defaultGroup.var(name); +} + +function has(name) { + return defaultGroup.has(name); +} + +if (global.Shiny) { + global.Shiny.addCustomMessageHandler("update-client-value", function (message) { + if (typeof message.group === "string") { + (0, _group2.default)(message.group).var(message.name).set(message.value); + } else { + var_(message.name).set(message.value); + } + }); +} + +var crosstalk = { + group: _group2.default, + var: var_, + has: has, + SelectionHandle: _selection.SelectionHandle, + FilterHandle: _filter.FilterHandle +}; + +/** + * @namespace crosstalk + */ +exports.default = crosstalk; + +global.crosstalk = crosstalk; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.register = register; +var $ = global.jQuery; + +var bindings = {}; + +function register(reg) { + bindings[reg.className] = reg; + if (global.document && global.document.readyState !== "complete") { + $(function () { + bind(); + }); + } else if (global.document) { + setTimeout(bind, 100); + } +} + +function bind() { + Object.keys(bindings).forEach(function (className) { + var binding = bindings[className]; + $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) { + bindInstance(binding, el); + }); + }); +} + +// Escape jQuery identifier +function $escape(val) { + return val.replace(/([!"#$%&'()*+,.\/:;<=>?@\[\\\]^`{|}~])/g, "\\$1"); +} + +function bindEl(el) { + var $el = $(el); + Object.keys(bindings).forEach(function (className) { + if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) { + var binding = bindings[className]; + bindInstance(binding, el); + } + }); +} + +function bindInstance(binding, el) { + var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']"); + var data = JSON.parse(jsonEl[0].innerText); + + var instance = binding.factory(el, data); + $(el).data("crosstalk-instance", instance); + $(el).addClass("crosstalk-input-bound"); +} + +if (global.Shiny) { + (function () { + var inputBinding = new global.Shiny.InputBinding(); + var $ = global.jQuery; + $.extend(inputBinding, { + find: function find(scope) { + return $(scope).find(".crosstalk-input"); + }, + initialize: function initialize(el) { + if (!$(el).hasClass("crosstalk-input-bound")) { + bindEl(el); + } + }, + getId: function getId(el) { + return el.id; + }, + getValue: function getValue(el) {}, + setValue: function setValue(el, value) {}, + receiveMessage: function receiveMessage(el, data) {}, + subscribe: function subscribe(el, callback) { + $(el).data("crosstalk-instance").resume(); + }, + unsubscribe: function unsubscribe(el) { + $(el).data("crosstalk-instance").suspend(); + } + }); + global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding"); + })(); +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{}],7:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-checkboxgroup", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + var $el = $(el); + $el.on("change", "input[type='checkbox']", function () { + var checked = $el.find("input[type='checkbox']:checked"); + if (checked.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + (function () { + var keys = {}; + checked.each(function () { + data.map[this.value].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + })(); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],8:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-select", + + factory: function factory(el, data) { + /* + * items: {value: [...], label: [...]} + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + + var first = [{ value: "", label: "(All)" }]; + var items = util.dataframeToD3(data.items); + var opts = { + options: first.concat(items), + valueField: "value", + labelField: "label", + searchField: "label" + }; + + var select = $(el).find("select")[0]; + + var selectize = $(select).selectize(opts)[0].selectize; + + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + selectize.on("change", function () { + if (selectize.items.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + (function () { + var keys = {}; + selectize.items.forEach(function (group) { + data.map[group].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + })(); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }(); + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; +var strftime = global.strftime; + +input.register({ + className: "crosstalk-input-slider", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var opts = {}; + var $el = $(el).find("input"); + var dataType = $el.data("data-type"); + var timeFormat = $el.data("time-format"); + var timeFormatter = void 0; + + // Set up formatting functions + if (dataType === "date") { + timeFormatter = strftime.utc(); + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "datetime") { + var timezone = $el.data("timezone"); + if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime; + + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } + + $el.ionRangeSlider(opts); + + function getValue() { + var result = $el.data("ionRangeSlider").result; + + // Function for converting numeric value from slider to appropriate type. + var convert = void 0; + var dataType = $el.data("data-type"); + if (dataType === "date") { + convert = function convert(val) { + return formatDateUTC(new Date(+val)); + }; + } else if (dataType === "datetime") { + convert = function convert(val) { + // Convert ms to s + return +val / 1000; + }; + } else { + convert = function convert(val) { + return +val; + }; + } + + if ($el.data("ionRangeSlider").options.type === "double") { + return [convert(result.from), convert(result.to)]; + } else { + return convert(result.from); + } + } + + var lastKnownKeys = null; + + $el.on("change.crosstalkSliderInput", function (event) { + if (!$el.data("updating") && !$el.data("animating")) { + var _getValue = getValue(), + _getValue2 = _slicedToArray(_getValue, 2), + from = _getValue2[0], + to = _getValue2[1]; + + var keys = []; + for (var i = 0; i < data.values.length; i++) { + var val = data.values[i]; + if (val >= from && val <= to) { + keys.push(data.keys[i]); + } + } + keys.sort(); + ctHandle.set(keys); + lastKnownKeys = keys; + } + }); + + // let $el = $(el); + // $el.on("change", "input[type="checkbox"]", function() { + // let checked = $el.find("input[type="checkbox"]:checked"); + // if (checked.length === 0) { + // ctHandle.clear(); + // } else { + // let keys = {}; + // checked.each(function() { + // data.map[this.value].forEach(function(key) { + // keys[key] = true; + // }); + // }); + // let keyArray = Object.keys(keys); + // keyArray.sort(); + // ctHandle.set(keyArray); + // } + // }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +// Convert a number to a string with leading zeros +function padZeros(n, digits) { + var str = n.toString(); + while (str.length < digits) { + str = "0" + str; + }return str; +} + +// Given a Date object, return a string in yyyy-mm-dd format, using the +// UTC date. This may be a day off from the date in the local time zone. +function formatDateUTC(date) { + if (date instanceof Date) { + return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2); + } else { + return null; + } +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],10:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.SelectionHandle = undefined; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var SelectionHandle = exports.SelectionHandle = function () { + + /** + * @classdesc + * Use this class to read and write (and listen for changes to) the selection + * for a Crosstalk group. This is intended to be used for linked brushing. + * + * If two (or more) `SelectionHandle` instances in the same webpage share the + * same group name, they will share the same state. Setting the selection using + * one `SelectionHandle` instance will result in the `value` property instantly + * changing across the others, and `"change"` event listeners on all instances + * (including the one that initiated the sending) will fire. + * + * @param {string} [group] - The name of the Crosstalk group, or if none, + * null or undefined (or any other falsy value). This can be changed later + * via the [SelectionHandle#setGroup](#setGroup) method. + * @param {Object} [extraInfo] - An object whose properties will be copied to + * the event object whenever an event is emitted. + */ + function SelectionHandle() { + var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null; + var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null; + + _classCallCheck(this, SelectionHandle); + + this._eventRelay = new _events2.default(); + this._emitter = new util.SubscriptionTracker(this._eventRelay); + + // Name of the group we're currently tracking, if any. Can change over time. + this._group = null; + // The Var we're currently tracking, if any. Can change over time. + this._var = null; + // The event handler subscription we currently have on var.on("change"). + this._varOnChangeSub = null; + + this._extraInfo = util.extend({ sender: this }, extraInfo); + + this.setGroup(group); + } + + /** + * Changes the Crosstalk group membership of this SelectionHandle. The group + * being switched away from (if any) will not have its selection value + * modified as a result of calling `setGroup`, even if this handle was the + * most recent handle to set the selection of the group. + * + * The group being switched to (if any) will also not have its selection value + * modified as a result of calling `setGroup`. If you want to set the + * selection value of the new group, call `set` explicitly. + * + * @param {string} group - The name of the Crosstalk group, or null (or + * undefined) to clear the group. + */ + + + _createClass(SelectionHandle, [{ + key: "setGroup", + value: function setGroup(group) { + var _this = this; + + // If group is unchanged, do nothing + if (this._group === group) return; + // Treat null, undefined, and other falsy values the same + if (!this._group && !group) return; + + if (this._var) { + this._var.off("change", this._varOnChangeSub); + this._var = null; + this._varOnChangeSub = null; + } + + this._group = group; + + if (group) { + this._var = (0, _group2.default)(group).var("selection"); + var sub = this._var.on("change", function (e) { + _this._eventRelay.trigger("change", e, _this); + }); + this._varOnChangeSub = sub; + } + } + + /** + * Retrieves the current selection for the group represented by this + * `SelectionHandle`. + * + * - If no selection is active, then this value will be falsy. + * - If a selection is active, but no data points are selected, then this + * value will be an empty array. + * - If a selection is active, and data points are selected, then the keys + * of the selected data points will be present in the array. + */ + + }, { + key: "_mergeExtraInfo", + + + /** + * Combines the given `extraInfo` (if any) with the handle's default + * `_extraInfo` (if any). + * @private + */ + value: function _mergeExtraInfo(extraInfo) { + // Important incidental effect: shallow clone is returned + return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see + * {@link SelectionHandle#value}). + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `SelectionHandle` constructor). + */ + + }, { + key: "set", + value: function set(selectedKeys, extraInfo) { + if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo)); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any that were passed + * into the `SelectionHandle` constructor). + */ + + }, { + key: "clear", + value: function clear(extraInfo) { + if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo)); + } + + /** + * Subscribes to events on this `SelectionHandle`. + * + * @param {string} eventType - Indicates the type of events to listen to. + * Currently, only `"change"` is supported. + * @param {SelectionHandle~listener} listener - The callback function that + * will be invoked when the event occurs. + * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel + * this subscription. + */ + + }, { + key: "on", + value: function on(eventType, listener) { + return this._emitter.on(eventType, listener); + } + + /** + * Cancels event subscriptions created by {@link SelectionHandle#on}. + * + * @param {string} eventType - The type of event to unsubscribe. + * @param {string|SelectionHandle~listener} listener - Either the callback + * function previously passed into {@link SelectionHandle#on}, or the + * string that was returned from {@link SelectionHandle#on}. + */ + + }, { + key: "off", + value: function off(eventType, listener) { + return this._emitter.off(eventType, listener); + } + + /** + * Shuts down the `SelectionHandle` object. + * + * Removes all event listeners that were added through this handle. + */ + + }, { + key: "close", + value: function close() { + this._emitter.removeAllListeners(); + this.setGroup(null); + } + + /** + * @callback SelectionHandle~listener + * @param {Object} event - An object containing details of the event. For + * `"change"` events, this includes the properties `value` (the new + * value of the selection, or `undefined` if no selection is active), + * `oldValue` (the previous value of the selection), and `sender` (the + * `SelectionHandle` instance that made the change). + */ + + /** + * @event SelectionHandle#change + * @type {object} + * @property {object} value - The new value of the selection, or `undefined` + * if no selection is active. + * @property {object} oldValue - The previous value of the selection. + * @property {SelectionHandle} sender - The `SelectionHandle` instance that + * changed the value. + */ + + }, { + key: "value", + get: function get() { + return this._var ? this._var.get() : null; + } + }]); + + return SelectionHandle; +}(); + +},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.extend = extend; +exports.checkSorted = checkSorted; +exports.diffSortedLists = diffSortedLists; +exports.dataframeToD3 = dataframeToD3; + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function extend(target) { + for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { + sources[_key - 1] = arguments[_key]; + } + + for (var i = 0; i < sources.length; i++) { + var src = sources[i]; + if (typeof src === "undefined" || src === null) continue; + + for (var key in src) { + if (src.hasOwnProperty(key)) { + target[key] = src[key]; + } + } + } + return target; +} + +function checkSorted(list) { + for (var i = 1; i < list.length; i++) { + if (list[i] <= list[i - 1]) { + throw new Error("List is not sorted or contains duplicate"); + } + } +} + +function diffSortedLists(a, b) { + var i_a = 0; + var i_b = 0; + + if (!a) a = []; + if (!b) b = []; + + var a_only = []; + var b_only = []; + + checkSorted(a); + checkSorted(b); + + while (i_a < a.length && i_b < b.length) { + if (a[i_a] === b[i_b]) { + i_a++; + i_b++; + } else if (a[i_a] < b[i_b]) { + a_only.push(a[i_a++]); + } else { + b_only.push(b[i_b++]); + } + } + + if (i_a < a.length) a_only = a_only.concat(a.slice(i_a)); + if (i_b < b.length) b_only = b_only.concat(b.slice(i_b)); + return { + removed: a_only, + added: b_only + }; +} + +// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... } +// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ] +function dataframeToD3(df) { + var names = []; + var length = void 0; + for (var name in df) { + if (df.hasOwnProperty(name)) names.push(name); + if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof length !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item = void 0; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; +} + +/** + * Keeps track of all event listener additions/removals and lets all active + * listeners be removed with a single operation. + * + * @private + */ + +var SubscriptionTracker = exports.SubscriptionTracker = function () { + function SubscriptionTracker(emitter) { + _classCallCheck(this, SubscriptionTracker); + + this._emitter = emitter; + this._subs = {}; + } + + _createClass(SubscriptionTracker, [{ + key: "on", + value: function on(eventType, listener) { + var sub = this._emitter.on(eventType, listener); + this._subs[sub] = eventType; + return sub; + } + }, { + key: "off", + value: function off(eventType, listener) { + var sub = this._emitter.off(eventType, listener); + if (sub) { + delete this._subs[sub]; + } + return sub; + } + }, { + key: "removeAllListeners", + value: function removeAllListeners() { + var _this = this; + + var current_subs = this._subs; + this._subs = {}; + Object.keys(current_subs).forEach(function (sub) { + _this._emitter.off(current_subs[sub], sub); + }); + } + }]); + + return SubscriptionTracker; +}(); + +},{}],12:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var Var = function () { + function Var(group, name, /*optional*/value) { + _classCallCheck(this, Var); + + this._group = group; + this._name = name; + this._value = value; + this._events = new _events2.default(); + } + + _createClass(Var, [{ + key: "get", + value: function get() { + return this._value; + } + }, { + key: "set", + value: function set(value, /*optional*/event) { + if (this._value === value) { + // Do nothing; the value hasn't changed + return; + } + var oldValue = this._value; + this._value = value; + // Alert JavaScript listeners that the value has changed + var evt = {}; + if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") { + for (var k in event) { + if (event.hasOwnProperty(k)) evt[k] = event[k]; + } + } + evt.oldValue = oldValue; + evt.value = value; + this._events.trigger("change", evt, this); + + // TODO: Make this extensible, to let arbitrary back-ends know that + // something has changed + if (global.Shiny && global.Shiny.onInputChange) { + global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value); + } + } + }, { + key: "on", + value: function on(eventType, listener) { + return this._events.on(eventType, listener); + } + }, { + key: "off", + value: function off(eventType, listener) { + return this._events.off(eventType, listener); + } + }]); + + return Var; +}(); + +exports.default = Var; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./events":1}]},{},[5]) +//# sourceMappingURL=crosstalk.js.map diff --git a/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js.map b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js.map new file mode 100644 index 0000000..508b24f --- /dev/null +++ b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.js.map @@ -0,0 +1,37 @@ +{ + "version": 3, + "sources": [ + "node_modules/browser-pack/_prelude.js", + "javascript/src/events.js", + "javascript/src/filter.js", + "javascript/src/filterset.js", + "javascript/src/group.js", + "javascript/src/index.js", + "javascript/src/input.js", + "javascript/src/input_checkboxgroup.js", + "javascript/src/input_selectize.js", + "javascript/src/input_slider.js", + "javascript/src/selection.js", + "javascript/src/util.js", + "javascript/src/var.js" + ], + "names": [], + "mappings": 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+ "file": "generated.js", + "sourceRoot": "", + "sourcesContent": [ + "(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n /**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n}\n", + "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n", + "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n", + "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n", + "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nfunction bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,.\\/:;<=>?@\\[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n", + "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nexport class SelectionHandle {\n\n /**\n * @classdesc\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n\n /**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n /**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n}\n", + "export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n", + "import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n" + ] +} \ No newline at end of file diff --git a/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.min.js b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.min.js new file mode 100644 index 0000000..55262e8 --- /dev/null +++ b/docs/articles/Outbreaks_files/crosstalk-1.0.0/js/crosstalk.min.js @@ -0,0 +1,2 @@ +!function a(b,c,d){function e(g,h){if(!c[g]){if(!b[g]){var i="function"==typeof require&&require;if(!h&&i)return i(g,!0);if(f)return f(g,!0);var j=new Error("Cannot find module '"+g+"'");throw j.code="MODULE_NOT_FOUND",j}var k=c[g]={exports:{}};b[g][0].call(k.exports,function(a){var c=b[g][1][a];return e(c?c:a)},k,k.exports,a,b,c,d)}return c[g].exports}for(var f="function"==typeof require&&require,g=0;gb?1:void 0}Object.defineProperty(c,"__esModule",{value:!0});var f=function(){function a(a,b){for(var c=0;c0&&void 0!==arguments[0]?arguments[0]:this._allKeys,b=Object.keys(this._handles).length;if(0===b)this._value=null;else{this._value=[];for(var c=0;c?@\[\\\]^`{|}~])/g,"\\$1")}function f(a){var b=h(a);Object.keys(i).forEach(function(c){if(b.hasClass(c)&&!b.hasClass("crosstalk-input-bound")){var d=i[c];g(d,a)}})}function g(a,b){var c=h(b).find("script[type='application/json'][data-for='"+e(b.id)+"']"),d=JSON.parse(c[0].innerText),f=a.factory(b,d);h(b).data("crosstalk-instance",f),h(b).addClass("crosstalk-input-bound")}Object.defineProperty(c,"__esModule",{value:!0}),c.register=b;var h=a.jQuery,i={};a.Shiny&&!function(){var b=new a.Shiny.InputBinding,c=a.jQuery;c.extend(b,{find:function(a){return c(a).find(".crosstalk-input")},initialize:function(a){c(a).hasClass("crosstalk-input-bound")||f(a)},getId:function(a){return a.id},getValue:function(a){},setValue:function(a,b){},receiveMessage:function(a,b){},subscribe:function(a,b){c(a).data("crosstalk-instance").resume()},unsubscribe:function(a){c(a).data("crosstalk-instance").suspend()}}),a.Shiny.inputBindings.register(b,"crosstalk.inputBinding")}()}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(a,b,c){(function(b){"use strict";function c(a){if(a&&a.__esModule)return a;var b={};if(null!=a)for(var c in a)Object.prototype.hasOwnProperty.call(a,c)&&(b[c]=a[c]);return b.default=a,b}var d=a("./input"),e=c(d),f=a("./filter"),g=b.jQuery;e.register({className:"crosstalk-input-checkboxgroup",factory:function(a,b){var c=new f.FilterHandle(b.group),d=void 0,e=g(a);return e.on("change","input[type='checkbox']",function(){var a=e.find("input[type='checkbox']:checked");0===a.length?(d=null,c.clear()):!function(){var e={};a.each(function(){b.map[this.value].forEach(function(a){e[a]=!0})});var f=Object.keys(e);f.sort(),d=f,c.set(f)}()}),{suspend:function(){c.clear()},resume:function(){d&&c.set(d)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(a,b,c){(function(b){"use strict";function c(a){if(a&&a.__esModule)return a;var b={};if(null!=a)for(var c in a)Object.prototype.hasOwnProperty.call(a,c)&&(b[c]=a[c]);return b.default=a,b}var d=a("./input"),e=c(d),f=a("./util"),g=c(f),h=a("./filter"),i=b.jQuery;e.register({className:"crosstalk-input-select",factory:function(a,b){var c=[{value:"",label:"(All)"}],d=g.dataframeToD3(b.items),e={options:c.concat(d),valueField:"value",labelField:"label",searchField:"label"},f=i(a).find("select")[0],j=i(f).selectize(e)[0].selectize,k=new h.FilterHandle(b.group),l=void 0;return j.on("change",function(){0===j.items.length?(l=null,k.clear()):!function(){var a={};j.items.forEach(function(c){b.map[c].forEach(function(b){a[b]=!0})});var c=Object.keys(a);c.sort(),l=c,k.set(c)}()}),{suspend:function(){k.clear()},resume:function(){l&&k.set(l)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6,"./util":11}],9:[function(a,b,c){(function(b){"use strict";function c(a){if(a&&a.__esModule)return a;var b={};if(null!=a)for(var c in a)Object.prototype.hasOwnProperty.call(a,c)&&(b[c]=a[c]);return b.default=a,b}function d(a,b){for(var c=a.toString();c.length=i&&m<=j&&k.push(b.keys[l])}k.sort(),d.set(k),p=k}}),{suspend:function(){d.clear()},resume:function(){p&&d.set(p)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],10:[function(a,b,c){"use strict";function d(a){if(a&&a.__esModule)return a;var b={};if(null!=a)for(var c in a)Object.prototype.hasOwnProperty.call(a,c)&&(b[c]=a[c]);return b.default=a,b}function e(a){return a&&a.__esModule?a:{default:a}}function f(a,b){if(!(a instanceof b))throw new TypeError("Cannot call a class as a function")}Object.defineProperty(c,"__esModule",{value:!0}),c.SelectionHandle=void 0;var g=function(){function a(a,b){for(var c=0;c0&&void 0!==arguments[0]?arguments[0]:null,c=arguments.length>1&&void 0!==arguments[1]?arguments[1]:null;f(this,a),this._eventRelay=new i.default,this._emitter=new m.SubscriptionTracker(this._eventRelay),this._group=null,this._var=null,this._varOnChangeSub=null,this._extraInfo=m.extend({sender:this},c),this.setGroup(b)}return g(a,[{key:"setGroup",value:function(a){var b=this;if(this._group!==a&&(this._group||a)&&(this._var&&(this._var.off("change",this._varOnChangeSub),this._var=null,this._varOnChangeSub=null),this._group=a,a)){this._var=(0,k.default)(a).var("selection");var c=this._var.on("change",function(a){b._eventRelay.trigger("change",a,b)});this._varOnChangeSub=c}}},{key:"_mergeExtraInfo",value:function(a){return m.extend({},this._extraInfo?this._extraInfo:null,a?a:null)}},{key:"set",value:function(a,b){this._var&&this._var.set(a,this._mergeExtraInfo(b))}},{key:"clear",value:function(a){this._var&&this.set(void 0,this._mergeExtraInfo(a))}},{key:"on",value:function(a,b){return this._emitter.on(a,b)}},{key:"off",value:function(a,b){return this._emitter.off(a,b)}},{key:"close",value:function(){this._emitter.removeAllListeners(),this.setGroup(null)}},{key:"value",get:function(){return this._var?this._var.get():null}}]),a}()},{"./events":1,"./group":4,"./util":11}],11:[function(a,b,c){"use strict";function d(a,b){if(!(a instanceof b))throw new TypeError("Cannot call a class as a function")}function e(a){for(var b=arguments.length,c=Array(b>1?b-1:0),d=1;d {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n /**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n}\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nfunction bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,.\\/:;<=>?@\\[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nexport class SelectionHandle {\n\n /**\n * @classdesc\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n\n /**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n /**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n}\n","export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n"]} \ No newline at end of file diff --git a/docs/articles/Outbreaks_files/datatables-binding-0.12/datatables.js b/docs/articles/Outbreaks_files/datatables-binding-0.12/datatables.js new file mode 100644 index 0000000..7c12ebc --- /dev/null +++ b/docs/articles/Outbreaks_files/datatables-binding-0.12/datatables.js @@ -0,0 +1,1323 @@ +(function() { + +// some helper functions: using a global object DTWidget so that it can be used +// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's +// dynamic scoping, when 'code' is eval()'ed, JavaScript does not know objects +// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made +// a global object +var DTWidget = {}; + +// 123456666.7890 -> 123,456,666.7890 +var markInterval = function(d, digits, interval, mark, decMark, precision) { + x = precision ? d.toPrecision(digits) : d.toFixed(digits); + if (!/^-?[\d.]+$/.test(x)) return x; + var xv = x.split('.'); + if (xv.length > 2) return x; // should have at most one decimal point + xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark); + return xv.join(decMark); +}; + +DTWidget.formatCurrency = function(thiz, row, data, col, currency, digits, interval, mark, decMark, before) { + var d = parseFloat(data[col]); + if (isNaN(d)) return; + var res = markInterval(d, digits, interval, mark, decMark); + res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) : + res + currency; + $(thiz.api().cell(row, col).node()).html(res); +}; + +DTWidget.formatString = function(thiz, row, data, col, prefix, suffix) { + var d = data[col]; + if (d === null) return; + var cell = $(thiz.api().cell(row, col).node()); + cell.html(prefix + cell.html() + suffix); +}; + +DTWidget.formatPercentage = function(thiz, row, data, col, digits, interval, mark, decMark) { + var d = parseFloat(data[col]); + if (isNaN(d)) return; + $(thiz.api().cell(row, col).node()) + .html(markInterval(d * 100, digits, interval, mark, decMark) + '%'); +}; + +DTWidget.formatRound = function(thiz, row, data, col, digits, interval, mark, decMark) { + var d = parseFloat(data[col]); + if (isNaN(d)) return; + $(thiz.api().cell(row, col).node()).html(markInterval(d, digits, interval, mark, decMark)); +}; + +DTWidget.formatSignif = function(thiz, row, data, col, digits, interval, mark, decMark) { + var d = parseFloat(data[col]); + if (isNaN(d)) return; + $(thiz.api().cell(row, col).node()) + .html(markInterval(d, digits, interval, mark, decMark, true)); +}; + +DTWidget.formatDate = function(thiz, row, data, col, method, params) { + var d = data[col]; + if (d === null) return; + // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the + // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)', + // i.e. the date-only string is treated as UTC time instead of local time + if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) { + d = d.split(/\D/); + d = new Date(d[0], d[1] - 1, d[2]); + } else { + d = new Date(d); + } + $(thiz.api().cell(row, col).node()).html(d[method].apply(d, params)); +}; + +window.DTWidget = DTWidget; + +var transposeArray2D = function(a) { + return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a); +}; + +var crosstalkPluginsInstalled = false; + +function maybeInstallCrosstalkPlugins() { + if (crosstalkPluginsInstalled) + return; + crosstalkPluginsInstalled = true; + + $.fn.dataTable.ext.afnFiltering.push( + function(oSettings, aData, iDataIndex) { + var ctfilter = oSettings.nTable.ctfilter; + if (ctfilter && !ctfilter[iDataIndex]) + return false; + + var ctselect = oSettings.nTable.ctselect; + if (ctselect && !ctselect[iDataIndex]) + return false; + + return true; + } + ); +} + +HTMLWidgets.widget({ + name: "datatables", + type: "output", + renderOnNullValue: true, + initialize: function(el, width, height) { + $(el).html(' '); + return { + data: null, + ctfilterHandle: new crosstalk.FilterHandle(), + ctfilterSubscription: null, + ctselectHandle: new crosstalk.SelectionHandle(), + ctselectSubscription: null + }; + }, + renderValue: function(el, data, instance) { + if (el.offsetWidth === 0 || el.offsetHeight === 0) { + instance.data = data; + return; + } + instance.data = null; + var $el = $(el); + $el.empty(); + + if (data === null) { + $el.append(' '); + // clear previous Shiny inputs (if any) + for (var i in instance.clearInputs) instance.clearInputs[i](); + instance.clearInputs = {}; + return; + } + + var crosstalkOptions = data.crosstalkOptions; + if (!crosstalkOptions) crosstalkOptions = { + 'key': null, 'group': null + }; + if (crosstalkOptions.group) { + maybeInstallCrosstalkPlugins(); + instance.ctfilterHandle.setGroup(crosstalkOptions.group); + instance.ctselectHandle.setGroup(crosstalkOptions.group); + } + + // If we are in a flexdashboard scroll layout then we: + // (a) Always want to use pagination (otherwise we'll have + // a "double scroll bar" effect on the phone); and + // (b) Never want to fill the container (we want the pagination + // level to determine the size of the container) + if (window.FlexDashboard && !window.FlexDashboard.isFillPage()) { + data.options.bPaginate = true; + data.fillContainer = false; + } + + // if we are in the viewer then we always want to fillContainer and + // and autoHideNavigation (unless the user has explicitly set these) + if (window.HTMLWidgets.viewerMode) { + if (!data.hasOwnProperty("fillContainer")) + data.fillContainer = true; + if (!data.hasOwnProperty("autoHideNavigation")) + data.autoHideNavigation = true; + } + + // propagate fillContainer to instance (so we have it in resize) + instance.fillContainer = data.fillContainer; + + var cells = data.data; + + if (cells instanceof Array) cells = transposeArray2D(cells); + + $el.append(data.container); + var $table = $el.find('table'); + if (data.class) $table.addClass(data.class); + if (data.caption) $table.prepend(data.caption); + + if (!data.selection) data.selection = { + mode: 'none', selected: null, target: 'row' + }; + if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' && + data.selection.target === 'row+column') { + if ($table.children('tfoot').length === 0) { + $table.append($('')); + $table.find('thead tr').clone().appendTo($table.find('tfoot')); + } + } + + // column filters + var filterRow; + switch (data.filter) { + case 'top': + $table.children('thead').append(data.filterHTML); + filterRow = $table.find('thead tr:last td'); + break; + case 'bottom': + if ($table.children('tfoot').length === 0) { + $table.append($('')); + } + $table.children('tfoot').prepend(data.filterHTML); + filterRow = $table.find('tfoot tr:first td'); + break; + } + + var options = { searchDelay: 1000 }; + if (cells !== null) $.extend(options, { + data: cells + }); + + // options for fillContainer + var bootstrapActive = typeof($.fn.popover) != 'undefined'; + if (instance.fillContainer) { + + // force scrollX/scrollY and turn off autoWidth + options.scrollX = true; + options.scrollY = "100px"; // can be any value, we'll adjust below + + // if we aren't paginating then move around the info/filter controls + // to save space at the bottom and rephrase the info callback + if (data.options.bPaginate === false) { + + // we know how to do this cleanly for bootstrap, not so much + // for other themes/layouts + if (bootstrapActive) { + options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" + + "<'row'<'col-sm-12'tr>>"; + } + + options.fnInfoCallback = function(oSettings, iStart, iEnd, + iMax, iTotal, sPre) { + return Number(iTotal).toLocaleString() + " records"; + }; + } + } + + // auto hide navigation if requested + if (data.autoHideNavigation === true) { + if (bootstrapActive && data.options.bPaginate !== false) { + // strip all nav if length >= cells + if ((cells instanceof Array) && data.options.iDisplayLength >= cells.length) + options.dom = "<'row'<'col-sm-12'tr>>"; + // alternatively lean things out for flexdashboard mobile portrait + else if (window.FlexDashboard && window.FlexDashboard.isMobilePhone()) + options.dom = "<'row'<'col-sm-12'f>>" + + "<'row'<'col-sm-12'tr>>" + + "<'row'<'col-sm-12'p>>"; + } + } + + $.extend(true, options, data.options || {}); + + var searchCols = options.searchCols; + if (searchCols) { + searchCols = searchCols.map(function(x) { + return x === null ? '' : x.search; + }); + // FIXME: this means I don't respect the escapeRegex setting + delete options.searchCols; + } + + // server-side processing? + var server = options.serverSide === true; + + // use the dataSrc function to pre-process JSON data returned from R + var DT_rows_all = [], DT_rows_current = []; + if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' && + /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) { + options.ajax.dataSrc = function(json) { + DT_rows_all = $.makeArray(json.DT_rows_all); + DT_rows_current = $.makeArray(json.DT_rows_current); + var data = json.data; + if (!colReorderEnabled()) return data; + var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row; + for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false; + if (flag) return data; + for (i = 0; i < data.length; ++i) { + row = data[i].slice(); + for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]]; + } + return data; + }; + } + + var thiz = this; + if (instance.fillContainer) $table.on('init.dt', function(e) { + thiz.fillAvailableHeight(el, $(el).innerHeight()); + }); + // If the page contains serveral datatables and one of which enables colReorder, + // the table.colReorder.order() function will exist but throws error when called. + // So it seems like the only way to know if colReorder is enabled or not is to + // check the options. + var colReorderEnabled = function() { return "colReorder" in options; }; + var table = $table.DataTable(options); + $el.data('datatable', table); + + // Unregister previous Crosstalk event subscriptions, if they exist + if (instance.ctfilterSubscription) { + instance.ctfilterHandle.off("change", instance.ctfilterSubscription); + instance.ctfilterSubscription = null; + } + if (instance.ctselectSubscription) { + instance.ctselectHandle.off("change", instance.ctselectSubscription); + instance.ctselectSubscription = null; + } + + if (!crosstalkOptions.group) { + $table[0].ctfilter = null; + $table[0].ctselect = null; + } else { + var key = crosstalkOptions.key; + function keysToMatches(keys) { + if (!keys) { + return null; + } else { + var selectedKeys = {}; + for (var i = 0; i < keys.length; i++) { + selectedKeys[keys[i]] = true; + } + var matches = {}; + for (var j = 0; j < key.length; j++) { + if (selectedKeys[key[j]]) + matches[j] = true; + } + return matches; + } + } + + function applyCrosstalkFilter(e) { + $table[0].ctfilter = keysToMatches(e.value); + table.draw(); + } + instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter); + applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys}); + + function applyCrosstalkSelection(e) { + if (e.sender !== instance.ctselectHandle) { + table + .rows('.' + selClass, {search: 'applied'}) + .nodes() + .to$() + .removeClass(selClass); + if (selectedRows) + changeInput('rows_selected', selectedRows(), void 0, true); + } + + if (e.sender !== instance.ctselectHandle && e.value && e.value.length) { + var matches = keysToMatches(e.value); + + // persistent selection with plotly (& leaflet) + var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {}; + if (ctOpts.persistent === true) { + var matches = $.extend(matches, $table[0].ctselect); + } + + $table[0].ctselect = matches; + table.draw(); + } else { + if ($table[0].ctselect) { + $table[0].ctselect = null; + table.draw(); + } + } + } + instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection); + // TODO: This next line doesn't seem to work when renderDataTable is used + applyCrosstalkSelection({value: instance.ctselectHandle.value}); + } + + var inArray = function(val, array) { + return $.inArray(val, $.makeArray(array)) > -1; + }; + + // encode + to %2B when searching in the table on server side, because + // shiny::parseQueryString() treats + as spaces, and DataTables does not + // encode + to %2B (or % to %25) when sending the request + var encode_plus = function(x) { + return server ? x.replace(/%/g, '%25').replace(/\+/g, '%2B') : x; + }; + + // search the i-th column + var searchColumn = function(i, value) { + var regex = false, ci = true; + if (options.search) { + regex = options.search.regex, + ci = options.search.caseInsensitive !== false; + } + return table.column(i).search(encode_plus(value), regex, !regex, ci); + }; + + if (data.filter !== 'none') { + + filterRow.each(function(i, td) { + + var $td = $(td), type = $td.data('type'), filter; + var $input = $td.children('div').first().children('input'); + $input.prop('disabled', !table.settings()[0].aoColumns[i].bSearchable || type === 'disabled'); + $input.on('input blur', function() { + $input.next('span').toggle(Boolean($input.val())); + }); + // Bootstrap sets pointer-events to none and we won't be able to click + // the clear button + $input.next('span').css('pointer-events', 'auto').hide().click(function() { + $(this).hide().prev('input').val('').trigger('input').focus(); + }); + var searchCol; // search string for this column + if (searchCols && searchCols[i]) { + searchCol = searchCols[i]; + $input.val(searchCol).trigger('input'); + } + var $x = $td.children('div').last(); + + // remove the overflow: hidden attribute of the scrollHead + // (otherwise the scrolling table body obscures the filters) + // The workaround and the discussion from + // https://github.com/rstudio/DT/issues/554#issuecomment-518007347 + // Otherwise the filter selection will not be anchored to the values + // when the columns number is many and scrollX is enabled. + var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot'); + var cssOverflowHead = scrollHead.css('overflow'); + var scrollBody = $(el).find('.dataTables_scrollBody'); + var cssOverflowBody = scrollBody.css('overflow'); + var scrollTable = $(el).find('.dataTables_scroll'); + var cssOverflowTable = scrollTable.css('overflow'); + if (cssOverflowHead === 'hidden') { + $x.on('show hide', function(e) { + if (e.type === 'show') { + scrollHead.css('overflow', 'visible'); + scrollBody.css('overflow', 'visible'); + scrollTable.css('overflow-x', 'scroll'); + } else { + scrollHead.css('overflow', cssOverflowHead); + scrollBody.css('overflow', cssOverflowBody); + scrollTable.css('overflow-x', cssOverflowTable); + } + }); + $x.css('z-index', 25); + } + + if (inArray(type, ['factor', 'logical'])) { + $input.on({ + click: function() { + $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus(); + }, + input: function() { + if ($input.val() === '') filter[0].selectize.setValue([]); + } + }); + var $input2 = $x.children('select'); + filter = $input2.selectize({ + options: $input2.data('options').map(function(v, i) { + return ({text: v, value: v}); + }), + plugins: ['remove_button'], + hideSelected: true, + onChange: function(value) { + if (value === null) value = []; // compatibility with jQuery 3.0 + $input.val(value.length ? JSON.stringify(value) : ''); + if (value.length) $input.trigger('input'); + $input.attr('title', $input.val()); + if (server) { + table.column(i).search(value.length ? encode_plus(JSON.stringify(value)) : '').draw(); + return; + } + // turn off filter if nothing selected + $td.data('filter', value.length > 0); + table.draw(); // redraw table, and filters will be applied + } + }); + if (searchCol) filter[0].selectize.setValue(JSON.parse(searchCol)); + filter[0].selectize.on('blur', function() { + $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur'); + }); + filter.next('div').css('margin-bottom', 'auto'); + } else if (type === 'character') { + var fun = function() { + searchColumn(i, $input.val()).draw(); + }; + if (server) { + fun = $.fn.dataTable.util.throttle(fun, options.searchDelay); + } + $input.on('input', fun); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + var $x0 = $x; + $x = $x0.children('div').first(); + $x0.css({ + 'background-color': '#fff', + 'border': '1px #ddd solid', + 'border-radius': '4px', + 'padding': '20px 20px 10px 20px' + }); + var $spans = $x0.children('span').css({ + 'margin-top': '10px', + 'white-space': 'nowrap' + }); + var $span1 = $spans.first(), $span2 = $spans.last(); + var r1 = +$x.data('min'), r2 = +$x.data('max'); + // when the numbers are too small or have many decimal places, the + // slider may have numeric precision problems (#150) + var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0)); + r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale); + var scaleBack = function(x, scale) { + if (scale === 1) return x; + var d = Math.round(Math.log(scale) / Math.log(10)); + // to avoid problems like 3.423/100 -> 0.034230000000000003 + return (x / scale).toFixed(d); + }; + $input.on({ + focus: function() { + $x0.show().trigger('show'); + // first, make sure the slider div leaves at least 20px between + // the two (slider value) span's + $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20)); + // then, if the input is really wide, make the slider the same + // width as the input + if ($x0.outerWidth() < $input.outerWidth()) { + $x0.outerWidth($input.outerWidth()); + } + // make sure the slider div does not reach beyond the right margin + if ($(window).width() < $x0.offset().left + $x0.width()) { + $x0.offset({ + 'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth() + }); + } + }, + blur: function() { + $x0.hide().trigger('hide'); + }, + input: function() { + if ($input.val() === '') filter.val([r1, r2]); + }, + change: function() { + var v = $input.val().replace(/\s/g, ''); + if (v === '') return; + v = v.split('...'); + if (v.length !== 2) { + $input.parent().addClass('has-error'); + return; + } + if (v[0] === '') v[0] = r1; + if (v[1] === '') v[1] = r2; + $input.parent().removeClass('has-error'); + // treat date as UTC time at midnight + var strTime = function(x) { + var s = type === 'date' ? 'T00:00:00Z' : ''; + var t = new Date(x + s).getTime(); + // add 10 minutes to date since it does not hurt the date, and + // it helps avoid the tricky floating point arithmetic problems, + // e.g. sometimes the date may be a few milliseconds earlier + // than the midnight due to precision problems in noUiSlider + return type === 'date' ? t + 3600000 : t; + }; + if (inArray(type, ['date', 'time'])) { + v[0] = strTime(v[0]); + v[1] = strTime(v[1]); + } + if (v[0] != r1) v[0] *= scale; + if (v[1] != r2) v[1] *= scale; + filter.val(v); + } + }); + var formatDate = function(d, isoFmt) { + d = scaleBack(d, scale); + if (type === 'number') return d; + if (type === 'integer') return parseInt(d); + var x = new Date(+d); + var fmt = ('filterDateFmt' in data) ? data.filterDateFmt[i] : undefined; + if (fmt !== undefined && isoFmt === false) return x[fmt.method].apply(x, fmt.params); + if (type === 'date') { + var pad0 = function(x) { + return ('0' + x).substr(-2, 2); + }; + return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth()) + + '-' + pad0(x.getUTCDate()); + } else { + return x.toISOString(); + } + }; + var opts = type === 'date' ? { step: 60 * 60 * 1000 } : + type === 'integer' ? { step: 1 } : {}; + filter = $x.noUiSlider($.extend({ + start: [r1, r2], + range: {min: r1, max: r2}, + connect: true + }, opts)); + if (scale > 1) (function() { + var t1 = r1, t2 = r2; + var val = filter.val(); + while (val[0] > r1 || val[1] < r2) { + if (val[0] > r1) { + t1 -= val[0] - r1; + } + if (val[1] < r2) { + t2 += r2 - val[1]; + } + filter = $x.noUiSlider($.extend({ + start: [t1, t2], + range: {min: t1, max: t2}, + connect: true + }, opts), true); + val = filter.val(); + } + r1 = t1; r2 = t2; + })(); + var updateSliderText = function(v1, v2) { + $span1.text(formatDate(v1, false)); $span2.text(formatDate(v2, false)); + }; + updateSliderText(r1, r2); + var updateSlider = function(e) { + var val = filter.val(); + // turn off filter if in full range + $td.data('filter', val[0] > r1 || val[1] < r2); + var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival; + if ($td.data('filter')) { + ival = v1 + ' ... ' + v2; + $input.attr('title', ival).val(ival).trigger('input'); + } else { + $input.attr('title', '').val(''); + } + updateSliderText(val[0], val[1]); + if (e.type === 'slide') return; // no searching when sliding only + if (server) { + table.column(i).search($td.data('filter') ? ival : '').draw(); + return; + } + table.draw(); + }; + filter.on({ + set: updateSlider, + slide: updateSlider + }); + } + + // server-side processing will be handled by R (or whatever server + // language you use); the following code is only needed for client-side + // processing + if (server) { + // if a search string has been pre-set, search now + if (searchCol) searchColumn(i, searchCol).draw(); + return; + } + + var customFilter = function(settings, data, dataIndex) { + // there is no way to attach a search function to a specific table, + // and we need to make sure a global search function is not applied to + // all tables (i.e. a range filter in a previous table should not be + // applied to the current table); we use the settings object to + // determine if we want to perform searching on the current table, + // since settings.sTableId will be different to different tables + if (table.settings()[0] !== settings) return true; + // no filter on this column or no need to filter this column + if (typeof filter === 'undefined' || !$td.data('filter')) return true; + + var r = filter.val(), v, r0, r1; + var i_data = function(i) { + if (!colReorderEnabled()) return i; + var order = table.colReorder.order(), k; + for (k = 0; k < order.length; ++k) if (order[k] === i) return k; + return i; // in theory it will never be here... + } + v = data[i_data(i)]; + if (type === 'number' || type === 'integer') { + v = parseFloat(v); + // how to handle NaN? currently exclude these rows + if (isNaN(v)) return(false); + r0 = parseFloat(scaleBack(r[0], scale)) + r1 = parseFloat(scaleBack(r[1], scale)); + if (v >= r0 && v <= r1) return true; + } else if (type === 'date' || type === 'time') { + v = new Date(v); + r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale); + if (v >= r0 && v <= r1) return true; + } else if (type === 'factor') { + if (r.length === 0 || inArray(v, r)) return true; + } else if (type === 'logical') { + if (r.length === 0) return true; + if (inArray(v === '' ? 'na' : v, r)) return true; + } + return false; + }; + + $.fn.dataTable.ext.search.push(customFilter); + + // search for the preset search strings if it is non-empty + if (searchCol) { + if (inArray(type, ['factor', 'logical'])) { + filter[0].selectize.setValue(JSON.parse(searchCol)); + } else if (type === 'character') { + $input.trigger('input'); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + $input.trigger('change'); + } + } + + }); + + } + + // highlight search keywords + var highlight = function() { + var body = $(table.table().body()); + // removing the old highlighting first + body.unhighlight(); + + // don't highlight the "not found" row, so we get the rows using the api + if (table.rows({ filter: 'applied' }).data().length === 0) return; + // highlight global search keywords + body.highlight($.trim(table.search()).split(/\s+/)); + // then highlight keywords from individual column filters + if (filterRow) filterRow.each(function(i, td) { + var $td = $(td), type = $td.data('type'); + if (type !== 'character') return; + var $input = $td.children('div').first().children('input'); + var column = table.column(i).nodes().to$(), + val = $.trim($input.val()); + if (type !== 'character' || val === '') return; + column.highlight(val.split(/\s+/)); + }); + }; + + if (options.searchHighlight) { + table + .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight) + .on('destroy', function() { + // remove event handler + table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth'); + }); + + // Set the option for escaping regex characters in our search string. This will be used + // for all future matching. + jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex); + + // initial highlight for state saved conditions and initial states + highlight(); + } + + // run the callback function on the table instance + if (typeof data.callback === 'function') data.callback(table); + + // double click to edit the cell, row, column, or all cells + if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) { + // only bring up the editor when the cell itself is dbclicked, and ignore + // other dbclick events bubbled up (e.g. from the ) + if (e.target !== this) return; + var target = [], immediate = false; + switch (data.editable.target) { + case 'cell': + target = [this]; + immediate = true; // edit will take effect immediately + break; + case 'row': + target = table.cells(table.cell(this).index().row, '*').nodes(); + break; + case 'column': + target = table.cells('*', table.cell(this).index().column).nodes(); + break; + case 'all': + target = table.cells().nodes(); + break; + default: + throw 'The editable parameter must be "cell", "row", "column", or "all"'; + } + var disableCols = data.editable.disable ? data.editable.disable.columns : null; + for (var i = 0; i < target.length; i++) { + (function(cell, current) { + var $cell = $(cell), html = $cell.html(); + var _cell = table.cell(cell), value = _cell.data(); + var $input = $(''), changed = false; + if (!immediate) { + $cell.data('input', $input).data('html', html); + $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel'); + } + $input.val(value); + if (inArray(_cell.index().column, disableCols)) { + $input.attr('readonly', '').css('filter', 'invert(25%)'); + } + $cell.empty().append($input); + if (cell === current) $input.focus(); + $input.css('width', '100%'); + + if (immediate) $input.on('change', function() { + changed = true; + var valueNew = $input.val(); + if (valueNew != value) { + _cell.data(valueNew); + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: "event"}); + } + // for server-side processing, users have to call replaceData() to update the table + if (!server) table.draw(false); + } else { + $cell.html(html); + } + $input.remove(); + }).on('blur', function() { + if (!changed) $input.trigger('change'); + }).on('keyup', function(e) { + // hit Escape to cancel editing + if (e.keyCode === 27) $input.trigger('blur'); + }); + + // bulk edit (row, column, or all) + if (!immediate) $input.on('keyup', function(e) { + var removeInput = function($cell, restore) { + $cell.data('input').remove(); + if (restore) $cell.html($cell.data('html')); + } + if (e.keyCode === 27) { + for (var i = 0; i < target.length; i++) { + removeInput($(target[i]), true); + } + } else if (e.keyCode === 13 && e.ctrlKey) { + // Ctrl + Enter + var cell, $cell, _cell, cellData = []; + for (var i = 0; i < target.length; i++) { + cell = target[i]; $cell = $(cell); _cell = table.cell(cell); + _cell.data($cell.data('input').val()); + HTMLWidgets.shinyMode && cellData.push(cellInfo(cell)); + removeInput($cell, false); + } + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"}); + } + if (!server) table.draw(false); + } + }); + })(target[i], this); + } + }); + + // interaction with shiny + if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return; + + var methods = {}; + var shinyData = {}; + + methods.updateCaption = function(caption) { + if (!caption) return; + $table.children('caption').replaceWith(caption); + } + + // register clear functions to remove input values when the table is removed + instance.clearInputs = {}; + + var changeInput = function(id, value, type, noCrosstalk, opts) { + var event = id; + id = el.id + '_' + id; + if (type) id = id + ':' + type; + // do not update if the new value is the same as old value + if (event !== 'cell_edit' && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value)) + return; + shinyData[id] = JSON.stringify(value); + if (HTMLWidgets.shinyMode && Shiny.setInputValue) { + Shiny.setInputValue(id, value, opts); + if (!instance.clearInputs[id]) instance.clearInputs[id] = function() { + Shiny.setInputValue(id, null); + } + } + + // HACK + if (event === "rows_selected" && !noCrosstalk) { + if (crosstalkOptions.group) { + var keys = crosstalkOptions.key; + var selectedKeys = null; + if (value) { + selectedKeys = []; + for (var i = 0; i < value.length; i++) { + // The value array's contents use 1-based row numbers, so we must + // convert to 0-based before indexing into the keys array. + selectedKeys.push(keys[value[i] - 1]); + } + } + instance.ctselectHandle.set(selectedKeys); + } + } + }; + + var addOne = function(x) { + return x.map(function(i) { return 1 + i; }); + }; + + var unique = function(x) { + var ux = []; + $.each(x, function(i, el){ + if ($.inArray(el, ux) === -1) ux.push(el); + }); + return ux; + } + + // change the row index of a cell + var tweakCellIndex = function(cell) { + var info = cell.index(); + // some cell may not be valid. e.g, #759 + // when using the RowGroup extension, datatables will + // generate the row label and the cells are not part of + // the data thus contain no row/col info + if (info === undefined) + return {row: null, col: null}; + if (server) { + info.row = DT_rows_current[info.row]; + } else { + info.row += 1; + } + return {row: info.row, col: info.column}; + } + + // a flag to indicates if select extension is initialized or not + var flagSelectExt = table.settings()[0]._select !== undefined; + // the Select extension should only be used in the client mode and + // when the selection.mode is set to none + if (data.selection.mode === 'none' && !server && flagSelectExt) { + var updateRowsSelected = function() { + var rows = table.rows({selected: true}); + var selected = []; + $.each(rows.indexes().toArray(), function(i, v) { + selected.push(v + 1); + }); + changeInput('rows_selected', selected); + } + var updateColsSelected = function() { + var columns = table.columns({selected: true}); + changeInput('columns_selected', columns.indexes().toArray()); + } + var updateCellsSelected = function() { + var cells = table.cells({selected: true}); + var selected = []; + cells.every(function() { + var row = this.index().row; + var col = this.index().column; + selected = selected.concat([[row + 1, col]]); + }); + changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix'); + } + table.on('select deselect', function(e, dt, type, indexes) { + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + }) + } + + var selMode = data.selection.mode, selTarget = data.selection.target; + if (inArray(selMode, ['single', 'multiple'])) { + var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected'; + var selected = data.selection.selected, selected1, selected2; + // selected1: row indices; selected2: column indices + if (selected === null) { + selected1 = selected2 = []; + } else if (selTarget === 'row') { + selected1 = $.makeArray(selected); + } else if (selTarget === 'column') { + selected2 = $.makeArray(selected); + } else if (selTarget === 'row+column') { + selected1 = $.makeArray(selected.rows); + selected2 = $.makeArray(selected.cols); + } + + // After users reorder the rows or filter the table, we cannot use the table index + // directly. Instead, we need this function to find out the rows between the two clicks. + // If user filter the table again between the start click and the end click, the behavior + // would be undefined, but it should not be a problem. + var shiftSelRowsIndex = function(start, end) { + var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray(); + start = indexes.indexOf(start); end = indexes.indexOf(end); + // if start is larger than end, we need to swap + if (start > end) { + var tmp = end; end = start; start = tmp; + } + return indexes.slice(start, end + 1); + } + + var serverRowIndex = function(clientRowIndex) { + return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1; + } + + // row, column, or cell selection + var lastClickedRow; + if (inArray(selTarget, ['row', 'row+column'])) { + var selectedRows = function() { + var rows = table.rows('.' + selClass); + var idx = rows.indexes().toArray(); + if (!server) return addOne(idx); + idx = idx.map(function(i) { + return DT_rows_current[i]; + }); + selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx; + return selected1; + } + table.on('mousedown.dt', 'tbody tr', function(e) { + var $this = $(this), thisRow = table.row(this); + if (selMode === 'multiple') { + if (e.shiftKey && lastClickedRow !== undefined) { + // select or de-select depends on the last clicked row's status + var flagSel = !$this.hasClass(selClass); + var crtClickedRow = serverRowIndex(thisRow.index()); + if (server) { + var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow); + // update current page's selClass + rowsIndex.map(function(i) { + var rowIndex = DT_rows_current.indexOf(i); + if (rowIndex >= 0) { + var row = table.row(rowIndex).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + } + }); + // update selected1 + if (flagSel) { + selected1 = unique(selected1.concat(rowsIndex)); + } else { + selected1 = selected1.filter(function(index) { + return !inArray(index, rowsIndex); + }); + } + } else { + // js starts from 0 + shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) { + var row = table.row(value).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + }); + } + e.preventDefault(); + } else { + $this.toggleClass(selClass); + } + } else { + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + } else { + table.$('tr.' + selClass).removeClass(selClass); + $this.addClass(selClass); + } + } + if (server && !$this.hasClass(selClass)) { + var id = DT_rows_current[thisRow.index()]; + // remove id from selected1 since its class .selected has been removed + if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1); + } + changeInput('rows_selected', selectedRows()); + changeInput('row_last_clicked', serverRowIndex(thisRow.index())); + lastClickedRow = serverRowIndex(thisRow.index()); + }); + changeInput('rows_selected', selected1); + var selectRows = function() { + table.$('tr.' + selClass).removeClass(selClass); + if (selected1.length === 0) return; + if (server) { + table.rows({page: 'current'}).every(function() { + if (inArray(DT_rows_current[this.index()], selected1)) { + $(this.node()).addClass(selClass); + } + }); + } else { + var selected0 = selected1.map(function(i) { return i - 1; }); + $(table.rows(selected0).nodes()).addClass(selClass); + } + } + selectRows(); // in case users have specified pre-selected rows + // restore selected rows after the table is redrawn (e.g. sort/search/page); + // client-side tables will preserve the selections automatically; for + // server-side tables, we have to *real* row indices are in `selected1` + if (server) table.on('draw.dt', selectRows); + methods.selectRows = function(selected) { + selected1 = $.makeArray(selected); + selectRows(); + changeInput('rows_selected', selected1); + } + } + + if (inArray(selTarget, ['column', 'row+column'])) { + if (selTarget === 'row+column') { + $(table.columns().footer()).css('cursor', 'pointer'); + } + var callback = function() { + var colIdx = selTarget === 'column' ? table.cell(this).index().column : + $.inArray(this, table.columns().footer()), + thisCol = $(table.column(colIdx).nodes()); + if (colIdx === -1) return; + if (thisCol.hasClass(selClass)) { + thisCol.removeClass(selClass); + selected2.splice($.inArray(colIdx, selected2), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + thisCol.addClass(selClass); + selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx])); + } + changeInput('columns_selected', selected2); + } + if (selTarget === 'column') { + $(table.table().body()).on('click.dt', 'td', callback); + } else { + $(table.table().footer()).on('click.dt', 'tr th', callback); + } + changeInput('columns_selected', selected2); + var selectCols = function() { + table.columns().nodes().flatten().to$().removeClass(selClass); + if (selected2.length > 0) + table.columns(selected2).nodes().flatten().to$().addClass(selClass); + } + selectCols(); // in case users have specified pre-selected columns + if (server) table.on('draw.dt', selectCols); + methods.selectColumns = function(selected) { + selected2 = $.makeArray(selected); + selectCols(); + changeInput('columns_selected', selected2); + } + } + + if (selTarget === 'cell') { + var selected3; + if (selected === null) { + selected3 = []; + } else { + selected3 = selected; + } + var findIndex = function(ij) { + for (var i = 0; i < selected3.length; i++) { + if (ij[0] === selected3[i][0] && ij[1] === selected3[i][1]) return i; + } + return -1; + } + table.on('click.dt', 'tbody td', function() { + var $this = $(this), info = tweakCellIndex(table.cell(this)); + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + selected3.splice(findIndex([info.row, info.col]), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + $this.addClass(selClass); + selected3 = selMode === 'single' ? [[info.row, info.col]] : + unique(selected3.concat([[info.row, info.col]])); + } + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + }); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + var selectCells = function() { + table.$('td.' + selClass).removeClass(selClass); + if (selected3.length === 0) return; + if (server) { + table.cells({page: 'current'}).every(function() { + var info = tweakCellIndex(this); + if (findIndex([info.row, info.col], selected3) > -1) + $(this.node()).addClass(selClass); + }); + } else { + selected3.map(function(ij) { + $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass); + }); + } + }; + selectCells(); // in case users have specified pre-selected columns + if (server) table.on('draw.dt', selectCells); + methods.selectCells = function(selected) { + selected3 = selected ? selected : []; + selectCells(); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + } + } + } + + // expose some table info to Shiny + var updateTableInfo = function(e, settings) { + // TODO: is anyone interested in the page info? + // changeInput('page_info', table.page.info()); + var updateRowInfo = function(id, modifier) { + var idx; + if (server) { + idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all; + } else { + var rows = table.rows($.extend({ + search: 'applied', + page: 'all' + }, modifier)); + idx = addOne(rows.indexes().toArray()); + } + changeInput('rows' + '_' + id, idx); + }; + updateRowInfo('current', {page: 'current'}); + updateRowInfo('all', {}); + } + table.on('draw.dt', updateTableInfo); + updateTableInfo(); + + // state info + table.on('draw.dt column-visibility.dt', function() { + changeInput('state', table.state()); + }); + changeInput('state', table.state()); + + // search info + var updateSearchInfo = function() { + changeInput('search', table.search()); + if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) { + return $(td).find('input').first().val(); + })); + } + table.on('draw.dt', updateSearchInfo); + updateSearchInfo(); + + var cellInfo = function(thiz) { + var info = tweakCellIndex(table.cell(thiz)); + info.value = table.cell(thiz).data(); + return info; + } + // the current cell clicked on + table.on('click.dt', 'tbody td', function() { + changeInput('cell_clicked', cellInfo(this)); + }) + changeInput('cell_clicked', {}); + + // do not trigger table selection when clicking on links unless they have classes + table.on('click.dt', 'tbody td a', function(e) { + if (this.className === '') e.stopPropagation(); + }); + + methods.addRow = function(data, rowname) { + var data0 = table.row(0).data(), n = data0.length, d = n - data.length; + if (d === 1) { + data = rowname.concat(data) + } else if (d !== 0) { + console.log(data); + console.log(data0); + throw 'New data must be of the same length as current data (' + n + ')'; + }; + table.row.add(data).draw(); + } + + methods.updateSearch = function(keywords) { + if (keywords.global !== null) + $(table.table().container()).find('input[type=search]').first() + .val(keywords.global).trigger('input'); + var columns = keywords.columns; + if (!filterRow || columns === null) return; + filterRow.toArray().map(function(td, i) { + var v = typeof columns === 'string' ? columns : columns[i]; + if (typeof v === 'undefined') { + console.log('The search keyword for column ' + i + ' is undefined') + return; + } + $(td).find('input').first().val(v); + searchColumn(i, v); + }); + table.draw(); + } + + methods.hideCols = function(hide, reset) { + if (reset) table.columns().visible(true, false); + table.columns(hide).visible(false); + } + + methods.showCols = function(show, reset) { + if (reset) table.columns().visible(false, false); + table.columns(show).visible(true); + } + + methods.colReorder = function(order, origOrder) { + table.colReorder.order(order, origOrder); + } + + methods.selectPage = function(page) { + if (table.page.info().pages < page || page < 1) { + throw 'Selected page is out of range'; + }; + table.page(page - 1).draw(false); + } + + methods.reloadData = function(resetPaging, clearSelection) { + // empty selections first if necessary + if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]); + if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]); + if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]); + table.ajax.reload(null, resetPaging); + } + + table.shinyMethods = methods; + }, + resize: function(el, width, height, instance) { + if (instance.data) this.renderValue(el, instance.data, instance); + + // dynamically adjust height if fillContainer = TRUE + if (instance.fillContainer) + this.fillAvailableHeight(el, height); + + this.adjustWidth(el); + }, + + // dynamically set the scroll body to fill available height + // (used with fillContainer = TRUE) + fillAvailableHeight: function(el, availableHeight) { + + // see how much of the table is occupied by header/footer elements + // and use that to compute a target scroll body height + var dtWrapper = $(el).find('div.dataTables_wrapper'); + var dtScrollBody = $(el).find($('div.dataTables_scrollBody')); + var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight(); + var scrollBodyHeight = availableHeight - framingHeight; + + // set the height + dtScrollBody.height(scrollBodyHeight + 'px'); + }, + + // adjust the width of columns; remove the hard-coded widths on table and the + // scroll header when scrollX/Y are enabled + adjustWidth: function(el) { + var $el = $(el), table = $el.data('datatable'); + if (table) table.columns.adjust(); + $el.find('.dataTables_scrollHeadInner').css('width', '') + .children('table').css('margin-left', ''); + } +}); + + if (!HTMLWidgets.shinyMode) return; + + Shiny.addCustomMessageHandler('datatable-calls', function(data) { + var id = data.id; + var el = document.getElementById(id); + var table = el ? $(el).data('datatable') : null; + if (!table) { + console.log("Couldn't find table with id " + id); + return; + } + + var methods = table.shinyMethods, call = data.call; + if (methods[call.method]) { + methods[call.method].apply(table, call.args); + } else { + console.log("Unknown method " + call.method); + } + }); + +})(); diff --git a/docs/articles/Outbreaks_files/datatables-css-0.0.0/datatables-crosstalk.css b/docs/articles/Outbreaks_files/datatables-css-0.0.0/datatables-crosstalk.css new file mode 100644 index 0000000..43422d2 --- /dev/null +++ b/docs/articles/Outbreaks_files/datatables-css-0.0.0/datatables-crosstalk.css @@ -0,0 +1,7 @@ +.dt-crosstalk-fade { + opacity: 0.2; +} + +html body div.DTS div.dataTables_scrollBody { + background: none; +} diff --git a/docs/articles/Outbreaks_files/dt-core-1.10.20/css/jquery.dataTables.extra.css b/docs/articles/Outbreaks_files/dt-core-1.10.20/css/jquery.dataTables.extra.css new file mode 100644 index 0000000..dbbac6d --- /dev/null +++ b/docs/articles/Outbreaks_files/dt-core-1.10.20/css/jquery.dataTables.extra.css @@ -0,0 +1,8 @@ +/* Selected rows/cells */ +table.dataTable tr.selected td, table.dataTable td.selected { + background-color: #b0bed9 !important; +} +/* In case of scrollX/Y or 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+f.extend(q.ext.classes,{sTable:"dataTable",sNoFooter:"no-footer",sPageButton:"paginate_button",sPageButtonActive:"current",sPageButtonDisabled:"disabled",sStripeOdd:"odd",sStripeEven:"even",sRowEmpty:"dataTables_empty",sWrapper:"dataTables_wrapper",sFilter:"dataTables_filter",sInfo:"dataTables_info",sPaging:"dataTables_paginate paging_",sLength:"dataTables_length",sProcessing:"dataTables_processing",sSortAsc:"sorting_asc",sSortDesc:"sorting_desc",sSortable:"sorting",sSortableAsc:"sorting_asc_disabled", +sSortableDesc:"sorting_desc_disabled",sSortableNone:"sorting_disabled",sSortColumn:"sorting_",sFilterInput:"",sLengthSelect:"",sScrollWrapper:"dataTables_scroll",sScrollHead:"dataTables_scrollHead",sScrollHeadInner:"dataTables_scrollHeadInner",sScrollBody:"dataTables_scrollBody",sScrollFoot:"dataTables_scrollFoot",sScrollFootInner:"dataTables_scrollFootInner",sHeaderTH:"",sFooterTH:"",sSortJUIAsc:"",sSortJUIDesc:"",sSortJUI:"",sSortJUIAscAllowed:"",sSortJUIDescAllowed:"",sSortJUIWrapper:"",sSortIcon:"", +sJUIHeader:"",sJUIFooter:""});var Pb=q.ext.pager;f.extend(Pb,{simple:function(a,b){return["previous","next"]},full:function(a,b){return["first","previous","next","last"]},numbers:function(a,b){return[ka(a,b)]},simple_numbers:function(a,b){return["previous",ka(a,b),"next"]},full_numbers:function(a,b){return["first","previous",ka(a,b),"next","last"]},first_last_numbers:function(a,b){return["first",ka(a,b),"last"]},_numbers:ka,numbers_length:7});f.extend(!0,q.ext.renderer,{pageButton:{_:function(a,b, +c,d,e,h){var g=a.oClasses,k=a.oLanguage.oPaginate,l=a.oLanguage.oAria.paginate||{},n,m,q=0,t=function(b,d){var p,r=g.sPageButtonDisabled,u=function(b){Xa(a,b.data.action,!0)};var w=0;for(p=d.length;w").appendTo(b);t(x,v)}else{n=null;m=v;x=a.iTabIndex;switch(v){case "ellipsis":b.append('…');break;case "first":n=k.sFirst;0===e&&(x=-1,m+=" "+r);break;case "previous":n=k.sPrevious;0===e&&(x=-1,m+= +" "+r);break;case "next":n=k.sNext;e===h-1&&(x=-1,m+=" "+r);break;case "last":n=k.sLast;e===h-1&&(x=-1,m+=" "+r);break;default:n=v+1,m=e===v?g.sPageButtonActive:""}null!==n&&(x=f("",{"class":g.sPageButton+" "+m,"aria-controls":a.sTableId,"aria-label":l[v],"data-dt-idx":q,tabindex:x,id:0===c&&"string"===typeof v?a.sTableId+"_"+v:null}).html(n).appendTo(b),$a(x,{action:v},u),q++)}}};try{var v=f(b).find(y.activeElement).data("dt-idx")}catch(mc){}t(f(b).empty(),d);v!==p&&f(b).find("[data-dt-idx="+ +v+"]").focus()}}});f.extend(q.ext.type.detect,[function(a,b){b=b.oLanguage.sDecimal;return db(a,b)?"num"+b:null},function(a,b){if(a&&!(a instanceof Date)&&!cc.test(a))return null;b=Date.parse(a);return null!==b&&!isNaN(b)||P(a)?"date":null},function(a,b){b=b.oLanguage.sDecimal;return db(a,b,!0)?"num-fmt"+b:null},function(a,b){b=b.oLanguage.sDecimal;return Ub(a,b)?"html-num"+b:null},function(a,b){b=b.oLanguage.sDecimal;return Ub(a,b,!0)?"html-num-fmt"+b:null},function(a,b){return P(a)||"string"=== +typeof a&&-1!==a.indexOf("<")?"html":null}]);f.extend(q.ext.type.search,{html:function(a){return P(a)?a:"string"===typeof a?a.replace(Rb," ").replace(Ea,""):""},string:function(a){return P(a)?a:"string"===typeof a?a.replace(Rb," "):a}});var Da=function(a,b,c,d){if(0!==a&&(!a||"-"===a))return-Infinity;b&&(a=Tb(a,b));a.replace&&(c&&(a=a.replace(c,"")),d&&(a=a.replace(d,"")));return 1*a};f.extend(C.type.order,{"date-pre":function(a){a=Date.parse(a);return isNaN(a)?-Infinity:a},"html-pre":function(a){return P(a)? +"":a.replace?a.replace(/<.*?>/g,"").toLowerCase():a+""},"string-pre":function(a){return P(a)?"":"string"===typeof a?a.toLowerCase():a.toString?a.toString():""},"string-asc":function(a,b){return ab?1:0},"string-desc":function(a,b){return ab?-1:0}});Ha("");f.extend(!0,q.ext.renderer,{header:{_:function(a,b,c,d){f(a.nTable).on("order.dt.DT",function(e,f,g,k){a===f&&(e=c.idx,b.removeClass(c.sSortingClass+" "+d.sSortAsc+" "+d.sSortDesc).addClass("asc"==k[e]?d.sSortAsc:"desc"==k[e]?d.sSortDesc: +c.sSortingClass))})},jqueryui:function(a,b,c,d){f("
    ").addClass(d.sSortJUIWrapper).append(b.contents()).append(f("").addClass(d.sSortIcon+" "+c.sSortingClassJUI)).appendTo(b);f(a.nTable).on("order.dt.DT",function(e,f,g,k){a===f&&(e=c.idx,b.removeClass(d.sSortAsc+" "+d.sSortDesc).addClass("asc"==k[e]?d.sSortAsc:"desc"==k[e]?d.sSortDesc:c.sSortingClass),b.find("span."+d.sSortIcon).removeClass(d.sSortJUIAsc+" "+d.sSortJUIDesc+" "+d.sSortJUI+" "+d.sSortJUIAscAllowed+" "+d.sSortJUIDescAllowed).addClass("asc"== +k[e]?d.sSortJUIAsc:"desc"==k[e]?d.sSortJUIDesc:c.sSortingClassJUI))})}}});var ib=function(a){return"string"===typeof a?a.replace(//g,">").replace(/"/g,"""):a};q.render={number:function(a,b,c,d,e){return{display:function(f){if("number"!==typeof f&&"string"!==typeof f)return f;var g=0>f?"-":"",h=parseFloat(f);if(isNaN(h))return ib(f);h=h.toFixed(c);f=Math.abs(h);h=parseInt(f,10);f=c?b+(f-h).toFixed(c).substring(2):"";return g+(d||"")+h.toString().replace(/\B(?=(\d{3})+(?!\d))/g, +a)+f+(e||"")}}},text:function(){return{display:ib,filter:ib}}};f.extend(q.ext.internal,{_fnExternApiFunc:Qb,_fnBuildAjax:va,_fnAjaxUpdate:qb,_fnAjaxParameters:zb,_fnAjaxUpdateDraw:Ab,_fnAjaxDataSrc:wa,_fnAddColumn:Ia,_fnColumnOptions:ma,_fnAdjustColumnSizing:aa,_fnVisibleToColumnIndex:ba,_fnColumnIndexToVisible:ca,_fnVisbleColumns:W,_fnGetColumns:oa,_fnColumnTypes:Ka,_fnApplyColumnDefs:nb,_fnHungarianMap:H,_fnCamelToHungarian:L,_fnLanguageCompat:Ga,_fnBrowserDetect:lb,_fnAddData:R,_fnAddTr:pa,_fnNodeToDataIndex:function(a, +b){return b._DT_RowIndex!==p?b._DT_RowIndex:null},_fnNodeToColumnIndex:function(a,b,c){return f.inArray(c,a.aoData[b].anCells)},_fnGetCellData:I,_fnSetCellData:ob,_fnSplitObjNotation:Na,_fnGetObjectDataFn:U,_fnSetObjectDataFn:Q,_fnGetDataMaster:Oa,_fnClearTable:qa,_fnDeleteIndex:ra,_fnInvalidate:ea,_fnGetRowElements:Ma,_fnCreateTr:La,_fnBuildHead:pb,_fnDrawHead:ha,_fnDraw:S,_fnReDraw:V,_fnAddOptionsHtml:sb,_fnDetectHeader:fa,_fnGetUniqueThs:ua,_fnFeatureHtmlFilter:ub,_fnFilterComplete:ia,_fnFilterCustom:Db, +_fnFilterColumn:Cb,_fnFilter:Bb,_fnFilterCreateSearch:Ta,_fnEscapeRegex:Ua,_fnFilterData:Eb,_fnFeatureHtmlInfo:xb,_fnUpdateInfo:Hb,_fnInfoMacros:Ib,_fnInitialise:ja,_fnInitComplete:xa,_fnLengthChange:Va,_fnFeatureHtmlLength:tb,_fnFeatureHtmlPaginate:yb,_fnPageChange:Xa,_fnFeatureHtmlProcessing:vb,_fnProcessingDisplay:K,_fnFeatureHtmlTable:wb,_fnScrollDraw:na,_fnApplyToChildren:N,_fnCalculateColumnWidths:Ja,_fnThrottle:Sa,_fnConvertToWidth:Jb,_fnGetWidestNode:Kb,_fnGetMaxLenString:Lb,_fnStringToCss:B, +_fnSortFlatten:Y,_fnSort:rb,_fnSortAria:Nb,_fnSortListener:Za,_fnSortAttachListener:Qa,_fnSortingClasses:Aa,_fnSortData:Mb,_fnSaveState:Ba,_fnLoadState:Ob,_fnSettingsFromNode:Ca,_fnLog:O,_fnMap:M,_fnBindAction:$a,_fnCallbackReg:E,_fnCallbackFire:A,_fnLengthOverflow:Wa,_fnRenderer:Ra,_fnDataSource:D,_fnRowAttributes:Pa,_fnExtend:ab,_fnCalculateEnd:function(){}});f.fn.dataTable=q;q.$=f;f.fn.dataTableSettings=q.settings;f.fn.dataTableExt=q.ext;f.fn.DataTable=function(a){return f(this).dataTable(a).api()}; +f.each(q,function(a,b){f.fn.DataTable[a]=b});return f.fn.dataTable}); diff --git a/docs/articles/Outbreaks_files/htmlwidgets-1.5.1/htmlwidgets.js b/docs/articles/Outbreaks_files/htmlwidgets-1.5.1/htmlwidgets.js new file mode 100644 index 0000000..6f3d672 --- /dev/null +++ b/docs/articles/Outbreaks_files/htmlwidgets-1.5.1/htmlwidgets.js @@ -0,0 +1,903 @@ +(function() { + // If window.HTMLWidgets is already defined, then use it; otherwise create a + // new object. This allows preceding code to set options that affect the + // initialization process (though none currently exist). + window.HTMLWidgets = window.HTMLWidgets || {}; + + // See if we're running in a viewer pane. If not, we're in a web browser. + var viewerMode = window.HTMLWidgets.viewerMode = + /\bviewer_pane=1\b/.test(window.location); + + // See if we're running in Shiny mode. If not, it's a static document. + // Note that static widgets can appear in both Shiny and static modes, but + // obviously, Shiny widgets can only appear in Shiny apps/documents. + var shinyMode = window.HTMLWidgets.shinyMode = + typeof(window.Shiny) !== "undefined" && !!window.Shiny.outputBindings; + + // We can't count on jQuery being available, so we implement our own + // version if necessary. + function querySelectorAll(scope, selector) { + if (typeof(jQuery) !== "undefined" && scope instanceof jQuery) { + return scope.find(selector); + } + if (scope.querySelectorAll) { + return scope.querySelectorAll(selector); + } + } + + function asArray(value) { + if (value === null) + return []; + if ($.isArray(value)) + return value; + return [value]; + } + + // Implement jQuery's extend + function extend(target /*, ... */) { + if (arguments.length == 1) { + return target; + } + for (var i = 1; i < arguments.length; i++) { + var source = arguments[i]; + for (var prop in source) { + if (source.hasOwnProperty(prop)) { + target[prop] = source[prop]; + } + } + } + return target; + } + + // IE8 doesn't support Array.forEach. + function forEach(values, callback, thisArg) { + if (values.forEach) { + values.forEach(callback, thisArg); + } else { + for (var i = 0; i < values.length; i++) { + callback.call(thisArg, values[i], i, values); + } + } + } + + // Replaces the specified method with the return value of funcSource. + // + // Note that funcSource should not BE the new method, it should be a function + // that RETURNS the new method. funcSource receives a single argument that is + // the overridden method, it can be called from the new method. The overridden + // method can be called like a regular function, it has the target permanently + // bound to it so "this" will work correctly. + function overrideMethod(target, methodName, funcSource) { + var superFunc = target[methodName] || function() {}; + var superFuncBound = function() { + return superFunc.apply(target, arguments); + }; + target[methodName] = funcSource(superFuncBound); + } + + // Add a method to delegator that, when invoked, calls + // delegatee.methodName. If there is no such method on + // the delegatee, but there was one on delegator before + // delegateMethod was called, then the original version + // is invoked instead. + // For example: + // + // var a = { + // method1: function() { console.log('a1'); } + // method2: function() { console.log('a2'); } + // }; + // var b = { + // method1: function() { console.log('b1'); } + // }; + // delegateMethod(a, b, "method1"); + // delegateMethod(a, b, "method2"); + // a.method1(); + // a.method2(); + // + // The output would be "b1", "a2". + function delegateMethod(delegator, delegatee, methodName) { + var inherited = delegator[methodName]; + delegator[methodName] = function() { + var target = delegatee; + var method = delegatee[methodName]; + + // The method doesn't exist on the delegatee. Instead, + // call the method on the delegator, if it exists. + if (!method) { + target = delegator; + method = inherited; + } + + if (method) { + return method.apply(target, arguments); + } + }; + } + + // Implement a vague facsimilie of jQuery's data method + function elementData(el, name, value) { + if (arguments.length == 2) { + return el["htmlwidget_data_" + name]; + } else if (arguments.length == 3) { + el["htmlwidget_data_" + name] = value; + return el; + } else { + throw new Error("Wrong number of arguments for elementData: " + + arguments.length); + } + } + + // http://stackoverflow.com/questions/3446170/escape-string-for-use-in-javascript-regex + function escapeRegExp(str) { + return str.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g, "\\$&"); + } + + function hasClass(el, className) { + var re = new RegExp("\\b" + escapeRegExp(className) + "\\b"); + return re.test(el.className); + } + + // elements - array (or array-like object) of HTML elements + // className - class name to test for + // include - if true, only return elements with given className; + // if false, only return elements *without* given className + function filterByClass(elements, className, include) { + var results = []; + for (var i = 0; i < elements.length; i++) { + if (hasClass(elements[i], className) == include) + results.push(elements[i]); + } + return results; + } + + function on(obj, eventName, func) { + if (obj.addEventListener) { + obj.addEventListener(eventName, func, false); + } else if (obj.attachEvent) { + obj.attachEvent(eventName, func); + } + } + + function off(obj, eventName, func) { + if (obj.removeEventListener) + obj.removeEventListener(eventName, func, false); + else if (obj.detachEvent) { + obj.detachEvent(eventName, func); + } + } + + // Translate array of values to top/right/bottom/left, as usual with + // the "padding" CSS property + // https://developer.mozilla.org/en-US/docs/Web/CSS/padding + function unpackPadding(value) { + if (typeof(value) === "number") + value = [value]; + if (value.length === 1) { + return {top: value[0], right: value[0], bottom: value[0], left: value[0]}; + } + if (value.length === 2) { + return {top: value[0], right: value[1], bottom: value[0], left: value[1]}; + } + if (value.length === 3) { + return {top: value[0], right: value[1], bottom: value[2], left: value[1]}; + } + if (value.length === 4) { + return {top: value[0], right: value[1], bottom: value[2], left: value[3]}; + } + } + + // Convert an unpacked padding object to a CSS value + function paddingToCss(paddingObj) { + return paddingObj.top + "px " + paddingObj.right + "px " + paddingObj.bottom + "px " + paddingObj.left + "px"; + } + + // Makes a number suitable for CSS + function px(x) { + if (typeof(x) === "number") + return x + "px"; + else + return x; + } + + // Retrieves runtime widget sizing information for an element. + // The return value is either null, or an object with fill, padding, + // defaultWidth, defaultHeight fields. + function sizingPolicy(el) { + var sizingEl = document.querySelector("script[data-for='" + el.id + "'][type='application/htmlwidget-sizing']"); + if (!sizingEl) + return null; + var sp = JSON.parse(sizingEl.textContent || sizingEl.text || "{}"); + if (viewerMode) { + return sp.viewer; + } else { + return sp.browser; + } + } + + // @param tasks Array of strings (or falsy value, in which case no-op). + // Each element must be a valid JavaScript expression that yields a + // function. Or, can be an array of objects with "code" and "data" + // properties; in this case, the "code" property should be a string + // of JS that's an expr that yields a function, and "data" should be + // an object that will be added as an additional argument when that + // function is called. + // @param target The object that will be "this" for each function + // execution. + // @param args Array of arguments to be passed to the functions. (The + // same arguments will be passed to all functions.) + function evalAndRun(tasks, target, args) { + if (tasks) { + forEach(tasks, function(task) { + var theseArgs = args; + if (typeof(task) === "object") { + theseArgs = theseArgs.concat([task.data]); + task = task.code; + } + var taskFunc = tryEval(task); + if (typeof(taskFunc) !== "function") { + throw new Error("Task must be a function! Source:\n" + task); + } + taskFunc.apply(target, theseArgs); + }); + } + } + + // Attempt eval() both with and without enclosing in parentheses. + // Note that enclosing coerces a function declaration into + // an expression that eval() can parse + // (otherwise, a SyntaxError is thrown) + function tryEval(code) { + var result = null; + try { + result = eval(code); + } catch(error) { + if (!error instanceof SyntaxError) { + throw error; + } + try { + result = eval("(" + code + ")"); + } catch(e) { + if (e instanceof SyntaxError) { + throw error; + } else { + throw e; + } + } + } + return result; + } + + function initSizing(el) { + var sizing = sizingPolicy(el); + if (!sizing) + return; + + var cel = document.getElementById("htmlwidget_container"); + if (!cel) + return; + + if (typeof(sizing.padding) !== "undefined") { + document.body.style.margin = "0"; + document.body.style.padding = paddingToCss(unpackPadding(sizing.padding)); + } + + if (sizing.fill) { + document.body.style.overflow = "hidden"; + document.body.style.width = "100%"; + document.body.style.height = "100%"; + document.documentElement.style.width = "100%"; + document.documentElement.style.height = "100%"; + if (cel) { + cel.style.position = "absolute"; + var pad = unpackPadding(sizing.padding); + cel.style.top = pad.top + "px"; + cel.style.right = pad.right + "px"; + cel.style.bottom = pad.bottom + "px"; + cel.style.left = pad.left + "px"; + el.style.width = "100%"; + el.style.height = "100%"; + } + + return { + getWidth: function() { return cel.offsetWidth; }, + getHeight: function() { return cel.offsetHeight; } + }; + + } else { + el.style.width = px(sizing.width); + el.style.height = px(sizing.height); + + return { + getWidth: function() { return el.offsetWidth; }, + getHeight: function() { return el.offsetHeight; } + }; + } + } + + // Default implementations for methods + var defaults = { + find: function(scope) { + return querySelectorAll(scope, "." + this.name); + }, + renderError: function(el, err) { + var $el = $(el); + + this.clearError(el); + + // Add all these error classes, as Shiny does + var errClass = "shiny-output-error"; + if (err.type !== null) { + // use the classes of the error condition as CSS class names + errClass = errClass + " " + $.map(asArray(err.type), function(type) { + return errClass + "-" + type; + }).join(" "); + } + errClass = errClass + " htmlwidgets-error"; + + // Is el inline or block? If inline or inline-block, just display:none it + // and add an inline error. + var display = $el.css("display"); + $el.data("restore-display-mode", display); + + if (display === "inline" || display === "inline-block") { + $el.hide(); + if (err.message !== "") { + var errorSpan = $("").addClass(errClass); + errorSpan.text(err.message); + $el.after(errorSpan); + } + } else if (display === "block") { + // If block, add an error just after the el, set visibility:none on the + // el, and position the error to be on top of the el. + // Mark it with a unique ID and CSS class so we can remove it later. + $el.css("visibility", "hidden"); + if (err.message !== "") { + var errorDiv = $("
    ").addClass(errClass).css("position", "absolute") + .css("top", el.offsetTop) + .css("left", el.offsetLeft) + // setting width can push out the page size, forcing otherwise + // unnecessary scrollbars to appear and making it impossible for + // the element to shrink; so use max-width instead + .css("maxWidth", el.offsetWidth) + .css("height", el.offsetHeight); + errorDiv.text(err.message); + $el.after(errorDiv); + + // Really dumb way to keep the size/position of the error in sync with + // the parent element as the window is resized or whatever. + var intId = setInterval(function() { + if (!errorDiv[0].parentElement) { + clearInterval(intId); + return; + } + errorDiv + .css("top", el.offsetTop) + .css("left", el.offsetLeft) + .css("maxWidth", el.offsetWidth) + .css("height", el.offsetHeight); + }, 500); + } + } + }, + clearError: function(el) { + var $el = $(el); + var display = $el.data("restore-display-mode"); + $el.data("restore-display-mode", null); + + if (display === "inline" || display === "inline-block") { + if (display) + $el.css("display", display); + $(el.nextSibling).filter(".htmlwidgets-error").remove(); + } else if (display === "block"){ + $el.css("visibility", "inherit"); + $(el.nextSibling).filter(".htmlwidgets-error").remove(); + } + }, + sizing: {} + }; + + // Called by widget bindings to register a new type of widget. The definition + // object can contain the following properties: + // - name (required) - A string indicating the binding name, which will be + // used by default as the CSS classname to look for. + // - initialize (optional) - A function(el) that will be called once per + // widget element; if a value is returned, it will be passed as the third + // value to renderValue. + // - renderValue (required) - A function(el, data, initValue) that will be + // called with data. Static contexts will cause this to be called once per + // element; Shiny apps will cause this to be called multiple times per + // element, as the data changes. + window.HTMLWidgets.widget = function(definition) { + if (!definition.name) { + throw new Error("Widget must have a name"); + } + if (!definition.type) { + throw new Error("Widget must have a type"); + } + // Currently we only support output widgets + if (definition.type !== "output") { + throw new Error("Unrecognized widget type '" + definition.type + "'"); + } + // TODO: Verify that .name is a valid CSS classname + + // Support new-style instance-bound definitions. Old-style class-bound + // definitions have one widget "object" per widget per type/class of + // widget; the renderValue and resize methods on such widget objects + // take el and instance arguments, because the widget object can't + // store them. New-style instance-bound definitions have one widget + // object per widget instance; the definition that's passed in doesn't + // provide renderValue or resize methods at all, just the single method + // factory(el, width, height) + // which returns an object that has renderValue(x) and resize(w, h). + // This enables a far more natural programming style for the widget + // author, who can store per-instance state using either OO-style + // instance fields or functional-style closure variables (I guess this + // is in contrast to what can only be called C-style pseudo-OO which is + // what we required before). + if (definition.factory) { + definition = createLegacyDefinitionAdapter(definition); + } + + if (!definition.renderValue) { + throw new Error("Widget must have a renderValue function"); + } + + // For static rendering (non-Shiny), use a simple widget registration + // scheme. We also use this scheme for Shiny apps/documents that also + // contain static widgets. + window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || []; + // Merge defaults into the definition; don't mutate the original definition. + var staticBinding = extend({}, defaults, definition); + overrideMethod(staticBinding, "find", function(superfunc) { + return function(scope) { + var results = superfunc(scope); + // Filter out Shiny outputs, we only want the static kind + return filterByClass(results, "html-widget-output", false); + }; + }); + window.HTMLWidgets.widgets.push(staticBinding); + + if (shinyMode) { + // Shiny is running. Register the definition with an output binding. + // The definition itself will not be the output binding, instead + // we will make an output binding object that delegates to the + // definition. This is because we foolishly used the same method + // name (renderValue) for htmlwidgets definition and Shiny bindings + // but they actually have quite different semantics (the Shiny + // bindings receive data that includes lots of metadata that it + // strips off before calling htmlwidgets renderValue). We can't + // just ignore the difference because in some widgets it's helpful + // to call this.renderValue() from inside of resize(), and if + // we're not delegating, then that call will go to the Shiny + // version instead of the htmlwidgets version. + + // Merge defaults with definition, without mutating either. + var bindingDef = extend({}, defaults, definition); + + // This object will be our actual Shiny binding. + var shinyBinding = new Shiny.OutputBinding(); + + // With a few exceptions, we'll want to simply use the bindingDef's + // version of methods if they are available, otherwise fall back to + // Shiny's defaults. NOTE: If Shiny's output bindings gain additional + // methods in the future, and we want them to be overrideable by + // HTMLWidget binding definitions, then we'll need to add them to this + // list. + delegateMethod(shinyBinding, bindingDef, "getId"); + delegateMethod(shinyBinding, bindingDef, "onValueChange"); + delegateMethod(shinyBinding, bindingDef, "onValueError"); + delegateMethod(shinyBinding, bindingDef, "renderError"); + delegateMethod(shinyBinding, bindingDef, "clearError"); + delegateMethod(shinyBinding, bindingDef, "showProgress"); + + // The find, renderValue, and resize are handled differently, because we + // want to actually decorate the behavior of the bindingDef methods. + + shinyBinding.find = function(scope) { + var results = bindingDef.find(scope); + + // Only return elements that are Shiny outputs, not static ones + var dynamicResults = results.filter(".html-widget-output"); + + // It's possible that whatever caused Shiny to think there might be + // new dynamic outputs, also caused there to be new static outputs. + // Since there might be lots of different htmlwidgets bindings, we + // schedule execution for later--no need to staticRender multiple + // times. + if (results.length !== dynamicResults.length) + scheduleStaticRender(); + + return dynamicResults; + }; + + // Wrap renderValue to handle initialization, which unfortunately isn't + // supported natively by Shiny at the time of this writing. + + shinyBinding.renderValue = function(el, data) { + Shiny.renderDependencies(data.deps); + // Resolve strings marked as javascript literals to objects + if (!(data.evals instanceof Array)) data.evals = [data.evals]; + for (var i = 0; data.evals && i < data.evals.length; i++) { + window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]); + } + if (!bindingDef.renderOnNullValue) { + if (data.x === null) { + el.style.visibility = "hidden"; + return; + } else { + el.style.visibility = "inherit"; + } + } + if (!elementData(el, "initialized")) { + initSizing(el); + + elementData(el, "initialized", true); + if (bindingDef.initialize) { + var result = bindingDef.initialize(el, el.offsetWidth, + el.offsetHeight); + elementData(el, "init_result", result); + } + } + bindingDef.renderValue(el, data.x, elementData(el, "init_result")); + evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]); + }; + + // Only override resize if bindingDef implements it + if (bindingDef.resize) { + shinyBinding.resize = function(el, width, height) { + // Shiny can call resize before initialize/renderValue have been + // called, which doesn't make sense for widgets. + if (elementData(el, "initialized")) { + bindingDef.resize(el, width, height, elementData(el, "init_result")); + } + }; + } + + Shiny.outputBindings.register(shinyBinding, bindingDef.name); + } + }; + + var scheduleStaticRenderTimerId = null; + function scheduleStaticRender() { + if (!scheduleStaticRenderTimerId) { + scheduleStaticRenderTimerId = setTimeout(function() { + scheduleStaticRenderTimerId = null; + window.HTMLWidgets.staticRender(); + }, 1); + } + } + + // Render static widgets after the document finishes loading + // Statically render all elements that are of this widget's class + window.HTMLWidgets.staticRender = function() { + var bindings = window.HTMLWidgets.widgets || []; + forEach(bindings, function(binding) { + var matches = binding.find(document.documentElement); + forEach(matches, function(el) { + var sizeObj = initSizing(el, binding); + + if (hasClass(el, "html-widget-static-bound")) + return; + el.className = el.className + " html-widget-static-bound"; + + var initResult; + if (binding.initialize) { + initResult = binding.initialize(el, + sizeObj ? sizeObj.getWidth() : el.offsetWidth, + sizeObj ? sizeObj.getHeight() : el.offsetHeight + ); + elementData(el, "init_result", initResult); + } + + if (binding.resize) { + var lastSize = { + w: sizeObj ? sizeObj.getWidth() : el.offsetWidth, + h: sizeObj ? sizeObj.getHeight() : el.offsetHeight + }; + var resizeHandler = function(e) { + var size = { + w: sizeObj ? sizeObj.getWidth() : el.offsetWidth, + h: sizeObj ? sizeObj.getHeight() : el.offsetHeight + }; + if (size.w === 0 && size.h === 0) + return; + if (size.w === lastSize.w && size.h === lastSize.h) + return; + lastSize = size; + binding.resize(el, size.w, size.h, initResult); + }; + + on(window, "resize", resizeHandler); + + // This is needed for cases where we're running in a Shiny + // app, but the widget itself is not a Shiny output, but + // rather a simple static widget. One example of this is + // an rmarkdown document that has runtime:shiny and widget + // that isn't in a render function. Shiny only knows to + // call resize handlers for Shiny outputs, not for static + // widgets, so we do it ourselves. + if (window.jQuery) { + window.jQuery(document).on( + "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets", + resizeHandler + ); + window.jQuery(document).on( + "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets", + resizeHandler + ); + } + + // This is needed for the specific case of ioslides, which + // flips slides between display:none and display:block. + // Ideally we would not have to have ioslide-specific code + // here, but rather have ioslides raise a generic event, + // but the rmarkdown package just went to CRAN so the + // window to getting that fixed may be long. + if (window.addEventListener) { + // It's OK to limit this to window.addEventListener + // browsers because ioslides itself only supports + // such browsers. + on(document, "slideenter", resizeHandler); + on(document, "slideleave", resizeHandler); + } + } + + var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']"); + if (scriptData) { + var data = JSON.parse(scriptData.textContent || scriptData.text); + // Resolve strings marked as javascript literals to objects + if (!(data.evals instanceof Array)) data.evals = [data.evals]; + for (var k = 0; data.evals && k < data.evals.length; k++) { + window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]); + } + binding.renderValue(el, data.x, initResult); + evalAndRun(data.jsHooks.render, initResult, [el, data.x]); + } + }); + }); + + invokePostRenderHandlers(); + } + + + function has_jQuery3() { + if (!window.jQuery) { + return false; + } + var $version = window.jQuery.fn.jquery; + var $major_version = parseInt($version.split(".")[0]); + return $major_version >= 3; + } + + /* + / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's + / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now + / really means $(setTimeout(fn)). + / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous + / + / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny + / one tick later than it did before, which means staticRender() is + / called renderValue() earlier than (advanced) widget authors might be expecting. + / https://github.com/rstudio/shiny/issues/2630 + / + / For a concrete example, leaflet has some methods (e.g., updateBounds) + / which reference Shiny methods registered in initShiny (e.g., setInputValue). + / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to + / delay execution of those methods (until Shiny methods are ready) + / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268 + / + / Ideally widget authors wouldn't need to use this setTimeout() hack that + / leaflet uses to call Shiny methods on a staticRender(). In the long run, + / the logic initShiny should be broken up so that method registration happens + / right away, but binding happens later. + */ + function maybeStaticRenderLater() { + if (shinyMode && has_jQuery3()) { + window.jQuery(window.HTMLWidgets.staticRender); + } else { + window.HTMLWidgets.staticRender(); + } + } + + if (document.addEventListener) { + document.addEventListener("DOMContentLoaded", function() { + document.removeEventListener("DOMContentLoaded", arguments.callee, false); + maybeStaticRenderLater(); + }, false); + } else if (document.attachEvent) { + document.attachEvent("onreadystatechange", function() { + if (document.readyState === "complete") { + document.detachEvent("onreadystatechange", arguments.callee); + maybeStaticRenderLater(); + } + }); + } + + + window.HTMLWidgets.getAttachmentUrl = function(depname, key) { + // If no key, default to the first item + if (typeof(key) === "undefined") + key = 1; + + var link = document.getElementById(depname + "-" + key + "-attachment"); + if (!link) { + throw new Error("Attachment " + depname + "/" + key + " not found in document"); + } + return link.getAttribute("href"); + }; + + window.HTMLWidgets.dataframeToD3 = function(df) { + var names = []; + var length; + for (var name in df) { + if (df.hasOwnProperty(name)) + names.push(name); + if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof(length) !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; + }; + + window.HTMLWidgets.transposeArray2D = function(array) { + if (array.length === 0) return array; + var newArray = array[0].map(function(col, i) { + return array.map(function(row) { + return row[i] + }) + }); + return newArray; + }; + // Split value at splitChar, but allow splitChar to be escaped + // using escapeChar. Any other characters escaped by escapeChar + // will be included as usual (including escapeChar itself). + function splitWithEscape(value, splitChar, escapeChar) { + var results = []; + var escapeMode = false; + var currentResult = ""; + for (var pos = 0; pos < value.length; pos++) { + if (!escapeMode) { + if (value[pos] === splitChar) { + results.push(currentResult); + currentResult = ""; + } else if (value[pos] === escapeChar) { + escapeMode = true; + } else { + currentResult += value[pos]; + } + } else { + currentResult += value[pos]; + escapeMode = false; + } + } + if (currentResult !== "") { + results.push(currentResult); + } + return results; + } + // Function authored by Yihui/JJ Allaire + window.HTMLWidgets.evaluateStringMember = function(o, member) { + var parts = splitWithEscape(member, '.', '\\'); + for (var i = 0, l = parts.length; i < l; i++) { + var part = parts[i]; + // part may be a character or 'numeric' member name + if (o !== null && typeof o === "object" && part in o) { + if (i == (l - 1)) { // if we are at the end of the line then evalulate + if (typeof o[part] === "string") + o[part] = tryEval(o[part]); + } else { // otherwise continue to next embedded object + o = o[part]; + } + } + } + }; + + // Retrieve the HTMLWidget instance (i.e. the return value of an + // HTMLWidget binding's initialize() or factory() function) + // associated with an element, or null if none. + window.HTMLWidgets.getInstance = function(el) { + return elementData(el, "init_result"); + }; + + // Finds the first element in the scope that matches the selector, + // and returns the HTMLWidget instance (i.e. the return value of + // an HTMLWidget binding's initialize() or factory() function) + // associated with that element, if any. If no element matches the + // selector, or the first matching element has no HTMLWidget + // instance associated with it, then null is returned. + // + // The scope argument is optional, and defaults to window.document. + window.HTMLWidgets.find = function(scope, selector) { + if (arguments.length == 1) { + selector = scope; + scope = document; + } + + var el = scope.querySelector(selector); + if (el === null) { + return null; + } else { + return window.HTMLWidgets.getInstance(el); + } + }; + + // Finds all elements in the scope that match the selector, and + // returns the HTMLWidget instances (i.e. the return values of + // an HTMLWidget binding's initialize() or factory() function) + // associated with the elements, in an array. If elements that + // match the selector don't have an associated HTMLWidget + // instance, the returned array will contain nulls. + // + // The scope argument is optional, and defaults to window.document. + window.HTMLWidgets.findAll = function(scope, selector) { + if (arguments.length == 1) { + selector = scope; + scope = document; + } + + var nodes = scope.querySelectorAll(selector); + var results = []; + for (var i = 0; i < nodes.length; i++) { + results.push(window.HTMLWidgets.getInstance(nodes[i])); + } + return results; + }; + + var postRenderHandlers = []; + function invokePostRenderHandlers() { + while (postRenderHandlers.length) { + var handler = postRenderHandlers.shift(); + if (handler) { + handler(); + } + } + } + + // Register the given callback function to be invoked after the + // next time static widgets are rendered. + window.HTMLWidgets.addPostRenderHandler = function(callback) { + postRenderHandlers.push(callback); + }; + + // Takes a new-style instance-bound definition, and returns an + // old-style class-bound definition. This saves us from having + // to rewrite all the logic in this file to accomodate both + // types of definitions. + function createLegacyDefinitionAdapter(defn) { + var result = { + name: defn.name, + type: defn.type, + initialize: function(el, width, height) { + return defn.factory(el, width, height); + }, + renderValue: function(el, x, instance) { + return instance.renderValue(x); + }, + resize: function(el, width, height, instance) { + return instance.resize(width, height); + } + }; + + if (defn.find) + result.find = defn.find; + if (defn.renderError) + result.renderError = defn.renderError; + if (defn.clearError) + result.clearError = defn.clearError; + + return result; + } +})(); + diff --git a/docs/articles/Outbreaks_files/jquery-1.12.4/LICENSE.txt b/docs/articles/Outbreaks_files/jquery-1.12.4/LICENSE.txt new file mode 100644 index 0000000..5bf4f5e --- /dev/null +++ b/docs/articles/Outbreaks_files/jquery-1.12.4/LICENSE.txt @@ -0,0 +1,37 @@ +Copyright 2005, 2014 jQuery Foundation and other contributors, +https://jquery.org/ + +This software consists of voluntary contributions made by many +individuals. For exact contribution history, see the revision history +available at https://github.com/jquery/jquery + +The following license applies to all parts of this software except as +documented below: + +==== + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +==== + +All files located in the node_modules and external directories are +externally maintained libraries used by this software which have their +own licenses; we recommend you read them, as their terms may differ from +the terms above. diff --git a/docs/articles/Outbreaks_files/jquery-1.12.4/jquery.min.js b/docs/articles/Outbreaks_files/jquery-1.12.4/jquery.min.js new file mode 100644 index 0000000..e836475 --- /dev/null +++ b/docs/articles/Outbreaks_files/jquery-1.12.4/jquery.min.js @@ -0,0 +1,5 @@ +/*! jQuery v1.12.4 | (c) jQuery Foundation | jquery.org/license */ +!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery 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