version 0.2.6

DESCRIPTION

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+Package: prodigenr
+Title: Research Project Directory Generator
+Version: 0.2.6
+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,
+    as well as for them to be standardized. Designed specifically with scientists
+    in mind (mainly bio-medical researchers, but likely applies to other fields).
+Depends: R (>= 3.1.2)
+License: MIT + file LICENSE
+LazyData: true
+Suggests: rmarkdown, git2r, packrat, knitr, testthat
+RoxygenNote: 5.0.1
+VignetteBuilder: knitr
+URL: https://github.com/lwjohnst86/prodigenr
+BugReports: https://github.com/lwjohnst86/prodigenr/issues
+NeedsCompilation: no
+Packaged: 2016-04-29 17:00:58 UTC; luke
+Author: Luke Johnston [aut, cre]
+Maintainer: Luke Johnston <lwjohnst@gmail.com>
+Repository: CRAN
+Date/Publication: 2016-04-30 00:16:00

LICENSE

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+YEAR: 2015-2016
+COPYRIGHT HOLDER: Luke W. Johnston

MD5

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+90c17f84d693b77792afa99e9aa4b23a *DESCRIPTION
+ddb53d8ec14a4592849266ac05157e5e *LICENSE
+8faea9a4680950417c132141bfee75bc *NAMESPACE
+ce221787641d1ed5844f28754184f4dc *R/list_templates.R
+0477f91b27e684ae413c53482f41c3f1 *R/prodigen.R
+f49e52a95dbc55b7b1c0856c3755e30f *README.md
+9074b79483d35651b2642f68e2c28f15 *build/vignette.rds
+3ff2055d4844bd21aab5b429efc415e1 *inst/doc/introduction.R
+f9128e5f5764852cf28d0fbf10948eb7 *inst/doc/introduction.Rmd
+06e247865cb9d673cba31dc6a11518f1 *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
+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
+2ffba69e65ca57623c926451edbcc829 *tests/testthat.R
+deb68e1c9003a63d9bca0820f422d5d9 *tests/testthat/test-projects.R
+f9128e5f5764852cf28d0fbf10948eb7 *vignettes/introduction.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(list_templates)
+export(prodigen)

R/list_templates.R

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+#' List project templates within \pkg{prodigenr}.
+#'
+#' Get a list of available templates in a package.
+#'
+#' @param type Type of template (file or directory, aka project)
+#' @param package Name of package
+#' @return Vector of templates available
+#' @export
+#' @examples
+#'
+#' list_templates('projects')
+#' list_templates()
+#'
+list_templates <- function(type = 'projects', package = 'prodigenr') {
+    temp.type <- match.arg(type)
+    if (temp.type == 'projects') {
+        list.dirs(system.file('templates', temp.type, package = package),
+                  full.names = FALSE, recursive = FALSE)
+    }
+}

R/prodigen.R

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+##' 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.Rproj'),
+                file.path(proj_new, paste0(proj.name, '.Rproj')))
+
+    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')
+    }
+
+}

README.md

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+# prodigenr
+
+[![Build Status](https://travis-ci.org/lwjohnst86/prodigenr.svg?branch=master)](https://travis-ci.org/lwjohnst86/prodigenr)
+
+This is a *pro*ject *di*rectory *gen*erato*r* (`prodigenr`) that will
+create a project directory structure with template files necessary for
+managing and analyzing data for a variety of projects.  This allows
+for a standardized approach to having a modular research project.
+This package can be found at
+[on the GitHub `prodigenr` repo](https://github.com/lwjohnst86/prodigenr). Note,
+this is still in development.
+
+# How to install
+
+Install by forking or cloning this repo, or by using the R command:
+
+    devtools::install_github('lwjohnst86/prodigenr')
+
+# Usage
+
+The main function is the `prodigen` command.  So, for instance, if you
+want a manuscript project, type out:
+
+    library(prodigenr)
+    prodigen(proj.name = 'cancerAndToxins',
+        proj.type = 'manuscript', proj.path = '/path/to/new/project')
+
+This then creates a directory tree, with template files for starting
+your analysis!  The main secondary function is the `list_templates`
+command, which lists the available template projects and files (submit
+a PR if you want another template included!):
+
+    list_templates('projects') ## Shows project templates
+
+For a more detailed tutorial, see the vignette (still in development):
+
+    vignette('introduction', 'prodigenr')
+
+# Related packages or projects
+
+There are several ways of creating projects, each of which has it's pros and cons.
+
+- [`ProjectTemplate`](http://projecttemplate.net/) 
+- [`makeProject`](https://cran.r-project.org/package=makeProject)
+- R package structure via
+[`devtools`](https://cran.r-project.org/package=devtools), argued for in this
+[blog](https://rmflight.github.io/posts/2014/07/vignetteAnalysis.html) 
+
+`prodigenr` tries to use ideas from R packages/`devtools` while still being as simple
+as possible and be more specific to academic researchers primarily in
+biomedical/non-computer science fields. However, it can always improve! I
+welcome any suggestions, just submit a 
+[GitHub issue](https://github.com/lwjohnst86/prodigenr/issues)!

inst/doc/introduction.R

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+## ----templates, collapse=TRUE--------------------------------------------
+library(prodigenr)
+list_templates()
+
+## ---- eval=FALSE---------------------------------------------------------
+#  prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project')
+
+## ---- eval=FALSE---------------------------------------------------------
+#  prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project', git.init = TRUE)
+
+## ---- eval=FALSE---------------------------------------------------------
+#  prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project', packrat.init = TRUE)
+
+## ---- eval=FALSE---------------------------------------------------------
+#  prodigen('slides', 'PresentationName', '~/path')
+#  prodigen('abstract', 'Name', '.') # Current directory
+

inst/doc/introduction.Rmd

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+---
+title: "Introduction to prodigenr"
+author: "Luke W. Johnston"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Introduction to prodigenr}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+Are you an academic researcher who often writes up abstracts for conferences or
+submits manuscripts to journals? Do you often have to make slides or posters for
+presentations? Is your usual workflow to copy a previous project and start 
+replacing the old text for the new text? This R package was designed with you in
+mind!
+
+`prodigenr`, or *pro*ject *di*rectory *gen*erator, simplifies the process of
+creating these new projects and can help make your workflow more reproducible.
+Standard files and folders are created for specific projects (e.g. abstracts or
+manuscripts), along with a workflow that tries to be simple and easy to use.
+
+Because researchers often write or create many papers, slides, posters, and
+abstracts, it can quickly become tedious and messy to always make a new
+directory with all the necessary files and organization. 
+
+## The main command: `prodigen`
+
+To use `prodigenr`, you simply need to use the `prodigen` command. At present,
+there are only four template projects that you can view using:
+
+```{r templates, collapse=TRUE}
+library(prodigenr)
+list_templates()
+```
+
+These templates are projects that an academic researcher typically encounters.
+However, if you have a suggestion or want to add a template, please create a
+[Github issue](https://github.com/lwjohnst86/prodigenr/issues) or submit a [Pull Request](https://github.com/lwjohnst86/prodigenr/pulls)!
+
+Starting a manuscript? Create a project directory like so:
+
+```{r, eval=FALSE}
+prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project')
+```
+
+Do you use [Git](https://git-scm.com/)? You can start a git repository in the new project simply through the `git.init` argument:
+
+```{r, eval=FALSE}
+prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project', git.init = TRUE)
+```
+
+Or if you need to use [Packrat](https://rstudio.github.io/packrat/), start it with `packrat.init`:
+
+```{r, eval=FALSE}
+prodigen('manuscript', 'ManuscriptName', '~/path/to/new/project', packrat.init = TRUE)
+```
+
+The same procedure is used for making the other project templates.
+
+```{r, eval=FALSE}
+prodigen('slides', 'PresentationName', '~/path')
+prodigen('abstract', 'Name', '.') # Current directory
+```
+
+A `README.md` file is contained within each project that explains more about
+what each folder does and what some of the files do that were created.
+
+The end goal of each project is to be as self contained as possible. So that if
+you ever need to go back to the analysis, it is easy to re-run the code and get
+the results that you say you got. This is especially useful if others such as
+reviewers ask for something or want to confirm your results. For more
+information on good practices to use in making an analysis project, see 
+[here](http://stats.stackexchange.com/questions/2910/how-to-efficiently-manage-a-statistical-analysis-project)
+or 
+[here](http://www.r-bloggers.com/managing-a-statistical-analysis-project-%E2%80%93-guidelines-and-best-practices/))
+
+## Workflow when using projects created from `prodigenr`
+
+A typical workflow would be to:
+
+1. Write up your analysis and associated written explanations of the results, as
+you would for any research project, in the abstract, poster, slides, or
+manuscript `.Rmd` ([R Markdown](http://rmarkdown.rstudio.com/)) file.
+2. Any piece of code you use more than once or is fairly complex, convert it
+into a function. Put this new function into the `R/functions.R` file.
+3. Fetch and wrangle your data in the `R/fetch_data.R` and to use the data, load
+it using `load_data()`.
+4. Knit the `.Rmd` file. You now have your final abstract, poster, slides, or
+manuscript to use for your research.
+
+## Related packages or projects
+
+There are several ways of handling a project. There is at least two packages
+that have similar goals as `prodigenr` as well as through the use of the R
+package structure:
+
+- [`ProjectTemplate`](http://projecttemplate.net/) is well documented and still
+actively developed. Only downside is that it is fairly complicated to use and
+complex in the project workflow it creates.
+- [`makeProject`](https://cran.r-project.org/package=makeProject)
+is very simple and stripped down in what it creates and in it's use. Downside is
+that it wasn't updated since 2012.
+- Use of the R package structure via
+[`devtools`](https://cran.r-project.org/package=devtools),
+which is argued for in this
+[blog](https://rmflight.github.io/posts/2014/07/vignetteAnalysis.html) and
+compared to `ProjectTemplate` in this
+[blog](https://rmflight.github.io/posts/2014/07/zpackages_vs_projectTemplate.html)).
+
+It's up to you to decide which style to use. The goal behind creating 
+`prodigenr` was to incorporate the ideas behind R packages and mesh well with 
+RStudio, while also trying to be as simple as possible so it is in some ways a
+hybrid between `ProjectTemplate` and `makeProject`. It can always be improved, 
+so if you have suggestions just submit a 
+[GitHub issue](https://github.com/lwjohnst86/prodigenr/issues)!