Add function write_sessioninfo()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: inborutils
 Title: Collection of Useful R Utilities
-Version: 0.1.0.9061
+Version: 0.1.0.9062
 Description: While working on research projects, typical small functionalities 
     are useful across these projects. Instead of copy-pasting these functions in 
     all indidivual project repositories/folders, this package collects these 
@@ -15,6 +15,7 @@ Authors@R: c(
     person("Thierry", "Onkelinx", role = "ctb", email = "thierry.onkelinx@inbo.be", comment = c(ORCID = "0000-0001-8804-4216")),
     person("Floris", "Vanderhaeghe", role = "ctb", email = "floris.vanderhaeghe@inbo.be", comment = c(ORCID = "0000-0002-6378-6229")),
     person("Pieter", "Verschelde", role = "ctb", email = "pieter.verschelde@inbo.be", comment = c(ORCID = "0000-0002-9199-421X")),
+    person("Els", "De Bie", role = "ctb", email = "els.debie@inbo.be", comment = c(ORCID = "0000-0001-7679-743X")),
     person("Research Institute for Nature and Forest (INBO)", role = "cph", email = "info@inbo.be")
     )
 License: MIT + file LICENSE
@@ -41,6 +42,7 @@ Imports:
     rgdal,
     rlang,
     RSQLite,
+    sessioninfo,
     sp,
     sf,
     stats,

NAMESPACE

@@ -20,6 +20,7 @@ export(read_knmi_data)
 export(read_mow_data)
 export(reproject_coordinates)
 export(vif)
+export(write_sessioninfo)
 exportMethods(dbDisconnect)
 importFrom(DBI,dbConnect)
 importFrom(DBI,dbDisconnect)
@@ -104,6 +105,8 @@ importFrom(readr,read_delim_chunked)
 importFrom(rgbif,name_backbone)
 importFrom(rlang,"!!")
 importFrom(rlang,.data)
+importFrom(sessioninfo,package_info)
+importFrom(sessioninfo,platform_info)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
@@ -118,10 +121,13 @@ importFrom(stats,cov2cor)
 importFrom(stats,lm)
 importFrom(stats,model.matrix)
 importFrom(stats,vcov)
+importFrom(stringr,str_detect)
 importFrom(tibble,as_tibble)
 importFrom(tidyr,extract)
 importFrom(tidyr,separate)
 importFrom(tidyselect,ends_with)
 importFrom(tidyselect,enquo)
 importFrom(tidyselect,vars_pull)
+importFrom(utils,capture.output)
 importFrom(utils,getFromNamespace)
+importFrom(utils,write.table)

R/write_sessioninfo.R

@@ -0,0 +1,71 @@
+#' Write essential session info to a file or connection
+#'
+#' Writes essentials of
+#' \code{\link[sessioninfo:session_info]{sessioninfo::session_info()}}
+#' to a file or connection in order to
+#' maintain versionable documentation of a workflow and aid
+#' reproducibility.
+#'
+#' The following information is written:
+#' \itemize{
+#' \item{essential platform info: version, os, system, ctype}
+#' \item{essential info on loaded packages: package, loadedversion, date,
+#' source if different from CRAN.}
+#' }
+#'
+#' @param file A file path or a \code{\link[base]{connection}}.
+#'
+#' @importFrom sessioninfo
+#' platform_info
+#' package_info
+#' @importFrom stringr
+#' str_detect
+#' @importFrom utils
+#' write.table
+#' capture.output
+#' @importFrom rlang
+#' .data
+#' @importFrom dplyr
+#' mutate
+#' select
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' write_sessioninfo(file = "sessioninfo.txt")
+#' }
+write_sessioninfo <- function(file) {
+
+  platform_info()[c("version",
+                    "os",
+                    "system",
+                    "ctype")] %>%
+    unlist %>%
+    as.matrix() %>%
+    write.table(file = file,
+                quote = FALSE,
+                col.names = FALSE,
+                sep = "\t")
+
+  capture.output(cat("\n"),
+                 file = file,
+                 append = TRUE)
+
+  package_info() %>%
+    as.data.frame %>%
+    mutate(non_cran = ifelse(str_detect(source, "CRAN"),
+                             "",
+                             source)) %>%
+    select(.data$package,
+           .data$loadedversion,
+           .data$date,
+           .data$non_cran) %>%
+    write.table(file = file,
+                quote = FALSE,
+                row.names = FALSE,
+                col.names = FALSE,
+                sep = " ",
+                append = TRUE)
+
+}

_pkgdown.yml

@@ -35,6 +35,10 @@ reference:
     contents:
       - df_factors_to_char
       - csv_to_sqlite
+  - title: "Enhancing transparency and reproducibility"
+    desc: "Functions to help in achieving transparency and reproducibility"
+    contents:
+      - write_sessioninfo
   - title: "Statistical modelling"
     desc: "Functions for handling statistical modelling tasks"
     contents:

inborutils.Rproj

@@ -18,3 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
+PackageRoxygenize: rd,collate,namespace