Merge pull request #57 from aghaynes/master

update template code
CTU-Bern · Mar 21, 2024 · ea27393 · ea27393
2 parents 8ba4b4b + fe6c80e
commit ea27393
Show file tree

Hide file tree

Showing 7 changed files with 38 additions and 7 deletions.
diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml
@@ -27,8 +27,8 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: 'oldrel-1'}
           #- {os: windows-latest, r: '3.6'}
-          # - {os: ubuntu-20.04,   r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-latest, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          #- {os: ubuntu-20.04,   r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-latest,   r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml
@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v2
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
       - name: Install rmarkdown, remotes, and the local package
         run: |
           install.packages(c("devtools", "badger"))

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CTUtemplate
 Title: Example RStudio Project Templates
 Author: Alan G. Haynes
-Maintainer: Alan G. Haynes <alan.haynes@ctu.unibe.ch>
-Version: 0.4.7
+Maintainer: Alan G. Haynes <[email protected]>
+Version: 0.5.0
 Description: Templates and functions for use in CTU Bern.
 Depends: 
   R (>= 3.3.2)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+CTUtemplate 0.5.0
+---------------------
+addition of template R code for saving data as CSV
+addition of example code for using groundhog
+
 CTUtemplate 0.4.7
 ---------------------
 addition of `coloured_text` for using in quarto/RMarkdown documents to more easily colour particular pieces of text

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 # `CTUtemplate` <img src='man/figures/sticker.png' align="right" width="200">
 
-[![](https://img.shields.io/badge/dev%20version-0.4.7-blue.svg)](https://github.com/CTU-Bern/CTUtemplate)
+[![](https://img.shields.io/badge/dev%20version-0.5.0-blue.svg)](https://github.com/CTU-Bern/CTUtemplate)
 
 `CTUtemplate` is a package to create a template directory structure (and
 files) and also includes the CTUs annual safety report function.
@@ -85,7 +85,7 @@ info.
 generic template with some examples of how to do things.
 
 | Function                    | Description                                                                          |
-| :-------------------------- | :----------------------------------------------------------------------------------- |
+|:----------------------------|:-------------------------------------------------------------------------------------|
 | `use_report_template`       | Opens a generic file with various examples                                           |
 | `use_ssreport_template`     | Opens a template for a sample size report                                            |
 | `use_recreport_template`    | Opens a template for a recruitment report                                            |

diff --git a/inst/extdata/R/dataprep.R b/inst/extdata/R/dataprep.R
@@ -5,6 +5,28 @@ mykeep()
 # dat <- read_secuTrial(paths$od("zipname.zip"))
 # dat < redcap_export_byform(readLines("O:/tokens/projNum.txt"),
 #                            "https://redcap.ctu.unibe.ch/api/")
+# alternative REDCap export code. also saves data as CSV
+# if(export_date == Sys.Date()){
+#   dat <- redcap_export_byform(readLines("O:/tokens/projNum.txt"),
+#                               "https://redcap.ctu.unibe.ch/api/")
+#   meta <- redcap_export_meta(readLines("O:/tokens/projNum.txt"),
+#                              "https://redcap.ctu.unibe.ch/api/")
+#   lapply(names(dat), function(x){
+#     write.csv(dat[[x]], paths$od(paste0(x, "-", export_date, ".csv")),
+#               na = "", row.names = FALSE)
+#     return(NULL)
+#   })
+#   lapply(names(meta), function(x){
+#     write.csv(meta[[x]], paths$od(paste0(x, "-", export_date, ".csv")),
+#               na = "", row.names = FALSE)
+#     return(NULL)
+#   })
+#   saveRDS(dat, paths$od(paste0("raw-", export_date, ".RDS")))
+#   saveRDS(meta, paths$od(paste0("meta-", export_date, ".RDS")))
+# }
+#
+# dat <- readRDS(paths$od(paste0("raw-", export_date, ".RDS")))
+# meta <- readRDS(paths$od(paste0("meta-", export_date, ".RDS")))
 
 # example using mtcars
 data(mtcars)

diff --git a/inst/extdata/R/packages_funs.R b/inst/extdata/R/packages_funs.R
@@ -10,6 +10,9 @@
 # install.packages("redcaptools", repos = "https://ctu-bern.r-universe.dev")
 # install.packages("secuTrialR")
 
+# install.packages("groundhog")
+# library.groundhog(" #UNCOMMENT TO USE GROUNDHOG
+
 ## Load packages ----
 # library(atable)
 # atable_options(format_to = "console", add_margins = TRUE)
@@ -31,6 +34,7 @@
 # library(btabler)
 # library(sse)
 
+# ", date = "2024-02-01") #UNCOMMENT TO USE GROUNDHOG
 
 # custom functions ----
 # function to retain only named objects (+ 'paths', pp and functions)