Merge pull request #40 from RaymondBalise/add_analysis_with_examples

Add analysis with examples
RaymondBalise · Feb 15, 2024 · b0e7cf8 · b0e7cf8
2 parents 26203d5 + 897f9ab
commit b0e7cf8
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Showing 10 changed files with 560 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rUM
 Title: R Templates from the University of Miami
-Version: 1.0.2
+Version: 1.1.0
 Authors@R: 
     c(
       person(
@@ -46,20 +46,23 @@ Depends:
 Imports:
     bookdown,
     conflicted,
+    glue,
+    gtsummary,
+    rio,
     rlang,
     rmarkdown,
     table1,
+    tidymodels,
     tidyverse,
     usethis
 Suggests:
     knitr,
-    tidymodels,
     tinytex
 License: MIT + file LICENSE
 URL: 
     https://raymondbalise.github.io/rUM/,
     https://github.com/RaymondBalise/rUM
 BugReports: https://github.com/RaymondBalise/rUM/issues
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,9 +3,13 @@
 export(make_project)
 importFrom(bookdown,html_document2)
 importFrom(conflicted,conflict_prefer)
+importFrom(glue,glue)
+importFrom(gtsummary,tbl_summary)
+importFrom(rio,import)
 importFrom(rlang,abort)
 importFrom(rmarkdown,html_document)
 importFrom(table1,t1kable)
+importFrom(tidymodels,tidymodels_prefer)
 importFrom(tidyverse,tidyverse_logo)
 importFrom(usethis,create_project)
 importFrom(utils,download.file)
diff --git a/R/make_project.R b/R/make_project.R
@@ -12,6 +12,7 @@
 #'    \code{./rstudio/templates/project/})
 #' @param type Choose between "Quarto (analysis.qmd)" or
 #'    "R Markdown (analysis.Rmd)"
+#' @param example Will the analysis file include an example table/figure?"
 #'
 #' @details Behind the scenes, this function used by research_project.dcf when
 #' a user selects New project... > New Directory > rUM Research Project Template
@@ -25,6 +26,10 @@
 #' @importFrom rlang abort
 #' @importFrom utils download.file
 #' @importFrom usethis create_project
+#' @importFrom glue glue
+#' @importFrom gtsummary tbl_summary
+#' @importFrom rio import
+#' @importFrom tidymodels tidymodels_prefer
 #'
 #' @return Returns nothing.  See description above.
 #'
@@ -40,7 +45,8 @@
 
 make_project <- function(
     path,
-    type = c("Quarto (analysis.qmd)", "R Markdown (analysis.Rmd)")
+    type = c("Quarto (analysis.qmd)", "R Markdown (analysis.Rmd)"),
+    example = FALSE
   ) {
 
   type <- match.arg(type)
@@ -65,6 +71,19 @@ make_project <- function(
     "ee3369492aafd001b59d4390177e8b44cd0ea088/analysis.qmd"
   )
 
+  gist_w_ex_path_rmd <- paste0(
+    "https://gist.githubusercontent.com/RaymondBalise/",
+    "c8399e7b3474a6022eeae373d059a042/",
+    "raw/094e854be27554e4e296c48e4323c4f0d1b5ba9c/analysis_with_example.Rmd"
+  )
+
+  gist_w_ex_path_qmd <- paste0(
+    "https://gist.githubusercontent.com/RaymondBalise/",
+    "40e8e1cc0dec94b225b7cb307f4fa959/raw/",
+    "f365198b41abe5b35ec7d7501d6f286f668a14d7/analysis_with_example.qmd"
+  )
+
+
   # Prevent user from overwriting an analysis file
   if (file.exists(paste0(path, "/analysis.Rmd")) ||
       file.exists(paste0(path, "/analysis.qmd"))
@@ -74,15 +93,30 @@ make_project <- function(
     )
   }
 
-  if (type == "R Markdown (analysis.Rmd)") {
-    download.file(gist_path_rmd, paste0(path, "/analysis.Rmd"))
-  } else if (type == "Quarto (analysis.qmd)") {
-    download.file(gist_path_qmd, paste0(path, "/analysis.qmd"))
-  } else {
-    abort(
-      "The type must be 'R Markdown (analysis.Rmd)' or 'Quarto (analysis.qmd)'"
-    )
+
+  if (example == FALSE){ # use old templates w/o an example
+    if (type == "R Markdown (analysis.Rmd)") {
+      download.file(gist_path_rmd, paste0(path, "/analysis.Rmd"))
+    } else if (type == "Quarto (analysis.qmd)") {
+      download.file(gist_path_qmd, paste0(path, "/analysis.qmd"))
+    } else {
+      abort(
+        "The type must be 'R Markdown (analysis.Rmd)' or 'Quarto (analysis.qmd)'"
+      )
+    }
+  } else { # use newer templates w an example
+    if (type == "R Markdown (analysis.Rmd)") {
+      download.file(gist_w_ex_path_rmd, paste0(path, "/analysis.Rmd"))
+    } else if (type == "Quarto (analysis.qmd)") {
+      download.file(gist_w_ex_path_qmd, paste0(path, "/analysis.qmd"))
+    } else {
+      abort(
+        "The type must be 'R Markdown (analysis.Rmd)' or 'Quarto (analysis.qmd)'"
+      )
+    }
   }
+
+
 
   dir.create(paste0(path, "/data"), recursive = TRUE, showWarnings = FALSE)
 

diff --git a/inst/gists/analysis_1_0_2_9001.Rmd b/inst/gists/analysis_1_0_2_9001.Rmd
@@ -5,6 +5,8 @@ date: "`r Sys.Date()`"
 output:
   bookdown::html_document2:
     number_sections: false
+bibliography: [references.bib, packages.bib]
+csl: the-new-england-journal-of-medicine.csl
 ---
 
 ```{r setup, echo=FALSE}
@@ -34,9 +36,9 @@ options(dplyr.summarise.inform = FALSE)
 
 ```{r other-packages}
 library(glue)  # for glue()
-library(rUM)  # needed for the bibliography
+library(rUM)  # needed for the bibliography to include the package
 library(rio)  # for import() 
-# library(table1)  # for table1()
+library(table1)  # for table1() if you want to use it instead of gtsummary
 
 # gtsummary for tbl_summary(), add_n(), add_p(), modify_header(), bold_labels()
 suppressPackageStartupMessages(library(gtsummary)) 
@@ -58,7 +60,7 @@ analysis <- mtcars |>
 # Introduction
 
 # Methods
-Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `table1` (`r packageVersion("table1")`) packages used to preprocess and summarize data.[@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-table1]
+Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `gtsummary` (`r packageVersion("gtsummary")`) packages used to preprocess and summarize data. [@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-gtsummary]
 
 # Results
 

diff --git a/inst/gists/analysis_1_0_2_9001.qmd b/inst/gists/analysis_1_0_2_9001.qmd
@@ -16,6 +16,8 @@ knitr:
     R.options:    
       digits: 3    # round to three digits
 editor: visual
+bibliography: [references.bib, packages.bib]
+csl: the-new-england-journal-of-medicine.csl
 ---
 
 ```{r tidyverse-tidymodels, echo=FALSE}
@@ -32,7 +34,7 @@ options(dplyr.summarise.inform = FALSE)
 library(glue)  # for glue()
 library(rUM)  # needed for the bibliography
 library(rio)  # for import() 
-# library(table1)  # for table1()
+library(table1)  # for table1()
 
 # gtsummary for tbl_summary(), add_n(), add_p(), modify_header(), bold_labels()
 suppressPackageStartupMessages(library(gtsummary)) 
@@ -55,7 +57,7 @@ analysis <- mtcars |>
 
 # Methods
 
-Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `table1` (`r packageVersion("table1")`) packages used to preprocess and summarize data.[@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-table1]
+Analyses were conducted with `r stringr::word(R.Version()$version.string, 1, 3)` with the `tidyverse` (`r packageVersion("tidyverse")`), `rUM` (`r packageVersion("rUM")`), `gtsummary` (`r packageVersion("gtsummary")`) packages used to preprocess and summarize data. [@R-base; @R-tidyverse; @tidyverse2019; @R-rUM; @R-gtsummary]
 
 # Results