R/thesis.R
In ykunisato/senshuRmd: Rmarkdown template for thesis format at Department of Psychology, Senshu University
Defines functions
set_analysis
senshu_thesis
Documented in
senshu_thesis
set_analysis
#' @title R Markdown output formats Template for thesis at Department of Psychology, Senshu University
#' @importFrom rmarkdown render
#' @importFrom rmarkdown pdf_document
#' @importFrom jpaRmd jpa_cite
#' @param Rmd_file file name of R Markdown file
#' @param Bib_file file name of Bib file
#' @export
senshu_thesis <- function(Rmd_file, Bib_file) {
jpa_cite(Rmd_file, Bib_file)
tmp_rmd <- paste0("tmp_", Rmd_file)
template_tex_file <- system.file("rmarkdown/templates/thesis_senshu/resources/senshu.tex",
package = 'senshuRmd')
format_pdf <- pdf_document(
latex_engine = "xelatex",
template = template_tex_file,
keep_tex = TRUE,
toc = TRUE,
toc_depth = 3,
highlight = "tango"
)
format_pdf$inherits <- "pdf_document"
output_file <- strsplit(Rmd_file, ".Rmd")[[1]]
render(tmp_rmd, format_pdf, output_file)
}
#' @title Research Compendium of Department of Psychology, Senshu University
#' @importFrom rstudioapi navigateToFile
#' @examples # set_rc()
#' @export
set_rc <- function (){
path = getwd()
# make README
if(!file.exists(file.path(path, "README.md"))){
file.create(file.path(path, "README.md"), showWarnings = FALSE)
writeLines("# SenshuRmd\u306e\u8aac\u660e\n\n## Research Compendium\u306e\u5185\u5bb9\n\nsenshuRmd\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u30fc\u69cb\u9020\u3092\u3082\u3063\u305fResearch Compendium\u3092\u7528\u610f\u3057\u307e\u3059\u3002\n\n\u5404\u30d5\u30a9\u30eb\u30c0\u306e\u6a5f\u80fd\u3092\u7406\u89e3\u3057\u305f\u4e0a\u3067\u30d5\u30a1\u30a4\u30eb\u3092\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\n- paper:\u5352\u8ad6\u30fb\u4fee\u8ad6\u7528\u306eRmd\u30d5\u30a1\u30a4\u30eb\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u307e\u3059\n\n- analysis\uff1a\u89e3\u6790\u7528\u30d5\u30a1\u30a4\u30eb\u3092\u5165\u308c\u308b\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) data\uff1a\u89e3\u6790\u7528\u30c7\u30fc\u30bf\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) function\uff1a\u89e3\u6790\u7528R\u306e\u95a2\u6570\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- materials\uff1a\u7814\u7a76\u3067\u4f7f\u3063\u305f\u6750\u6599\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- exercises\uff1a\u30bc\u30df\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- labnote\uff1a\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u4fdd\u7ba1\u3059\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n## \u6700\u521d\u306b\u3059\u308b\u3053\u3068\n\nset_rc()\u304bset_rc_ccp()\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0c\u3053\u306eREADME.md\u3068paper.Rmd\u304c\u958b\u304d\u307e\u3059\u3002\n\npaper.Rmd\u3068\u3044\u3046\u30bf\u30d6\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\uff0c\u305d\u306eKnit\u3063\u3066\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\n\n\u3057\u3070\u3089\u304f\u3059\u308b\u3068\uff0cpaper\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u5352\u8ad6\u30fb\u4fee\u8ad6\u306ePDF\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u5352\u8ad6\u30fb\u4fee\u8ad6\u306f\uff0cpaper.Rmd\u306b\u66f8\u304d\u8fbc\u3093\u3067\uff0cknit\u3057\u3066\u51fa\u529b\u3055\u308c\u305fPDF\u306b\u306a\u308a\u307e\u3059\u3002\n\n## \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u306eOSF\u3082\u3057\u304f\u306fGitHub\u306e\u8a2d\u5b9a\n\n\u4ee5\u4e0b\u3092\u53c2\u8003\u306b\u3057\u3066\uff0c\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u7814\u7a76\u5ba4\u306b\u3088\u3063\u3066OSF\u3092\u4f7f\u3046\u306e\u304bGitHub\u3092\u4f7f\u3046\u306e\u304b\u7570\u306a\u308a\u307e\u3059\u306e\u3067\uff0c\u6559\u54e1\u306b\u78ba\u8a8d\u3092\u3057\u3066\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\nhttps://github.com/ykunisato/eln4Rmd\n\n## \u65e5\u3005\u306e\u7814\u7a76\u6d3b\u52d5\u3067\u4f7f\u3046R\u30b3\u30de\u30f3\u30c9\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u4f5c\u6210(PDF)\n\nResearch Compendium\u306e\u4e00\u756a\u4e0a\u306e\u30d5\u30a9\u30eb\u30c0\u3092\u30ab\u30ec\u30f3\u30c8\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u3057\u3066\u3044\u308c\u3070\uff0clabnote\u30d5\u30a9\u30eb\u30c0\u306b\u30e9\u30dc\u30ce\u30fc\u30c8PD\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3092\u4f5c\u6210\u3057\u307e\u3059\n\neln4Rmd::elnjp_pdf(rc = TRUE)\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08OSF\u306e\u5834\u5408\uff09\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3068Research Compendium\u5185\u306e\u30d5\u30a1\u30a4\u30eb\u306e\u30d0\u30c3\u30af\u30a2\u30c3\u30d7\u3092\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\", rc_osf = \"OSF\u306eResearch Compendium\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n### GitHub\u3078\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\uff06\u30d7\u30c3\u30b7\u30e5\uff09\n\neln4Rmd::up_elnjp_git(rc = TRUE)\n\n## analysis\u30d5\u30a9\u30eb\u30c0\u306bRmd\u30d5\u30a1\u30a4\u30eb\u3092\u8ffd\u52a0\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0canalysis\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u89e3\u6790\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u3066\uff0c\u958b\u304b\u308c\u307e\u3059\u3002\n\nsenshuRmd::set_analysis(\"\u30d5\u30a1\u30a4\u30eb\u540d\")", "README.md")
navigateToFile(file.path(path, "README.md"))
}
# make paper.Rmd
if(!file.exists(file.path(path, "paper/paper.Rmd"))){
rmarkdown::draft(paste0("paper.Rmd"), template = "thesis_senshu", package = "senshuRmd", edit = FALSE)
navigateToFile(file.path(path, "paper/paper.Rmd"))
}
# make analysis directory
if(!dir.exists(file.path(path, "analysis"))){
dir.create(file.path(path, "analysis"), showWarnings = FALSE)
file.create(file.path(path, "analysis/README_analysis.md"), showWarnings = FALSE)
writeLines("README(analysis)\n\n\u89e3\u6790\u306b\u4f7f\u3046R\u3084Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3053\u3053\u306b\u7f6e\u304d\u307e\u3059\u3002\n\u30d5\u30a1\u30a4\u30eb\u540d\u306f\u89e3\u6790\u306e\u9806\u756a\u304c\u308f\u304b\u308b\u3088\u3046\u306b\u3064\u3051\u3066\u304f\u3060\u3055\u3044\u3002\nRmd\u30d5\u30a1\u30a4\u30eb\u306f\u89e3\u6790\u3068\u305d\u306e\u8aac\u660e\u3092\u307e\u3068\u3081\u3084\u3059\u3044\u306e\u3067\uff0c\u3067\u304d\u308b\u3060\u3051Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u4f7f\u3046\u3088\u3046\u306b\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/README_analysis.md")
}
# make data directory
if(!dir.exists(file.path(path, "analysis/data"))){
dir.create(file.path(path, "analysis/data"), showWarnings = FALSE)
file.create(file.path(path, "analysis/data/README_data.md"), showWarnings = FALSE)
writeLines("README(data)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046\u30c7\u30fc\u30bf\u3092\u7f6e\u304d\u307e\u3059\u3002OSF\u3084GitHub\u306b\u304a\u3044\u3066\u3082\u5927\u4e08\u592b\u306a\u30c7\u30fc\u30bf\u5316\u3069\u3046\u304b\u306f\u6307\u5c0e\u6559\u54e1\u306b\u76f8\u8ac7\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/data/README_data.md")
}
# make function directory
if(!dir.exists(file.path(path, "analysis/function"))){
dir.create(file.path(path, "analysis/function"), showWarnings = FALSE)
file.create(file.path(path, "analysis/function/README_function.md"), showWarnings = FALSE)
writeLines("README(function)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046R\u95a2\u6570\u3092\u7f6e\u304d\u307e\u3059\u3002\u95a2\u6570\u5316\u3057\u305f\u3082\u306e\u306f\u5225\u306b\u307e\u3068\u3081\u3066\u304a\u3044\u305f\u307b\u3046\u304c\u4fbf\u5229\u306a\u306e\u3067\uff0c\u3053\u3061\u3089\u3092\u5229\u7528\u304f\u3060\u3055\u3044\u3002", "analysis/function/README_function.md")
}
# make materials directory
if(!dir.exists(file.path(path, "materials"))){
dir.create(file.path(path, "materials"), showWarnings = FALSE)
file.create(file.path(path, "materials/README_materials.md"), showWarnings = FALSE)
writeLines("README(materials)\n\n\u7814\u7a76\u3067\u4f7f\u7528\u3057\u305f\u6750\u6599\uff08\u5b9f\u9a13\u8ab2\u984c\uff0c\u8cea\u554f\u7d19\uff0c\u5b9f\u9a13\u30fb\u8abf\u67fb\u30d7\u30ed\u30c8\u30b3\u30eb\uff0c\u502b\u7406\u7533\u8acb\u66f8\uff09\u306a\u3069\u3092\u3053\u3061\u3089\u306b\u4fdd\u7ba1\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "materials/README_materials.md")
}
# make labnote directory
if(!dir.exists(file.path(path, "labnote"))){
dir.create(file.path(path, "labnote"), showWarnings = FALSE)
file.create(file.path(path, "labnote/README_labnote.r"), showWarnings = FALSE)
writeLines("# README(labnote)\n\n# \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306f\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u307e\u305a\uff0csetwd()\u3067labnote\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u307e\u3059\u3002\nsetwd('labnote')\n# \u4ee5\u4e0b\u306eelnjp_pdf()\u3067\u30e9\u30dc\u30ce\u30fc\u30c8\u304c\u4f5c\u308c\u307e\u3059\u3002\neln4Rmd::elnjp_pdf()\n# \u4ee5\u4e0b\u306e\u30ea\u30f3\u30af\u5148\u3092\u307f\u3066\uff0cOSF\u304bGitHub\u306e\u8a2d\u5b9a\u3092\u3057\u307e\u3059\u3002\n# https://github.com/ykunisato/eln4Rmd\n#OSF\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_osf(eln_osf=\"OSF\u306eURL\")\n# GitHub\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\u3068\u30d7\u30c3\u30b7\u30e5\uff09\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_git()", "labnote/README_labnote.r")
}
}
#' @title Research Compendium of CCP Lab
#' @importFrom rstudioapi navigateToFile
#' @examples # set_rc_ccp()
#' @export
set_rc_ccp <- function (){
path = getwd()
# make README
if(!file.exists(file.path(path, "README.md"))){
file.create(file.path(path, "README.md"), showWarnings = FALSE)
writeLines("# SenshuRmd\u306e\u8aac\u660e\n\n## Research Compendium\u306e\u5185\u5bb9\n\nsenshuRmd\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u30fc\u69cb\u9020\u3092\u3082\u3063\u305fResearch Compendium\u3092\u7528\u610f\u3057\u307e\u3059\u3002\n\n\u5404\u30d5\u30a9\u30eb\u30c0\u306e\u6a5f\u80fd\u3092\u7406\u89e3\u3057\u305f\u4e0a\u3067\u30d5\u30a1\u30a4\u30eb\u3092\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\n- paper:\u5352\u8ad6\u30fb\u4fee\u8ad6\u7528\u306eRmd\u30d5\u30a1\u30a4\u30eb\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u307e\u3059\n\n- analysis\uff1a\u89e3\u6790\u7528\u30d5\u30a1\u30a4\u30eb\u3092\u5165\u308c\u308b\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) data\uff1a\u89e3\u6790\u7528\u30c7\u30fc\u30bf\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) function\uff1a\u89e3\u6790\u7528R\u306e\u95a2\u6570\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- materials\uff1a\u7814\u7a76\u3067\u4f7f\u3063\u305f\u6750\u6599\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- exercises\uff1a\u30bc\u30df\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- labnote\uff1a\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u4fdd\u7ba1\u3059\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n## \u6700\u521d\u306b\u3059\u308b\u3053\u3068\n\nset_rc()\u304bset_rc_ccp()\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0c\u3053\u306eREADME.md\u3068paper.Rmd\u304c\u958b\u304d\u307e\u3059\u3002\n\npaper.Rmd\u3068\u3044\u3046\u30bf\u30d6\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\uff0c\u305d\u306eKnit\u3063\u3066\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\n\n\u3057\u3070\u3089\u304f\u3059\u308b\u3068\uff0cpaper\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u5352\u8ad6\u30fb\u4fee\u8ad6\u306ePDF\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u5352\u8ad6\u30fb\u4fee\u8ad6\u306f\uff0cpaper.Rmd\u306b\u66f8\u304d\u8fbc\u3093\u3067\uff0cknit\u3057\u3066\u51fa\u529b\u3055\u308c\u305fPDF\u306b\u306a\u308a\u307e\u3059\u3002\n\n## \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u306eOSF\u3082\u3057\u304f\u306fGitHub\u306e\u8a2d\u5b9a\n\n\u4ee5\u4e0b\u3092\u53c2\u8003\u306b\u3057\u3066\uff0c\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u7814\u7a76\u5ba4\u306b\u3088\u3063\u3066OSF\u3092\u4f7f\u3046\u306e\u304bGitHub\u3092\u4f7f\u3046\u306e\u304b\u7570\u306a\u308a\u307e\u3059\u306e\u3067\uff0c\u6559\u54e1\u306b\u78ba\u8a8d\u3092\u3057\u3066\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\nhttps://github.com/ykunisato/eln4Rmd\n\n## \u65e5\u3005\u306e\u7814\u7a76\u6d3b\u52d5\u3067\u4f7f\u3046R\u30b3\u30de\u30f3\u30c9\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u4f5c\u6210(PDF)\n\nResearch Compendium\u306e\u4e00\u756a\u4e0a\u306e\u30d5\u30a9\u30eb\u30c0\u3092\u30ab\u30ec\u30f3\u30c8\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u3057\u3066\u3044\u308c\u3070\uff0clabnote\u30d5\u30a9\u30eb\u30c0\u306b\u30e9\u30dc\u30ce\u30fc\u30c8PD\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3092\u4f5c\u6210\u3057\u307e\u3059\n\neln4Rmd::elnjp_pdf(rc = TRUE)\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08OSF\u306e\u5834\u5408\uff09\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3068Research Compendium\u5185\u306e\u30d5\u30a1\u30a4\u30eb\u306e\u30d0\u30c3\u30af\u30a2\u30c3\u30d7\u3092\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\", rc_osf = \"OSF\u306eResearch Compendium\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n### GitHub\u3078\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\uff06\u30d7\u30c3\u30b7\u30e5\uff09\n\neln4Rmd::up_elnjp_git(rc = TRUE)\n\n## analysis\u30d5\u30a9\u30eb\u30c0\u306bRmd\u30d5\u30a1\u30a4\u30eb\u3092\u8ffd\u52a0\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0canalysis\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u89e3\u6790\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u3066\uff0c\u958b\u304b\u308c\u307e\u3059\u3002\n\nsenshuRmd::set_analysis(\"\u30d5\u30a1\u30a4\u30eb\u540d\")\n\n## jsPsych\u3067\u5b9f\u9a13\u8ab2\u984c\u3092\u4f5c\u6210\u3059\u308b\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0cexercises\u30d5\u30a9\u30eb\u30c0\u5185\u306bjsPsych\u8ab2\u984c\u7528\u30d5\u30a9\u30eb\u30c0\u3068\u30d5\u30a1\u30a4\u30eb\u4e00\u5f0f\u304c\u7528\u610f\u3055\u308c\u307e\u3059\u3002\n\njsPsychRmd::set_jsPsych(folder = \"\u8ab2\u984c\u540d\u3092\u82f1\u8a9e\u3067\u66f8\u304f\", rc = TRUE)", "README.md")
navigateToFile(file.path(path, "README.md"))
}
# make paper.Rmd
if(!file.exists(file.path(path, "paper/paper.Rmd"))){
rmarkdown::draft(paste0("paper.Rmd"), template = "thesis_senshu", package = "senshuRmd", edit = FALSE)
navigateToFile(file.path(path, "paper/paper.Rmd"))
}
# make analysis directory
if(!dir.exists(file.path(path, "analysis"))){
dir.create(file.path(path, "analysis"), showWarnings = FALSE)
file.create(file.path(path, "analysis/README_analysis.md"), showWarnings = FALSE)
writeLines("README(analysis)\n\n\u89e3\u6790\u306b\u4f7f\u3046R\u3084Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3053\u3053\u306b\u7f6e\u304d\u307e\u3059\u3002\n\u30d5\u30a1\u30a4\u30eb\u540d\u306f\u89e3\u6790\u306e\u9806\u756a\u304c\u308f\u304b\u308b\u3088\u3046\u306b\u3064\u3051\u3066\u304f\u3060\u3055\u3044\u3002\nRmd\u30d5\u30a1\u30a4\u30eb\u306f\u89e3\u6790\u3068\u305d\u306e\u8aac\u660e\u3092\u307e\u3068\u3081\u3084\u3059\u3044\u306e\u3067\uff0c\u3067\u304d\u308b\u3060\u3051Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u4f7f\u3046\u3088\u3046\u306b\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/README_analysis.md")
}
# make data directory
if(!dir.exists(file.path(path, "analysis/data"))){
dir.create(file.path(path, "analysis/data"), showWarnings = FALSE)
file.create(file.path(path, "analysis/data/README_data.md"), showWarnings = FALSE)
writeLines("README(data)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046\u30c7\u30fc\u30bf\u3092\u7f6e\u304d\u307e\u3059\u3002OSF\u3084GitHub\u306b\u304a\u3044\u3066\u3082\u5927\u4e08\u592b\u306a\u30c7\u30fc\u30bf\u5316\u3069\u3046\u304b\u306f\u6307\u5c0e\u6559\u54e1\u306b\u76f8\u8ac7\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/data/README_data.md")
}
# make function directory
if(!dir.exists(file.path(path, "analysis/function"))){
dir.create(file.path(path, "analysis/function"), showWarnings = FALSE)
file.create(file.path(path, "analysis/function/README_function.md"), showWarnings = FALSE)
writeLines("README(function)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046R\u95a2\u6570\u3092\u7f6e\u304d\u307e\u3059\u3002\u95a2\u6570\u5316\u3057\u305f\u3082\u306e\u306f\u5225\u306b\u307e\u3068\u3081\u3066\u304a\u3044\u305f\u307b\u3046\u304c\u4fbf\u5229\u306a\u306e\u3067\uff0c\u3053\u3061\u3089\u3092\u5229\u7528\u304f\u3060\u3055\u3044\u3002", "analysis/function/README_function.md")
}
# make materials directory
if(!dir.exists(file.path(path, "materials"))){
dir.create(file.path(path, "materials"), showWarnings = FALSE)
file.create(file.path(path, "materials/README_materials.md"), showWarnings = FALSE)
writeLines("README(materials)\n\n\u7814\u7a76\u3067\u4f7f\u7528\u3057\u305f\u6750\u6599\uff08\u5b9f\u9a13\u8ab2\u984c\uff0c\u8cea\u554f\u7d19\uff0c\u5b9f\u9a13\u30fb\u8abf\u67fb\u30d7\u30ed\u30c8\u30b3\u30eb\uff0c\u502b\u7406\u7533\u8acb\u66f8\uff09\u306a\u3069\u3092\u3053\u3061\u3089\u306b\u4fdd\u7ba1\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "materials/README_materials.md")
}
# make exercises directory
if(!dir.exists(file.path(path, "exercises"))){
dir.create(file.path(path, "exercises"), showWarnings = FALSE)
file.create(file.path(path, "exercises/README_exercises.r"), showWarnings = FALSE)
writeLines("# README(exercises)\n\n# \u56fd\u91cc\u7814\u7a76\u5ba4\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u306f\uff0c\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068exercises\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3067\u304d\u307e\u3059\u3002\r\nsetwd(\"exercises\")\n# exercises\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u305f\u3046\u3048\u3067\uff0c\u6f14\u7fd2\u8ab2\u984c\u306b\u53d6\u308a\u7d44\u3093\u3067\u304f\u3060\u3055\u3044\u3002\n# \u4ee5\u4e0b\u306eset_jsPsych()\u3092\u4f7f\u3046\u3068\uff0cjsPsych\u306e\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u3092\u4f5c\u3063\u3066\uff0c\u5fc5\u8981\u306a\u30d5\u30a1\u30a4\u30eb\u3092\u7528\u610f\u3057\u307e\u3059\u3002\njsPsychRmd::set_jsPsych(folder = 'hello')", "exercises/README_exercises.r")
}
# make labnote directory
if(!dir.exists(file.path(path, "labnote"))){
dir.create(file.path(path, "labnote"), showWarnings = FALSE)
file.create(file.path(path, "labnote/README_labnote.r"), showWarnings = FALSE)
writeLines("# README(labnote)\n\n# \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306f\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u307e\u305a\uff0csetwd()\u3067labnote\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u307e\u3059\u3002\nsetwd('labnote')\n# \u4ee5\u4e0b\u306eelnjp_pdf()\u3067\u30e9\u30dc\u30ce\u30fc\u30c8\u304c\u4f5c\u308c\u307e\u3059\u3002\neln4Rmd::elnjp_pdf()\n# \u4ee5\u4e0b\u306e\u30ea\u30f3\u30af\u5148\u3092\u307f\u3066\uff0cOSF\u304bGitHub\u306e\u8a2d\u5b9a\u3092\u3057\u307e\u3059\u3002\n# https://github.com/ykunisato/eln4Rmd\n#OSF\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_osf(eln_osf=\"OSF\u306eURL\")\n# GitHub\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\u3068\u30d7\u30c3\u30b7\u30e5\uff09\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_git()", "labnote/README_labnote.r")
}
}
#' @title R Markdown output formats template for analysis at Department of Psychology, Senshu University
#' @importFrom stringr str_replace
#' @importFrom rstudioapi navigateToFile
#' @param Rmd_file file name of R Markdown file
#' @param rc If you are using Research Compendium of senshuRmd,
#' you can create a Rmd file in the "analysis" directory from the current directory.
#' @export
set_analysis <- function(Rmd_file, rc = TRUE) {
if(missing(Rmd_file)){
stop("Rmd_file\u3000= \"\u30d5\u30a1\u30a4\u30eb\u540d\"\u3067\uff0c\u4f5c\u6210\u3059\u308bRmd\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u6307\u5b9a\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u30d5\u30a1\u30a4\u30eb\u540d\u306f\uff0cAnalysis01\u306e\u3088\u3046\u306b\u82f1\u8a9e\u3067\u6307\u5b9a\u304f\u3060\u3055\u3044\u3002")
}
path = getwd()
if(rc == TRUE){
path <- paste0(path, "/analysis")
}
file_path <- paste0(path,"/",Rmd_file,".Rmd")
if(!file.exists(file_path)){
path_skeleton <- system.file("rmarkdown/templates/analysis/skeleton/skeleton.Rmd",package = "senshuRmd")
text_skeleton <- readLines(path_skeleton, warn = F)
tmp_rmd <- file(file_path, "w")
for (i in 1:length(text_skeleton)) {
st <- text_skeleton[i]
st <- str_replace(st, pattern = "title: 'title'",
replacement = paste0("title: ", "'",Rmd_file,"'"))
writeLines(st, tmp_rmd)
}
close(tmp_rmd)
navigateToFile(file_path)
}else{
stop("\u6307\u5b9a\u3055\u308c\u305f\u30d5\u30a1\u30a4\u30eb\u540d\u306eRmd\u30d5\u30a1\u30a4\u30eb\u306f\u65e2\u306b\u5b58\u5728\u3057\u3066\u3044\u307e\u3059\u3002\u5225\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u3067\u4f5c\u6210\u304f\u3060\u3055\u3044\u3002")
}
}
ykunisato/senshuRmd documentation built on March 20, 2022, 11:53 p.m.
R Package Documentation
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Defines functions set_analysis senshu_thesis
Documented in senshu_thesis set_analysis
#' @title R Markdown output formats Template for thesis at Department of Psychology, Senshu University
#' @importFrom rmarkdown render
#' @importFrom rmarkdown pdf_document
#' @importFrom jpaRmd jpa_cite
#' @param Rmd_file file name of R Markdown file
#' @param Bib_file file name of Bib file
#' @export
senshu_thesis <- function(Rmd_file, Bib_file) {
jpa_cite(Rmd_file, Bib_file)
tmp_rmd <- paste0("tmp_", Rmd_file)
template_tex_file <- system.file("rmarkdown/templates/thesis_senshu/resources/senshu.tex",
package = 'senshuRmd')
format_pdf <- pdf_document(
latex_engine = "xelatex",
template = template_tex_file,
keep_tex = TRUE,
toc = TRUE,
toc_depth = 3,
highlight = "tango"
)
format_pdf$inherits <- "pdf_document"
output_file <- strsplit(Rmd_file, ".Rmd")[[1]]
render(tmp_rmd, format_pdf, output_file)
}
#' @title Research Compendium of Department of Psychology, Senshu University
#' @importFrom rstudioapi navigateToFile
#' @examples # set_rc()
#' @export
set_rc <- function (){
path = getwd()
# make README
if(!file.exists(file.path(path, "README.md"))){
file.create(file.path(path, "README.md"), showWarnings = FALSE)
writeLines("# SenshuRmd\u306e\u8aac\u660e\n\n## Research Compendium\u306e\u5185\u5bb9\n\nsenshuRmd\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u30fc\u69cb\u9020\u3092\u3082\u3063\u305fResearch Compendium\u3092\u7528\u610f\u3057\u307e\u3059\u3002\n\n\u5404\u30d5\u30a9\u30eb\u30c0\u306e\u6a5f\u80fd\u3092\u7406\u89e3\u3057\u305f\u4e0a\u3067\u30d5\u30a1\u30a4\u30eb\u3092\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\n- paper:\u5352\u8ad6\u30fb\u4fee\u8ad6\u7528\u306eRmd\u30d5\u30a1\u30a4\u30eb\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u307e\u3059\n\n- analysis\uff1a\u89e3\u6790\u7528\u30d5\u30a1\u30a4\u30eb\u3092\u5165\u308c\u308b\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) data\uff1a\u89e3\u6790\u7528\u30c7\u30fc\u30bf\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) function\uff1a\u89e3\u6790\u7528R\u306e\u95a2\u6570\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- materials\uff1a\u7814\u7a76\u3067\u4f7f\u3063\u305f\u6750\u6599\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- exercises\uff1a\u30bc\u30df\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- labnote\uff1a\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u4fdd\u7ba1\u3059\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n## \u6700\u521d\u306b\u3059\u308b\u3053\u3068\n\nset_rc()\u304bset_rc_ccp()\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0c\u3053\u306eREADME.md\u3068paper.Rmd\u304c\u958b\u304d\u307e\u3059\u3002\n\npaper.Rmd\u3068\u3044\u3046\u30bf\u30d6\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\uff0c\u305d\u306eKnit\u3063\u3066\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\n\n\u3057\u3070\u3089\u304f\u3059\u308b\u3068\uff0cpaper\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u5352\u8ad6\u30fb\u4fee\u8ad6\u306ePDF\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u5352\u8ad6\u30fb\u4fee\u8ad6\u306f\uff0cpaper.Rmd\u306b\u66f8\u304d\u8fbc\u3093\u3067\uff0cknit\u3057\u3066\u51fa\u529b\u3055\u308c\u305fPDF\u306b\u306a\u308a\u307e\u3059\u3002\n\n## \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u306eOSF\u3082\u3057\u304f\u306fGitHub\u306e\u8a2d\u5b9a\n\n\u4ee5\u4e0b\u3092\u53c2\u8003\u306b\u3057\u3066\uff0c\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u7814\u7a76\u5ba4\u306b\u3088\u3063\u3066OSF\u3092\u4f7f\u3046\u306e\u304bGitHub\u3092\u4f7f\u3046\u306e\u304b\u7570\u306a\u308a\u307e\u3059\u306e\u3067\uff0c\u6559\u54e1\u306b\u78ba\u8a8d\u3092\u3057\u3066\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\nhttps://github.com/ykunisato/eln4Rmd\n\n## \u65e5\u3005\u306e\u7814\u7a76\u6d3b\u52d5\u3067\u4f7f\u3046R\u30b3\u30de\u30f3\u30c9\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u4f5c\u6210(PDF)\n\nResearch Compendium\u306e\u4e00\u756a\u4e0a\u306e\u30d5\u30a9\u30eb\u30c0\u3092\u30ab\u30ec\u30f3\u30c8\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u3057\u3066\u3044\u308c\u3070\uff0clabnote\u30d5\u30a9\u30eb\u30c0\u306b\u30e9\u30dc\u30ce\u30fc\u30c8PD\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3092\u4f5c\u6210\u3057\u307e\u3059\n\neln4Rmd::elnjp_pdf(rc = TRUE)\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08OSF\u306e\u5834\u5408\uff09\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3068Research Compendium\u5185\u306e\u30d5\u30a1\u30a4\u30eb\u306e\u30d0\u30c3\u30af\u30a2\u30c3\u30d7\u3092\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\", rc_osf = \"OSF\u306eResearch Compendium\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n### GitHub\u3078\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\uff06\u30d7\u30c3\u30b7\u30e5\uff09\n\neln4Rmd::up_elnjp_git(rc = TRUE)\n\n## analysis\u30d5\u30a9\u30eb\u30c0\u306bRmd\u30d5\u30a1\u30a4\u30eb\u3092\u8ffd\u52a0\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0canalysis\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u89e3\u6790\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u3066\uff0c\u958b\u304b\u308c\u307e\u3059\u3002\n\nsenshuRmd::set_analysis(\"\u30d5\u30a1\u30a4\u30eb\u540d\")", "README.md")
navigateToFile(file.path(path, "README.md"))
}
# make paper.Rmd
if(!file.exists(file.path(path, "paper/paper.Rmd"))){
rmarkdown::draft(paste0("paper.Rmd"), template = "thesis_senshu", package = "senshuRmd", edit = FALSE)
navigateToFile(file.path(path, "paper/paper.Rmd"))
}
# make analysis directory
if(!dir.exists(file.path(path, "analysis"))){
dir.create(file.path(path, "analysis"), showWarnings = FALSE)
file.create(file.path(path, "analysis/README_analysis.md"), showWarnings = FALSE)
writeLines("README(analysis)\n\n\u89e3\u6790\u306b\u4f7f\u3046R\u3084Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3053\u3053\u306b\u7f6e\u304d\u307e\u3059\u3002\n\u30d5\u30a1\u30a4\u30eb\u540d\u306f\u89e3\u6790\u306e\u9806\u756a\u304c\u308f\u304b\u308b\u3088\u3046\u306b\u3064\u3051\u3066\u304f\u3060\u3055\u3044\u3002\nRmd\u30d5\u30a1\u30a4\u30eb\u306f\u89e3\u6790\u3068\u305d\u306e\u8aac\u660e\u3092\u307e\u3068\u3081\u3084\u3059\u3044\u306e\u3067\uff0c\u3067\u304d\u308b\u3060\u3051Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u4f7f\u3046\u3088\u3046\u306b\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/README_analysis.md")
}
# make data directory
if(!dir.exists(file.path(path, "analysis/data"))){
dir.create(file.path(path, "analysis/data"), showWarnings = FALSE)
file.create(file.path(path, "analysis/data/README_data.md"), showWarnings = FALSE)
writeLines("README(data)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046\u30c7\u30fc\u30bf\u3092\u7f6e\u304d\u307e\u3059\u3002OSF\u3084GitHub\u306b\u304a\u3044\u3066\u3082\u5927\u4e08\u592b\u306a\u30c7\u30fc\u30bf\u5316\u3069\u3046\u304b\u306f\u6307\u5c0e\u6559\u54e1\u306b\u76f8\u8ac7\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/data/README_data.md")
}
# make function directory
if(!dir.exists(file.path(path, "analysis/function"))){
dir.create(file.path(path, "analysis/function"), showWarnings = FALSE)
file.create(file.path(path, "analysis/function/README_function.md"), showWarnings = FALSE)
writeLines("README(function)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046R\u95a2\u6570\u3092\u7f6e\u304d\u307e\u3059\u3002\u95a2\u6570\u5316\u3057\u305f\u3082\u306e\u306f\u5225\u306b\u307e\u3068\u3081\u3066\u304a\u3044\u305f\u307b\u3046\u304c\u4fbf\u5229\u306a\u306e\u3067\uff0c\u3053\u3061\u3089\u3092\u5229\u7528\u304f\u3060\u3055\u3044\u3002", "analysis/function/README_function.md")
}
# make materials directory
if(!dir.exists(file.path(path, "materials"))){
dir.create(file.path(path, "materials"), showWarnings = FALSE)
file.create(file.path(path, "materials/README_materials.md"), showWarnings = FALSE)
writeLines("README(materials)\n\n\u7814\u7a76\u3067\u4f7f\u7528\u3057\u305f\u6750\u6599\uff08\u5b9f\u9a13\u8ab2\u984c\uff0c\u8cea\u554f\u7d19\uff0c\u5b9f\u9a13\u30fb\u8abf\u67fb\u30d7\u30ed\u30c8\u30b3\u30eb\uff0c\u502b\u7406\u7533\u8acb\u66f8\uff09\u306a\u3069\u3092\u3053\u3061\u3089\u306b\u4fdd\u7ba1\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "materials/README_materials.md")
}
# make labnote directory
if(!dir.exists(file.path(path, "labnote"))){
dir.create(file.path(path, "labnote"), showWarnings = FALSE)
file.create(file.path(path, "labnote/README_labnote.r"), showWarnings = FALSE)
writeLines("# README(labnote)\n\n# \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306f\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u307e\u305a\uff0csetwd()\u3067labnote\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u307e\u3059\u3002\nsetwd('labnote')\n# \u4ee5\u4e0b\u306eelnjp_pdf()\u3067\u30e9\u30dc\u30ce\u30fc\u30c8\u304c\u4f5c\u308c\u307e\u3059\u3002\neln4Rmd::elnjp_pdf()\n# \u4ee5\u4e0b\u306e\u30ea\u30f3\u30af\u5148\u3092\u307f\u3066\uff0cOSF\u304bGitHub\u306e\u8a2d\u5b9a\u3092\u3057\u307e\u3059\u3002\n# https://github.com/ykunisato/eln4Rmd\n#OSF\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_osf(eln_osf=\"OSF\u306eURL\")\n# GitHub\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\u3068\u30d7\u30c3\u30b7\u30e5\uff09\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_git()", "labnote/README_labnote.r")
}
}
#' @title Research Compendium of CCP Lab
#' @importFrom rstudioapi navigateToFile
#' @examples # set_rc_ccp()
#' @export
set_rc_ccp <- function (){
path = getwd()
# make README
if(!file.exists(file.path(path, "README.md"))){
file.create(file.path(path, "README.md"), showWarnings = FALSE)
writeLines("# SenshuRmd\u306e\u8aac\u660e\n\n## Research Compendium\u306e\u5185\u5bb9\n\nsenshuRmd\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u30fc\u69cb\u9020\u3092\u3082\u3063\u305fResearch Compendium\u3092\u7528\u610f\u3057\u307e\u3059\u3002\n\n\u5404\u30d5\u30a9\u30eb\u30c0\u306e\u6a5f\u80fd\u3092\u7406\u89e3\u3057\u305f\u4e0a\u3067\u30d5\u30a1\u30a4\u30eb\u3092\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\n- paper:\u5352\u8ad6\u30fb\u4fee\u8ad6\u7528\u306eRmd\u30d5\u30a1\u30a4\u30eb\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u307e\u3059\n\n- analysis\uff1a\u89e3\u6790\u7528\u30d5\u30a1\u30a4\u30eb\u3092\u5165\u308c\u308b\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) data\uff1a\u89e3\u6790\u7528\u30c7\u30fc\u30bf\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- (analysis\u5185) function\uff1a\u89e3\u6790\u7528R\u306e\u95a2\u6570\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- materials\uff1a\u7814\u7a76\u3067\u4f7f\u3063\u305f\u6750\u6599\u3092\u5165\u308c\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- exercises\uff1a\u30bc\u30df\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u7528\u306e\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n- labnote\uff1a\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u4fdd\u7ba1\u3059\u308b\u30d5\u30a9\u30eb\u30c0\u3067\u3059\n\n## \u6700\u521d\u306b\u3059\u308b\u3053\u3068\n\nset_rc()\u304bset_rc_ccp()\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0c\u3053\u306eREADME.md\u3068paper.Rmd\u304c\u958b\u304d\u307e\u3059\u3002\n\npaper.Rmd\u3068\u3044\u3046\u30bf\u30d6\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\uff0c\u305d\u306eKnit\u3063\u3066\u30dc\u30bf\u30f3\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\n\n\u3057\u3070\u3089\u304f\u3059\u308b\u3068\uff0cpaper\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u5352\u8ad6\u30fb\u4fee\u8ad6\u306ePDF\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u5352\u8ad6\u30fb\u4fee\u8ad6\u306f\uff0cpaper.Rmd\u306b\u66f8\u304d\u8fbc\u3093\u3067\uff0cknit\u3057\u3066\u51fa\u529b\u3055\u308c\u305fPDF\u306b\u306a\u308a\u307e\u3059\u3002\n\n## \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u306eOSF\u3082\u3057\u304f\u306fGitHub\u306e\u8a2d\u5b9a\n\n\u4ee5\u4e0b\u3092\u53c2\u8003\u306b\u3057\u3066\uff0c\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u7814\u7a76\u5ba4\u306b\u3088\u3063\u3066OSF\u3092\u4f7f\u3046\u306e\u304bGitHub\u3092\u4f7f\u3046\u306e\u304b\u7570\u306a\u308a\u307e\u3059\u306e\u3067\uff0c\u6559\u54e1\u306b\u78ba\u8a8d\u3092\u3057\u3066\u8a2d\u5b9a\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n\nhttps://github.com/ykunisato/eln4Rmd\n\n## \u65e5\u3005\u306e\u7814\u7a76\u6d3b\u52d5\u3067\u4f7f\u3046R\u30b3\u30de\u30f3\u30c9\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u4f5c\u6210(PDF)\n\nResearch Compendium\u306e\u4e00\u756a\u4e0a\u306e\u30d5\u30a9\u30eb\u30c0\u3092\u30ab\u30ec\u30f3\u30c8\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u3057\u3066\u3044\u308c\u3070\uff0clabnote\u30d5\u30a9\u30eb\u30c0\u306b\u30e9\u30dc\u30ce\u30fc\u30c8PD\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3092\u4f5c\u6210\u3057\u307e\u3059\n\neln4Rmd::elnjp_pdf(rc = TRUE)\n\n### \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08OSF\u306e\u5834\u5408\uff09\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u3092\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n\u4ee5\u4e0b\u3067\u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3068Research Compendium\u5185\u306e\u30d5\u30a1\u30a4\u30eb\u306e\u30d0\u30c3\u30af\u30a2\u30c3\u30d7\u3092\u3057\u307e\u3059\u3002\n\neln4Rmd::up_elnjp_osf(eln_osf = \"OSF\u306e\u30e9\u30dc\u30ce\u30fc\u30c8\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\", rc_osf = \"OSF\u306eResearch Compendium\u7528\u30b3\u30f3\u30dd\u30fc\u30cd\u30f3\u30c8\u306eURL\")\n\n### GitHub\u3078\u306e\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\uff06\u30d7\u30c3\u30b7\u30e5\uff09\n\neln4Rmd::up_elnjp_git(rc = TRUE)\n\n## analysis\u30d5\u30a9\u30eb\u30c0\u306bRmd\u30d5\u30a1\u30a4\u30eb\u3092\u8ffd\u52a0\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0canalysis\u30d5\u30a9\u30eb\u30c0\u5185\u306b\u89e3\u6790\u7528Rmd\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u3066\uff0c\u958b\u304b\u308c\u307e\u3059\u3002\n\nsenshuRmd::set_analysis(\"\u30d5\u30a1\u30a4\u30eb\u540d\")\n\n## jsPsych\u3067\u5b9f\u9a13\u8ab2\u984c\u3092\u4f5c\u6210\u3059\u308b\n\n\u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068\uff0cexercises\u30d5\u30a9\u30eb\u30c0\u5185\u306bjsPsych\u8ab2\u984c\u7528\u30d5\u30a9\u30eb\u30c0\u3068\u30d5\u30a1\u30a4\u30eb\u4e00\u5f0f\u304c\u7528\u610f\u3055\u308c\u307e\u3059\u3002\n\njsPsychRmd::set_jsPsych(folder = \"\u8ab2\u984c\u540d\u3092\u82f1\u8a9e\u3067\u66f8\u304f\", rc = TRUE)", "README.md")
navigateToFile(file.path(path, "README.md"))
}
# make paper.Rmd
if(!file.exists(file.path(path, "paper/paper.Rmd"))){
rmarkdown::draft(paste0("paper.Rmd"), template = "thesis_senshu", package = "senshuRmd", edit = FALSE)
navigateToFile(file.path(path, "paper/paper.Rmd"))
}
# make analysis directory
if(!dir.exists(file.path(path, "analysis"))){
dir.create(file.path(path, "analysis"), showWarnings = FALSE)
file.create(file.path(path, "analysis/README_analysis.md"), showWarnings = FALSE)
writeLines("README(analysis)\n\n\u89e3\u6790\u306b\u4f7f\u3046R\u3084Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u3053\u3053\u306b\u7f6e\u304d\u307e\u3059\u3002\n\u30d5\u30a1\u30a4\u30eb\u540d\u306f\u89e3\u6790\u306e\u9806\u756a\u304c\u308f\u304b\u308b\u3088\u3046\u306b\u3064\u3051\u3066\u304f\u3060\u3055\u3044\u3002\nRmd\u30d5\u30a1\u30a4\u30eb\u306f\u89e3\u6790\u3068\u305d\u306e\u8aac\u660e\u3092\u307e\u3068\u3081\u3084\u3059\u3044\u306e\u3067\uff0c\u3067\u304d\u308b\u3060\u3051Rmd\u30d5\u30a1\u30a4\u30eb\u3092\u4f7f\u3046\u3088\u3046\u306b\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/README_analysis.md")
}
# make data directory
if(!dir.exists(file.path(path, "analysis/data"))){
dir.create(file.path(path, "analysis/data"), showWarnings = FALSE)
file.create(file.path(path, "analysis/data/README_data.md"), showWarnings = FALSE)
writeLines("README(data)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046\u30c7\u30fc\u30bf\u3092\u7f6e\u304d\u307e\u3059\u3002OSF\u3084GitHub\u306b\u304a\u3044\u3066\u3082\u5927\u4e08\u592b\u306a\u30c7\u30fc\u30bf\u5316\u3069\u3046\u304b\u306f\u6307\u5c0e\u6559\u54e1\u306b\u76f8\u8ac7\u3092\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "analysis/data/README_data.md")
}
# make function directory
if(!dir.exists(file.path(path, "analysis/function"))){
dir.create(file.path(path, "analysis/function"), showWarnings = FALSE)
file.create(file.path(path, "analysis/function/README_function.md"), showWarnings = FALSE)
writeLines("README(function)\n\n\u3053\u3061\u3089\u306b\u89e3\u6790\u3067\u4f7f\u3046R\u95a2\u6570\u3092\u7f6e\u304d\u307e\u3059\u3002\u95a2\u6570\u5316\u3057\u305f\u3082\u306e\u306f\u5225\u306b\u307e\u3068\u3081\u3066\u304a\u3044\u305f\u307b\u3046\u304c\u4fbf\u5229\u306a\u306e\u3067\uff0c\u3053\u3061\u3089\u3092\u5229\u7528\u304f\u3060\u3055\u3044\u3002", "analysis/function/README_function.md")
}
# make materials directory
if(!dir.exists(file.path(path, "materials"))){
dir.create(file.path(path, "materials"), showWarnings = FALSE)
file.create(file.path(path, "materials/README_materials.md"), showWarnings = FALSE)
writeLines("README(materials)\n\n\u7814\u7a76\u3067\u4f7f\u7528\u3057\u305f\u6750\u6599\uff08\u5b9f\u9a13\u8ab2\u984c\uff0c\u8cea\u554f\u7d19\uff0c\u5b9f\u9a13\u30fb\u8abf\u67fb\u30d7\u30ed\u30c8\u30b3\u30eb\uff0c\u502b\u7406\u7533\u8acb\u66f8\uff09\u306a\u3069\u3092\u3053\u3061\u3089\u306b\u4fdd\u7ba1\u3057\u3066\u304f\u3060\u3055\u3044\u3002", "materials/README_materials.md")
}
# make exercises directory
if(!dir.exists(file.path(path, "exercises"))){
dir.create(file.path(path, "exercises"), showWarnings = FALSE)
file.create(file.path(path, "exercises/README_exercises.r"), showWarnings = FALSE)
writeLines("# README(exercises)\n\n# \u56fd\u91cc\u7814\u7a76\u5ba4\u3067\u884c\u3046\u6f14\u7fd2\u8ab2\u984c\u306f\uff0c\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u4ee5\u4e0b\u3092\u5b9f\u884c\u3059\u308b\u3068exercises\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3067\u304d\u307e\u3059\u3002\r\nsetwd(\"exercises\")\n# exercises\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u305f\u3046\u3048\u3067\uff0c\u6f14\u7fd2\u8ab2\u984c\u306b\u53d6\u308a\u7d44\u3093\u3067\u304f\u3060\u3055\u3044\u3002\n# \u4ee5\u4e0b\u306eset_jsPsych()\u3092\u4f7f\u3046\u3068\uff0cjsPsych\u306e\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u3092\u4f5c\u3063\u3066\uff0c\u5fc5\u8981\u306a\u30d5\u30a1\u30a4\u30eb\u3092\u7528\u610f\u3057\u307e\u3059\u3002\njsPsychRmd::set_jsPsych(folder = 'hello')", "exercises/README_exercises.r")
}
# make labnote directory
if(!dir.exists(file.path(path, "labnote"))){
dir.create(file.path(path, "labnote"), showWarnings = FALSE)
file.create(file.path(path, "labnote/README_labnote.r"), showWarnings = FALSE)
writeLines("# README(labnote)\n\n# \u96fb\u5b50\u30e9\u30dc\u30ce\u30fc\u30c8\u306f\u3053\u3061\u3089\u306b\u4fdd\u5b58\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n# \u307e\u305a\uff0csetwd()\u3067labnote\u3092\u4f5c\u696d\u30d5\u30a9\u30eb\u30c0\u306b\u3057\u307e\u3059\u3002\nsetwd('labnote')\n# \u4ee5\u4e0b\u306eelnjp_pdf()\u3067\u30e9\u30dc\u30ce\u30fc\u30c8\u304c\u4f5c\u308c\u307e\u3059\u3002\neln4Rmd::elnjp_pdf()\n# \u4ee5\u4e0b\u306e\u30ea\u30f3\u30af\u5148\u3092\u307f\u3066\uff0cOSF\u304bGitHub\u306e\u8a2d\u5b9a\u3092\u3057\u307e\u3059\u3002\n# https://github.com/ykunisato/eln4Rmd\n#OSF\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_osf(eln_osf=\"OSF\u306eURL\")\n# GitHub\u3092\u4f7f\u3046\u5834\u5408\u306f\uff0c\u4ee5\u4e0b\u3067\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\uff08\u30b3\u30df\u30c3\u30c8\u3068\u30d7\u30c3\u30b7\u30e5\uff09\u3057\u307e\u3059\u3002\neln4Rmd::up_elnjp_git()", "labnote/README_labnote.r")
}
}
#' @title R Markdown output formats template for analysis at Department of Psychology, Senshu University
#' @importFrom stringr str_replace
#' @importFrom rstudioapi navigateToFile
#' @param Rmd_file file name of R Markdown file
#' @param rc If you are using Research Compendium of senshuRmd,
#' you can create a Rmd file in the "analysis" directory from the current directory.
#' @export
set_analysis <- function(Rmd_file, rc = TRUE) {
if(missing(Rmd_file)){
stop("Rmd_file\u3000= \"\u30d5\u30a1\u30a4\u30eb\u540d\"\u3067\uff0c\u4f5c\u6210\u3059\u308bRmd\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u6307\u5b9a\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u30d5\u30a1\u30a4\u30eb\u540d\u306f\uff0cAnalysis01\u306e\u3088\u3046\u306b\u82f1\u8a9e\u3067\u6307\u5b9a\u304f\u3060\u3055\u3044\u3002")
}
path = getwd()
if(rc == TRUE){
path <- paste0(path, "/analysis")
}
file_path <- paste0(path,"/",Rmd_file,".Rmd")
if(!file.exists(file_path)){
path_skeleton <- system.file("rmarkdown/templates/analysis/skeleton/skeleton.Rmd",package = "senshuRmd")
text_skeleton <- readLines(path_skeleton, warn = F)
tmp_rmd <- file(file_path, "w")
for (i in 1:length(text_skeleton)) {
st <- text_skeleton[i]
st <- str_replace(st, pattern = "title: 'title'",
replacement = paste0("title: ", "'",Rmd_file,"'"))
writeLines(st, tmp_rmd)
}
close(tmp_rmd)
navigateToFile(file_path)
}else{
stop("\u6307\u5b9a\u3055\u308c\u305f\u30d5\u30a1\u30a4\u30eb\u540d\u306eRmd\u30d5\u30a1\u30a4\u30eb\u306f\u65e2\u306b\u5b58\u5728\u3057\u3066\u3044\u307e\u3059\u3002\u5225\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u3067\u4f5c\u6210\u304f\u3060\u3055\u3044\u3002")
}
}
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