From 53701f061544e91e7d1b3d48a57756922720aaff Mon Sep 17 00:00:00 2001 From: "George G. Vega Yon" Date: Fri, 31 May 2024 00:56:55 -0600 Subject: [PATCH] Addressing CRAN comments --- DESCRIPTION | 6 ++-- R/app.R | 2 +- R/functions-ui.R | 2 +- README.Rmd | 2 +- README.md | 75 +++++++++++++++++++++++----------------- man/epiworldRShiny.Rd | 2 +- man/epiworldrshiny-ui.Rd | 2 +- 7 files changed, 52 insertions(+), 39 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9366ecd..b029be9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: epiworldRShiny Type: Package -Title: An 'RShiny' Wrapper of the R Package 'epiworldR' +Title: A 'shiny' Wrapper of the R Package 'epiworldR' Version: 0.1-0 -Date: 2024-05-14 +Date: 2024-05-31 Authors@R: c( person("Derek", "Meyer", role=c("aut","cre"), email="derekmeyer37@gmail.com", comment = c(ORCID = "0009-0005-1350-6988")), @@ -17,7 +17,7 @@ Authors@R: c( person("Matthew", "Samore", role=c("ctb"), email="matthew.samore@hsc.utah.edu", comment = c(ORCID = "0000-0002-4862-9196")), person("Jay", "Love", role=c("ctb"), email="jay.love@utah.edu", comment = c(ORCID="0000-0002-9371-2466")), person("Kristina", "Stratford", role=c("ctb"), email="kristina.stratford@hsc.utah.edu")) -Description: This 'RShiny' wrapper provides a user-friendly interface to the Agent-Based Modeling (ABM) R package 'epiworldR' (Meyer et al., 2023) . Some of the main features of the package include the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Recovered (SIR), and the Susceptible-Exposed-Infected-Recovered (SEIR) models. 'epiworldRShiny' provides a web-based user interface for running various epidemiological ABMs, simulating interventions, and visualizing results interactively. +Description: R 'shiny' web apps for epidemiological Agent-Based Models. It provides a user-friendly interface to the Agent-Based Modeling (ABM) R package 'epiworldR' (Meyer et al., 2023) . Some of the main features of the package include the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Recovered (SIR), and Susceptible-Exposed-Infected-Recovered (SEIR) models. 'epiworldRShiny' provides a web-based user interface for running various epidemiological ABMs, simulating interventions, and visualizing results interactively. URL: https://github.com/UofUEpiBio/epiworldRShiny/, https://uofuepibio.github.io/epiworldRShiny/, BugReports: https://github.com/UofUEpiBio/epiworldRShiny/issues/ diff --git a/R/app.R b/R/app.R index 3926bc1..5f1b48c 100644 --- a/R/app.R +++ b/R/app.R @@ -14,7 +14,7 @@ #' @importFrom stats aggregate as.formula reshape #' @importFrom utils write.csv packageVersion #' -#' @return Loads and opens the RShiny app for the epiworldR package +#' @return Loads and opens the R shiny app for the epiworldR package #' @param ... Currently ignored. #' @export #' @name epiworldRShiny diff --git a/R/functions-ui.R b/R/functions-ui.R index 81d4ba8..cf0e70d 100644 --- a/R/functions-ui.R +++ b/R/functions-ui.R @@ -22,7 +22,7 @@ text_input_disease_name <- function(model_name) { #' @rdname epiworldrshiny-ui #' @export #' @examples -#' # slider_prevalence("SEIRD") +#' slider_prevalence("SEIRD") slider_prevalence <- function(model_name) { shiny::sliderInput( paste0(model_name, "_prevalence"), diff --git a/README.Rmd b/README.Rmd index c529322..119fa54 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,5 +1,5 @@ --- -title: "epiworldRShiny: An RShiny Application for the epiworldR Package" +title: "epiworldRShiny: A 'shiny' Wrapper of the R Package 'epiworldR'" output: github_document --- diff --git a/README.md b/README.md index e946e27..9ad72ea 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -epiworldRShiny: An RShiny Application for the epiworldR Package +epiworldRShiny: A ‘shiny’ Wrapper of the R Package ‘epiworldR’ ================ @@ -9,18 +9,20 @@ status](https://www.r-pkg.org/badges/version/epiworldRShiny)](https://CRAN.R-pro This R package provides a user-friendly application for -[epiworldR](https://github.com/UofUEpiBio/epiworldR), a wrapper of the -C++ library [epiworld](https://github.com/UofUEpiBio/epiworld). It -provides a general framework for modeling disease transmission using -[agent-based -models](https://en.wikipedia.org/w/index.php?title=Agent-based_model&oldid=1153634802). -Some of the main features include: - - - Fast simulation with an average of 30 million agents/day per second. - - 9 different epidemiological models to choose from. - - Built-in capability for user-defined interventions. - - Built-in capability to define population and disease parameters. - - Informative visualizations and tables after running each simulation. +epiworldR, a wrapper of the C++ library +epiworld. It provides a general framework for +modeling disease transmission using agent-based models. Some of the main features +include: + +- Fast simulation with an average of 30 million agents/day per second. +- 9 different epidemiological models to choose from. +- Built-in capability for user-defined interventions. +- Built-in capability to define population and disease parameters. +- Informative visualizations and tables after running each simulation. You can find more examples on the package’s website: @@ -61,13 +63,17 @@ number, a model summary, and a table of counts over time are displayed. This example features: - SEIR network model for COVID-19 The day of peak infections occurs on day 12, maxing at about 18,000 infections. -\- The disease spreads rapidly at the simulation’s beginning, -drastically decreasing over the first ten days. -\- Model summary -\- State counts table - -![example 1 -GIF](https://github.com/UofUEpiBio/epiworldRShiny/assets/105825983/f4e7d313-e3b6-4ebb-9c0a-ca4d53ef9cea) +- The disease spreads rapidly at the simulation’s beginning, drastically +decreasing over the first ten days. +- Model summary +- State counts table + +
+ + +
### Example \#2 @@ -76,15 +82,18 @@ closure interventions to curb disease spread. All model output can be interpreted using the same logic from example \#1. Key features: - SEIRD network model for COVID-19 -\- Vaccine prevalence = 70% -\- School closure prevalence = 50% -\- Day of school closure implementation = 7 -\- Significantly decreased number of infections and deaths. -\- The majority of the population recovered or was susceptible by day -30. - -![example 2 -GIF](https://github.com/UofUEpiBio/epiworldRShiny/assets/105825983/d5405162-f7fe-4a42-8a4c-e9a2ac31be73) +- Vaccine prevalence = 70% +- School closure prevalence = 50% +- Day of school closure implementation = 7 +- Significantly decreased number of infections and deaths. +- The majority of the population recovered or was susceptible by day 30. + +
+ + +
### Example \#3 @@ -98,5 +107,9 @@ population, 70% non-hispanic - 52% female population - 30% of population younger than 20 years old - 30% of population between 20 and 60 years old - 40% of population older than 60. -![example 3 -GIF](https://github.com/UofUEpiBio/epiworldRShiny/assets/105825983/20aeb62d-cb42-4882-8577-a3406f167bca) +
+ + +
diff --git a/man/epiworldRShiny.Rd b/man/epiworldRShiny.Rd index a999d4f..b1d1032 100644 --- a/man/epiworldRShiny.Rd +++ b/man/epiworldRShiny.Rd @@ -13,7 +13,7 @@ run_app(...) \item{...}{Currently ignored.} } \value{ -Loads and opens the RShiny app for the epiworldR package +Loads and opens the R shiny app for the epiworldR package } \description{ Fires up the R Shiny App. You can find more examples and documentation at diff --git a/man/epiworldrshiny-ui.Rd b/man/epiworldrshiny-ui.Rd index 966894b..d25c6a2 100644 --- a/man/epiworldrshiny-ui.Rd +++ b/man/epiworldrshiny-ui.Rd @@ -72,7 +72,7 @@ build the UI for the epiworldRShiny app. } \examples{ text_input_disease_name("SEIRD") -# slider_prevalence("SEIRD") +slider_prevalence("SEIRD") numeric_input_ndays("SEIRD") slider_input_rate("SEIRD", "transmission", value = 0.3, maxval = 1, input_label = NULL)