From 926ab95e82167c7cd44582909ef844f661adfbb7 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Thu, 21 Mar 2024 11:26:42 +0100 Subject: [PATCH 1/6] add template code --- NEWS.md | 5 +++++ inst/extdata/R/dataprep.R | 22 ++++++++++++++++++++++ inst/extdata/R/packages_funs.R | 4 ++++ 3 files changed, 31 insertions(+) diff --git a/NEWS.md b/NEWS.md index 5c860b7..9c9d9e4 100644 --- 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/inst/extdata/R/dataprep.R b/inst/extdata/R/dataprep.R index a81d2b8..9068401 100644 --- 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 index aa731a6..7886f4e 100644 --- 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) From 73c600f91d7fe5e883248a768414f25f1b7ab401 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Thu, 21 Mar 2024 11:26:56 +0100 Subject: [PATCH 2/6] upgrade action versions --- .github/workflows/render-readme.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml index f2c870b..d2c0934 100644 --- a/.github/workflows/render-readme.yaml +++ b/.github/workflows/render-readme.yaml @@ -15,8 +15,8 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-pandoc@v2 - name: Install rmarkdown, remotes, and the local package run: | install.packages(c("devtools", "badger")) From 22ca5c514c873d1fb832392dbd5aa08fec97101c Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Thu, 21 Mar 2024 11:51:53 +0100 Subject: [PATCH 3/6] update email, increment version --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0224bbe..e336ea6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: CTUtemplate Title: Example RStudio Project Templates Author: Alan G. Haynes -Maintainer: Alan G. Haynes -Version: 0.4.7 +Maintainer: Alan G. Haynes +Version: 0.5.0 Description: Templates and functions for use in CTU Bern. Depends: R (>= 3.3.2) From 5695fc10d0a60650c1c6e2497c534c4a261aba3c Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Thu, 21 Mar 2024 11:54:40 +0100 Subject: [PATCH 4/6] remove ubuntu tests --- .github/workflows/R-CMD-full.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index a590bed..c6a39a2 100644 --- 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, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From a585a17e87fbeac01c1971172f3aa6154c3d5449 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 21 Mar 2024 10:54:50 +0000 Subject: [PATCH 5/6] Re-build README.Rmd --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8a578dc..190c6c8 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ # `CTUtemplate` -[![](https://img.shields.io/badge/dev%20version-0.4.6-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 | From 7e25ce17e827e774f71960b586fd340077e570cb Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Thu, 21 Mar 2024 11:55:41 +0100 Subject: [PATCH 6/6] ubuntu as per redcaptools --- .github/workflows/R-CMD-full.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index c6a39a2..df61192 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -28,7 +28,7 @@ jobs: - {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-latest, r: 'release'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true