version 0.3.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: prodigenr
 Title: Research Project Directory Generator
-Version: 0.2.7
+Version: 0.3.0
 Authors@R: person("Luke", "Johnston", , "lwjohnst@gmail.com", c("aut", "cre"))
 Description: Create a project directory structure, along with typical files
     for that project.  This allows projects to be quickly and easily created,
@@ -9,14 +9,15 @@ Description: Create a project directory structure, along with typical files
 Depends: R (>= 3.1.2)
 License: MIT + file LICENSE
 LazyData: true
-Suggests: rmarkdown, git2r, packrat, knitr, testthat
+Suggests: rmarkdown, knitr, testthat, rvest, xml2, rfigshare
 RoxygenNote: 5.0.1
 VignetteBuilder: knitr
 URL: https://github.com/lwjohnst86/prodigenr
 BugReports: https://github.com/lwjohnst86/prodigenr/issues
+Imports: devtools, stats, utils
 NeedsCompilation: no
-Packaged: 2016-05-13 19:41:13 UTC; luke
+Packaged: 2016-07-29 02:42:23 UTC; luke
 Author: Luke Johnston [aut, cre]
 Maintainer: Luke Johnston <lwjohnst@gmail.com>
 Repository: CRAN
-Date/Publication: 2016-05-14 09:10:15
+Date/Publication: 2016-07-29 06:41:09

MD5

@@ -1,34 +1,35 @@
-e37abead8b388798535378184b86cd3d *DESCRIPTION
+ad069562c459fb5d22ead8755f2a5448 *DESCRIPTION
 ddb53d8ec14a4592849266ac05157e5e *LICENSE
-8faea9a4680950417c132141bfee75bc *NAMESPACE
-1454c005558cf700e29273d6492ef3a0 *NEWS.md
-ce221787641d1ed5844f28754184f4dc *R/list_templates.R
-4192a5c05e64f7666aab6a151ce75614 *R/prodigen.R
-14c889f3fa53d4051b0e6425898b540e *README.md
-060c3c6fc3d055687dd54b63ceaf6a82 *build/vignette.rds
-3ff2055d4844bd21aab5b429efc415e1 *inst/doc/introduction.R
-f9128e5f5764852cf28d0fbf10948eb7 *inst/doc/introduction.Rmd
-c7ac089975d291e84a0352343f6d39cc *inst/doc/introduction.html
-bb92aaaf3f0bbb1be7ce62e99da5a5ad *inst/templates/files/R/fetch_data.R
-b83f6ec5d25726cd87ef3189fdbed33b *inst/templates/files/R/functions.R
-d79fa66d7f1a85d11fbb18095bc48331 *inst/templates/files/R/load_data.R
-092ab4df59fd1ea8f984a4d58b59b834 *inst/templates/files/R/setup.R
-0f57d75254a0e7625d240f7443c9bd86 *inst/templates/files/README.md
-099a501ac2a4cd0f8093fc3a19281e10 *inst/templates/files/Rprofile
-4019fadb95f0337dd231ace5c6895f3b *inst/templates/files/rstudio
-fee8a18773f6a58061cf7aef69a6c9b6 *inst/templates/projects/abstract/README-append.md
-f3566f0b5172098d11d1f60ab7391f87 *inst/templates/projects/abstract/abstract.Rmd
-ac754814e641869e0d2ce4b76ac9402a *inst/templates/projects/manuscript/README-append.md
-55658a0e8e31ba29da81389cc53c054c *inst/templates/projects/manuscript/doc/manuscript.Rmd
-4c7635a8de8b8c4d9f57f48f7a70cb1b *inst/templates/projects/poster/README-append.md
-0902a70397f07d23b8aee6a14df41bf3 *inst/templates/projects/poster/beamerthemeCustomPoster.sty
-d40ce241c60b815789f69333621a8f1e *inst/templates/projects/poster/poster.Rmd
-fc71f152dec9d2fbcc04a17212e68428 *inst/templates/projects/poster/template.tex
-18a13da95db5d5dcfcf21647630dddf4 *inst/templates/projects/slides/README-append.md
-66ef33c363ef0e9d8e8fedf0353aeb77 *inst/templates/projects/slides/slides.Rmd
-b08302683d33c2deb73b2fbd566a5e09 *inst/templates/projects/slides/template.tex
-689560a39942f835159b1c9af082af6b *man/list_templates.Rd
-c0ef83876a625c902c099a9e5dac2240 *man/prodigen.Rd
+8ce13d783f49dcfb287f03a57f0b8c90 *NAMESPACE
+a5567f83a8dfc85e135b8756f9e7d3ad *NEWS.md
+566b9a92ad8934d988473bfec492f760 *R/includes.R
+9d302cb7beb20244c197e1a46e7235b1 *R/prodigen.R
+edf9e54d0c01ea34cec3ad230fff589c *R/template_list.R
+965d672dd08f0eba690463caa42db4b2 *R/utils.R
+e9bf3d2a04362adf5155375af303035d *README.md
+f43fa768e61ed4fabae7b3b2a929da97 *build/vignette.rds
+2a8bfc48281c61059480fa33421bb4e3 *inst/doc/introduction.R
+a6d1a3b347737486ca57f352f4adcd2c *inst/doc/introduction.Rmd
+907f73229bcbdca617f1850669d3573a *inst/doc/introduction.html
+cfbb5010b3e802b463be44b0658df36a *inst/templates/R/fetch_data.R
+dde2c6ee88469bce15696d20aedaae77 *inst/templates/R/functions.R
+175645936217c01e2e5ddd8b7f4d6d24 *inst/templates/R/load_data.R
+05946e941c66614264aab0d8ac73095b *inst/templates/R/setup.R
+f3566f0b5172098d11d1f60ab7391f87 *inst/templates/abstract/abstract.Rmd
+ca226ae8ea6e3b68c7640e0a2142734b *inst/templates/manuscript/manuscript.Rmd
+0902a70397f07d23b8aee6a14df41bf3 *inst/templates/poster/beamerthemeCustomPoster.sty
+d40ce241c60b815789f69333621a8f1e *inst/templates/poster/poster.Rmd
+fc71f152dec9d2fbcc04a17212e68428 *inst/templates/poster/template.tex
+065c1868f44eb317a7b0a8ac8a2d8a1e *inst/templates/readme/README.md
+19976612495ae36e940ec7208413fd2e *inst/templates/rfigshare/rfigshare.R
+66ef33c363ef0e9d8e8fedf0353aeb77 *inst/templates/slides/slides.Rmd
+b08302683d33c2deb73b2fbd566a5e09 *inst/templates/slides/template.tex
+68eccc45cb7e38f1146b82737df704b4 *man/include_mit_license.Rd
+68b13700f83b70747d6353ff3f72ab39 *man/include_rfigshare_script.Rd
+a3c0d7149c5ff6b4ac7bdf3817db118b *man/include_strobe.Rd
+4377444a3a00d49e84b1a4c8a451c138 *man/prodigen.Rd
+8fb573986cb7ea5c332b7913126b6384 *man/template_list.Rd
 2ffba69e65ca57623c926451edbcc829 *tests/testthat.R
-1096499c7940187ae91226d0db3f308b *tests/testthat/test-projects.R
-f9128e5f5764852cf28d0fbf10948eb7 *vignettes/introduction.Rmd
+d0ff5428f998342ea9ea78c28d9c12f1 *tests/testthat/test-projects.R
+c52db57710e3e1ea76626a3a3ff5c4eb *vignettes/file_structure.txt
+a6d1a3b347737486ca57f352f4adcd2c *vignettes/introduction.Rmd

NAMESPACE

@@ -1,4 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(list_templates)
+export(include_mit_license)
+export(include_rfigshare_script)
+export(include_strobe)
 export(prodigen)
+export(template_list)

NEWS.md

@@ -1,3 +1,15 @@
+# prodigenr 0.3.0
+
+## New features/functionality
+
+* `prodigen()` now creates a new project structure that mimics R package development
+more, specifically `devtools` (since it is well documented and actively
+maintained) (#18, #15, #14). The old style has been removed.
+* Added a function to include a [STROBE](http://www.strobe-statement.org/index.php?id=strobe-home) 
+checklist for  reporting guidelines (#21).
+* Added function to include an `rfigshare` script to send to [figshare](https://figshare.com/) (#19).
+* Added function to include a more complete MIT license (#20).
+
 # prodigenr 0.2.7
 
 * Added a `NEWS.md` file to track changes to the package.

R/includes.R

@@ -0,0 +1,78 @@
+
+include_readme <- function(path) {
+    message('* Adding a README.md file to the project.')
+    copy_template_files('readme', path)
+}
+
+include_project_document <- function(type, path) {
+    message('* Adding the main project ', type, ' document to the doc/ folder.')
+    dir.create(file.path(path, 'doc'))
+    copy_template_files(type, file.path(path, 'doc'))
+}
+
+include_extra_analyses <- function(path) {
+    message('* Creating a vignette file for documenting additional analyses.')
+    devtools::use_vignette('extra-analyses', path)
+}
+
+include_rbase_files <- function(path) {
+    message('* Adding some basic R functions to the R/ folder.')
+    copy_template_files('R', file.path(path, 'R'))
+}
+
+#' License the project under MIT.
+#'
+#' @param path Path to the project.
+#'
+#' @return Creates a MIT LICENSE file.
+#' @export
+include_mit_license <- function(path = '.') {
+    if (!requireNamespace('xml2', quietly = TRUE))
+        stop('Please install the `xml2` package.')
+    if (!requireNamespace('rvest', quietly = TRUE))
+        stop('Please install the `rvest` package.')
+    path <- devtools::as.package(path)$path
+    message("* Adding MIT license to project.")
+    mit <- xml2::read_html("http://choosealicense.com/licenses/mit/")
+    mit <- rvest::html_node(mit, "#license-text")
+    mit <- rvest::html_text(mit)
+    devtools::use_mit_license(path)
+    license_path <- file.path(path, 'LICENSE')
+    utils::capture.output(cat(readLines(license_path), mit, file = license_path))
+    invisible()
+}
+
+#' Add an R script to send code to figshare.
+#'
+#' @param path Path to the project.
+#'
+#' @return Creates an rfigshare script.
+#' @export
+include_rfigshare_script <- function(path = '.') {
+    if (!requireNamespace('rfigshare', quietly = TRUE))
+        stop('Please install the `rfigshare` package.')
+    message('* Adding rfigshare.R to the R/ folder. Use this to send code to figshare.')
+    path <- devtools::as.package(path)$path
+    devtools::use_package('rfigshare', pkg = path)
+    copy_template_files('rfigshare', file.path(path, 'R'))
+}
+
+#' Include a STROBE checklist in the project.
+#'
+#' @param path Path to the project.
+#'
+#' @return Creates a file with the STROBE checklist.
+#' @export
+include_strobe <- function(path = '.') {
+    if (!requireNamespace('xml2', quietly = TRUE))
+        stop('Please install the `xml2` package.')
+    if (!requireNamespace('rvest', quietly = TRUE))
+        stop('Please install the `rvest` package.')
+    path <- devtools::as.package(path)$path
+    message('* Adding the STROBE checklist to the vignettes/ folder (this is for observational research).')
+    strobe <- xml2::read_html('https://raw.githubusercontent.com/lwjohnst86/scientific-checklists/master/STROBE.md')
+    strobe <- rvest::html_text(strobe)
+    file_path <- file.path(path, 'vignettes', 'strobe-checklist.md')
+    utils::capture.output(cat(strobe, file = file_path))
+    invisible()
+}

R/prodigen.R

@@ -1,97 +1,57 @@
-##' Create a project directory and associated files.
-##'
-##' The main workhorse of the \pkg{prodigenr} package.  Creates a
-##' project directory layout, with template files and helper scripts.
-##' @title Create a project directory based on a template
-##'
-##' @param proj.type type of project to create, based on the templates found in
-##'   \code{\link[prodigenr]{list_templates}} function
-##' @param proj.name name of the new project directory
-##' @param proj.path location of where the new project will be created
-##' @param git.init Logical, whether to initialize the new project with git
-##' @param packrat.init Logical, whether to track the R package usage with
-##'   packrat.
-##' @return Creates a project directory with files and subdirectories
-##' @export
-##' @author Luke W. Johnston
-##' @examples
-##'
-##' \dontrun{
-##' ## Get a list of possible project templates
-##' list_templates('projects')
-##' # Create a project. Best done in a fresh R console.
-##' prodigen('poster', 'poster', 'dev/', TRUE, FALSE)
-##' prodigen('poster', 'poster', 'path/to/dir/', FALSE)
-##' prodigen('poster', 'posterName', git.init = FALSE)
-##' prodigen('slides', 'conference-presentation', packrat.init = FALSE)
-##' prodigen('abstract', 'name', './', FALSE)
-##' prodigen('manuscript', proj.path = './', git.init = TRUE)
-##' }
-prodigen <- function(proj.type, proj.name = NULL, proj.path = getwd(),
-                     git.init = FALSE, packrat.init = FALSE) {
-
-    proj.type <- match.arg(proj.type, list_templates())
-    if (is.null(proj.name)) {
-        proj.name <- proj.type
-    } else if (!is.character(proj.name)) {
-        stop('Please use a character string (ie. in quotes) for the project name.')
-    }
-
-    if (!dir.exists(proj.path))
-        stop('Please use a proj.path that currently exists on your computer.')
-
-    proj_old <- file.path(proj.path, proj.type)
-    proj_new <- file.path(proj.path, proj.name)
-
-    if (file.exists(proj_new))
-        stop('Project already exists, please use a different proj.name.')
-
-    proj.files <- system.file('templates', 'projects', proj.type, package = 'prodigenr')
-    file.copy(proj.files,
-              proj.path, recursive = TRUE)
-    file.rename(proj_old, proj_new)
-
-    # Copy over the RStudio, Rprofile, and R/ files
-    template.files <- system.file('templates', 'files',
-                                  package = 'prodigenr')
-    template.files <- list.files(template.files, all.files = TRUE,
-                                 full.names = TRUE,
-                                 include.dirs = FALSE)[-1:-2]
-    file.copy(template.files,
-              file.path(proj_new), recursive = TRUE)
-
-    file.rename(file.path(proj_new, 'rstudio'),
-                file.path(proj_new, paste0(proj.name, '.Rproj')))
-
-    file.rename(file.path(proj_new, 'Rprofile'),
-                file.path(proj_new, '.Rprofile'))
-
-    file.append(file.path(proj_new, 'README.md'),
-                file.path(proj_new, 'README-append.md'))
-    file.remove(file.path(proj_new, 'README-append.md'))
-
-    if (git.init & requireNamespace('git2r', quietly = TRUE)) {
-        repo <- git2r::init(proj_new)
-        gitignore.file <- file.path(proj_new, '.gitignore')
-        if (!file.exists(gitignore.file))
-            file.create(gitignore.file, showWarnings = FALSE)
-        write('.RData\n.Rout\ndata/\n.Rhistory\n.Rproj.user',
-              file = gitignore.file, append = TRUE)
-    }
-
-    if (packrat.init & requireNamespace('packrat', quietly = TRUE)) {
-        packrat::init(
-            proj_new, enter = FALSE,
-            options = list(
-                vcs.ignore.lib = TRUE,
-                vcs.ignore.src = TRUE
-            )
-        )
-    }
-
-    if (git.init & requireNamespace('git2r', quietly = TRUE)) {
-        git2r::add(repo, unlist(git2r::status(repo, verbose = FALSE)))
-        git2r::commit(repo, 'Initial commit')
+#' Create a project directory based on a template.
+#'
+#'
+#' Create a project directory and associated files. Is based on using RStudio
+#' and the \link[devtools]{devtools} package development way of working with
+#' files and code. So commands/keybindings like
+#' \code{\link[devtools]{load_all}} (Ctrl-Shift-L) and
+#' \code{\link[devtools]{document}} (Ctrl-Shift-D) work to update your code and
+#' allow an continuous and integrated approach to analyzing your data and
+#' writing up your research product.
+#'
+#' @param type type of project to create, based on the templates found in
+#'   \code{\link[prodigenr]{template_list}} function
+#' @param name name of the new project directory
+#' @param path location of where the new project will be created
+#' @param git.init Logical, whether to initialize the new project with git
+#' @return Creates a project directory with files and subdirectories
+#' @export
+#' @examples
+#'
+#' \dontrun{\donttest{
+#' # Get a list of possible project templates
+#' template_list
+#' # Create a project. Best done in a fresh R console.
+#' prodigen('poster', 'poster', 'dev/', TRUE, FALSE)
+#' prodigen('poster', 'poster', 'path/to/dir/', FALSE)
+#' prodigen('poster', 'posterName', git.init = FALSE)
+#' prodigen('abstract', 'name', './', FALSE)
+#' prodigen('manuscript', path = './', git.init = TRUE)
+#' }}
+prodigen <-
+    function(type,
+             name = NULL,
+             path = getwd(),
+             git.init = FALSE) {
+        type <- match.arg(type, template_list)
+        stopifnot(is.character(name))
+        if (is.null(name)) {
+            name <- type
+        }
+
+        proj_path <- file.path(path, name)
+        message("* Creating project '", name, "' in '", proj_path, "'.")
+        null <- utils::capture.output(suppressMessages(devtools::create(proj_path)))
+        include_readme(proj_path)
+        include_project_document(type, proj_path)
+        include_extra_analyses(proj_path)
+        include_rbase_files(proj_path)
+        suppressMessages(devtools::use_package('devtools', pkg = proj_path))
+        if (git.init) {
+            devtools::use_git(pkg = proj_path)
+        } else {
+            null <- file.remove(file.path(proj_path, '.gitignore'))
+        }
+        invisible(TRUE)
     }
 
-}

R/template_list.R

@@ -0,0 +1,10 @@
+#' List project templates within \pkg{prodigenr}.
+#'
+#' Get a list of available templates in a package.
+#'
+#' @return Vector of templates available
+#' @export
+#' @examples
+#' template_list
+#'
+template_list <- c('abstract', 'manuscript', 'poster', 'slides')

R/utils.R

@@ -0,0 +1,11 @@
+
+copy_template_files <- function(from, to) {
+    template_files <- system.file('templates', from,
+                                  package = 'prodigenr')
+    template_files <- list.files(template_files, all.files = TRUE,
+                                 full.names = TRUE,
+                                 include.dirs = FALSE)[-1:-2]
+    file.copy(template_files, to, recursive = TRUE)
+}
+
+