From f935776625e5f57372bf2df76b70b706a42d65e9 Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Tue, 27 Jun 2023 08:09:28 +0000 Subject: [PATCH 1/6] README updated for install.packages segment #177 --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3a8a3de..14d4253 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,11 @@ to apply a data cut to SDTM data in R. ## Installation -The package is available from CRAN and can be installed by running install.packages("datacutr"). +The package is available from CRAN and can be installed by running the following, + +```r +install.packages("datacutr") +``` To install the latest development version of the package directly from GitHub use the following code:: From 8895027a922e007ff0852e7b3217f653f330e246 Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Mon, 25 Sep 2023 09:09:43 +0000 Subject: [PATCH 2/6] Update lintr issues raised #177 --- R/date_cut.R | 2 +- vignettes/variable_cut.Rmd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/date_cut.R b/R/date_cut.R index 02989d4..3f323e4 100644 --- a/R/date_cut.R +++ b/R/date_cut.R @@ -92,7 +92,7 @@ date_cut <- function(dataset_sdtm, # Flag records to be removed - those occurring after cut date and patients not in dcut dataset dataset <- dataset_sdtm_pt %>% mutate(DCUT_TEMP_REMOVE = ifelse((DCUT_TEMP_SDTM_DATE > DCUT_TEMP_DCUTDTM) | - is.na(DCUT_TEMP_DCUTDTM), "Y", NA_character_)) + is.na(DCUT_TEMP_DCUTDTM), "Y", NA_character_)) dataset <- drop_temp_vars(dsin = dataset, drop_dcut_temp = FALSE) diff --git a/vignettes/variable_cut.Rmd b/vignettes/variable_cut.Rmd index d53cfdb..390f63f 100755 --- a/vignettes/variable_cut.Rmd +++ b/vignettes/variable_cut.Rmd @@ -81,8 +81,8 @@ sv <- tibble::tribble( dcut <- dcut %>% left_join(sv %>% - filter(VISIT == "WEEK24") %>% - select(USUBJID, SVSTDTC)) %>% + filter(VISIT == "WEEK24") %>% + select(USUBJID, SVSTDTC)) %>% mutate(DCUTDTC = as.character(ifelse(!is.na(SVSTDTC), SVSTDTC, as.character(DCUTDTC)))) %>% impute_dcutdtc(dsin = ., varin = DCUTDTC, varout = DCUTDTM) ``` From ce32bf969b18f16a2c5a46117c21e7922fec4f34 Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Mon, 25 Sep 2023 10:08:12 +0000 Subject: [PATCH 3/6] Reverse lintr update for styler #177 --- R/date_cut.R | 2 +- vignettes/variable_cut.Rmd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/date_cut.R b/R/date_cut.R index 3f323e4..02989d4 100644 --- a/R/date_cut.R +++ b/R/date_cut.R @@ -92,7 +92,7 @@ date_cut <- function(dataset_sdtm, # Flag records to be removed - those occurring after cut date and patients not in dcut dataset dataset <- dataset_sdtm_pt %>% mutate(DCUT_TEMP_REMOVE = ifelse((DCUT_TEMP_SDTM_DATE > DCUT_TEMP_DCUTDTM) | - is.na(DCUT_TEMP_DCUTDTM), "Y", NA_character_)) + is.na(DCUT_TEMP_DCUTDTM), "Y", NA_character_)) dataset <- drop_temp_vars(dsin = dataset, drop_dcut_temp = FALSE) diff --git a/vignettes/variable_cut.Rmd b/vignettes/variable_cut.Rmd index 390f63f..d53cfdb 100755 --- a/vignettes/variable_cut.Rmd +++ b/vignettes/variable_cut.Rmd @@ -81,8 +81,8 @@ sv <- tibble::tribble( dcut <- dcut %>% left_join(sv %>% - filter(VISIT == "WEEK24") %>% - select(USUBJID, SVSTDTC)) %>% + filter(VISIT == "WEEK24") %>% + select(USUBJID, SVSTDTC)) %>% mutate(DCUTDTC = as.character(ifelse(!is.na(SVSTDTC), SVSTDTC, as.character(DCUTDTC)))) %>% impute_dcutdtc(dsin = ., varin = DCUTDTC, varout = DCUTDTM) ``` From a9088f751b3a34bd4bd917bbd4167f3f948e7065 Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Mon, 25 Sep 2023 11:10:23 +0000 Subject: [PATCH 4/6] Updating lintr and styler to renv #177 --- renv.lock | 59 +++++++++++++++++++++++++++++++------------------------ 1 file changed, 33 insertions(+), 26 deletions(-) diff --git a/renv.lock b/renv.lock index 5eb137d..0d29f57 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "3.6.3", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", @@ -69,21 +69,28 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713" }, "assertthat": { "Package": "assertthat", "Version": "0.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "50c838a310445e954bc13f26f26a6ecf" }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c39fbec8a30d23e721980b8afb31984c" + }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc" }, "brew": { @@ -118,7 +125,7 @@ "Package": "cli", "Version": "3.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3177a5a16c243adc199ba33117bd9657" }, "clipr": { @@ -237,7 +244,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" }, "evaluate": { @@ -258,21 +265,21 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, "fs": { "Package": "fs", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "15e9634c0fcd294799e9b2e929ed1b86" }, "gert": { @@ -363,7 +370,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5aab57a3bd297eee1c1d862735972182" }, "jsonlite": { @@ -391,22 +398,22 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370" }, "lifecycle": { "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "001cecbeac1cff9301bdc3775ee46a86" }, "lintr": { "Package": "lintr", - "Version": "2.0.1", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "023cecbdc0a32f86ad3cb1734c018d2e" + "Hash": "b21ebd652d940f099915221f3328ab7b" }, "lubridate": { "Package": "lubridate", @@ -419,7 +426,7 @@ "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7ce2733a9826b3aeb1775d56fd305472" }, "memoise": { @@ -461,7 +468,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, "pkgdown": { @@ -482,14 +489,14 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f" }, "prettyunits": { "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e" }, "processx": { @@ -531,7 +538,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, "rcmdcheck": { @@ -559,7 +566,7 @@ "Package": "renv", "Version": "0.13.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9f10d9db5b50400c348920c5c603385e" }, "rex": { @@ -573,7 +580,7 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" }, "rmarkdown": { @@ -594,7 +601,7 @@ "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1de7ab598047a87bba48434ba35d497d" }, "rstudioapi": { @@ -648,10 +655,10 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c855e70eb69b3dd8883660b7110e0c44" + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", @@ -699,7 +706,7 @@ "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { @@ -762,7 +769,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "40682ed6a969ea5abfd351eb67833adc" }, "xmlparsedata": { From 924822bbedeb460247f51dc75f62eaf1610a404d Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Mon, 25 Sep 2023 12:29:13 +0000 Subject: [PATCH 5/6] Adds NEWS.md version notes #177 --- NEWS.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/NEWS.md b/NEWS.md index 4e75117..41199cd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,17 @@ +# datacutr 0.2.0 + +## New Features +- N/A + +## Updates of Existing Functions +- N/A + +## Breaking Changes +- N/A + +## Documentation +- Minor documentation updates #171 #173 #177 + # datacutr 0.1.0 ## New Features From 6e9407f130b761671a91f10288bf205e716e94ad Mon Sep 17 00:00:00 2001 From: Tim Barnett Date: Tue, 3 Oct 2023 15:56:43 +0000 Subject: [PATCH 6/6] Reset renv.lock repos #177 --- renv.lock | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/renv.lock b/renv.lock index 0d29f57..4fc65bb 100644 --- a/renv.lock +++ b/renv.lock @@ -69,28 +69,28 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e8a22846fff485f0be3770c2da758713" }, "assertthat": { "Package": "assertthat", "Version": "0.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "50c838a310445e954bc13f26f26a6ecf" }, "backports": { "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c39fbec8a30d23e721980b8afb31984c" }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "543776ae6848fde2f48ff3816d0628bc" }, "brew": { @@ -125,7 +125,7 @@ "Package": "cli", "Version": "3.6.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "3177a5a16c243adc199ba33117bd9657" }, "clipr": { @@ -244,7 +244,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" }, "evaluate": { @@ -265,21 +265,21 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, "fs": { "Package": "fs", "Version": "1.5.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", "Version": "0.1.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "15e9634c0fcd294799e9b2e929ed1b86" }, "gert": { @@ -370,7 +370,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5aab57a3bd297eee1c1d862735972182" }, "jsonlite": { @@ -398,14 +398,14 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d908914ae53b04d4c0c0fd72ecc35370" }, "lifecycle": { "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "001cecbeac1cff9301bdc3775ee46a86" }, "lintr": { @@ -426,7 +426,7 @@ "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "7ce2733a9826b3aeb1775d56fd305472" }, "memoise": { @@ -468,7 +468,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, "pkgdown": { @@ -489,14 +489,14 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a555924add98c99d2f411e37e7d25e9f" }, "prettyunits": { "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e" }, "processx": { @@ -538,7 +538,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, "rcmdcheck": { @@ -566,7 +566,7 @@ "Package": "renv", "Version": "0.13.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9f10d9db5b50400c348920c5c603385e" }, "rex": { @@ -580,7 +580,7 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" }, "rmarkdown": { @@ -601,7 +601,7 @@ "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "1de7ab598047a87bba48434ba35d497d" }, "rstudioapi": { @@ -706,7 +706,7 @@ "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { @@ -769,7 +769,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "40682ed6a969ea5abfd351eb67833adc" }, "xmlparsedata": {