Initial Commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+inst/doc

DESCRIPTION

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+Package: MakeAPackage
+Title: Steps to create and submit a package
+Version: 0.0.1
+Authors@R: person("Lori", "Shepherd", email = "[email protected]", role = c("aut", "cre"))
+Description: The vignette provided will have a basic sketch of the steps we 
+    interactively went through to build a package with devtools, version control 
+    with git, link to github, bioconductor advice, and submitting to bioconductor.
+Depends: R (>= 3.4.1)
+License: Artistic-2.0
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1
+Suggests: knitr,
+    rmarkdown
+VignetteBuilder: knitr

MakeAPackage.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+

vignettes/MakeAPackage.Rmd

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+---
+title: "Make A Package"
+author: "Lori Shepherd"
+date: "`r Sys.Date()`"
+output:
+  BiocStyle::html_document:
+    toc: true
+    toc_depth: 2
+vignette: >
+  %\VignetteIndexEntry{Make A Package}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+# Make A Package
+
+A package is a collection of functions that work together in a cohesive manner 
+to achieve a goal. It (should) include detailed documentation through man pages
+and vignettes and (should) be tested for accuracy and efficiency. 
+
+[Writing R extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html) 
+is a very detailed manual to writing packages and what the structure of a 
+package entails. 
+
+## Using `devtools` to create a package 
+
+The `devtools` package provides a lot of options and utility for helping to 
+construct a new package. You can get a list of all available devtools functions
+with `ls("package:devtools")`. 
+
+Some useful references for using devtools to build packages are [Rstudio Devtools Cheetsheet](https://www.rstudio.com/wp-content/uploads/2015/03/devtools-cheatsheet.pdf) and
+[Jennifer Bryan class](http://stat545.com/packages06_foofactors-package.html)
+
+### set up shell of a package 
+```{r, eval=FALSE}
+library(devtools)
+create("myFirstPackage")
+```
+
+Create will instantiate all the necessary files and sub-directories that are required
+by R to be a valid package: DESCRIPTION, NAMESPACE, and R directory. You 
+will have to edit the DESCRIPTION to insert the information pertinent to your package. 
+
+
+After running create, the package has a valid package structure and can installed
+and loaded: `install("myFirstPackage")`, `library("myFirstPackage")`, 
+`library(help="myFirstPackage")`.
+
+### version control
+
+It is an excellent idea to version control whenever creating a package and especially
+when collaborating on a project, where multiple users are allowed to make changes. It allows 
+for a constant record of changes that can be advanced or reverted if necessary.
+
+Only a project can be version controlled, to make a directory a project in Rstudio
+go to:  `File -> New Project` .  In this case we started creating the directory so 
+we follow the prompts for the option `Use Existing Directory`. Now that it is a 
+project we can go to `Tools -> Version Control -> Project Setup` Change the 
+`Version Control System` to `Git` and follow the prompts. Notice in the Rstudio 
+pane for environments/history/build there is a new tab Git. The package now can 
+start using `git` version control by making commits. To make a commit, you can go 
+to the Git tab, select the check box next to any files that have been modified, 
+added, or deleted that you would like to track, and select `commit`. Enter a new
+commit message in the window that pops up and select `commit`. 
+
+We coud stop here but we also would like put the package on GitHub. (This
+assumes you have a github account).  First, in Rstudio go to 
+`Tools -> Global Options` and select Git/SVN. Ensure the paths are correct. If you 
+have not linked a Rstudio project to Github, select `Create RSA key`. Close the 
+window. Click on `View public key` and copy the displayed public key.  Now in a 
+web browser, open your GitHub account. Go to `Settings` and `SSH and GPG keys`. 
+Click on the option for `New SSH key` and paste the public key that was copied. Also 
+on GitHub, create a new repository with the same name as the one you created in 
+Rstudio using `create()`.  Back in Rstudio, select `Tools -> Shell` and type the 
+following subsituting your github user.name and the package name. 
+```
+git remote add origin https://github.com/<github user.name>/<package repo name>.git
+git config remote.origin.url [email protected]:<github user.name>/<package repo name>.git
+git pull -u origin master
+git push -u origin master
+```
+For instance, my package repository on github is "myFirstPackage" and my git hub
+user.name is lshep: 
+```
+https://github.com/lshep/myFirstPackage.git
+[email protected]:lshep/myFirstPackage.git
+```
+Now if you look in the Rstudio tab for Git, the push and pull options are available. 
+You can now push and pull from/to the local version of your package and the GitHub
+repository version of the package. 
+
+### Back to making a valid package
+
+`devtools` proviodes built in functions for building, checking, and installing a
+package.  The package we created using `create` has a valid package structure but 
+if we did `check` we will find the DESCRIPTION needs updating. Update the 
+DESCRIPTION file to be appropriate for your package; throughout the development of
+your package you might have to update the DESCRIPTION for appropraite Depends, Imports, 
+and Suggest fields.  
+
+Now we want to start writing R functions. In Rstudio you can open an empty file
+by  `File -> New File` and selecting `R Script`. Save the file in the R directory. Write your functions and document. You can either document functions manually or if you use roxygen you can use the devtools function `document()`.  See the [Writing R extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html) for 
+manual creation of Rd files (located in the man directory) but roxygen is growing 
+increating popular. Some helpful links for roxygen tags can be found [Rstudio Devtools Cheetsheet](https://www.rstudio.com/wp-content/uploads/2015/03/devtools-cheatsheet.pdf) and 
+[Roxygen Help](https://cran.rstudio.com/web/packages/roxygen2/vignettes/rd.html).
+
+Some useful devtools commands while creating functions: 
+
+ * `load_all()` loads all package functions in environment to test
+ * `check()` checks the package (R CMD check)
+ * `document()` generates or updates andy documentation files
+
+and using the Rstudio options `Build -> Build And Reload` and `Build -> Clean and Rebuild`. 
+
+It is also recommended to have a man page for your package. devtools provides 
+framework for this and creates the file that needs to be modified by calling 
+`use_package_doc()`.
+
+If you import any functions in your code, don't forget to update the DESCRIPTION
+file for Depends, Imports, or Suggests. 
+
+### Testing
+
+It is highly recommended to add unit tests to your package. Unit test ensure the 
+package is working as expect. The two main ways to test are using `RUnit` or `testthat`. 
+testthat functionality is included in devtools. Using `use_testthat()` will set up
+the needed directory structure and add the package suggestion to the DESCRIPTION. 
+Here are some examples of the structure of tests for testthat: `expect_identical`, 
+`expect_true`, `expect_error`. There are other options as well that are discussed
+in [testthat Wickham](https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf)
+and [testthat](http://r-pkgs.had.co.nz/tests.html).
+
+
+### Vignettes
+
+Vignettes are another major documentation piece to a package and more and more 
+repository systems (CRAN, Bioconductor, ROpenSci) and making vignettes a standard
+requirement.  They are a more indepth description and examples of package usage. 
+devtools also provides the function `use_vignette()` to set up the directory structure
+and initial file for creating a vignette. For Bioconductor submissions we recommend
+changing the `output:` section of the vignette header to the following (this would
+require adding BiocStyle to the Suggest field in the DESCRIPTION):
+```
+output:
+  BiocStyle::html_document:
+    toc: true
+    toc_depth: 2
+```
+A helpful rmarkdown link, which is commonly used for vignette creation can be found 
+here: [rmarkdown cheetsheet](http://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf)
+
+
+## Bioconductor Standards 
+1. proper coding and efficient coding:
+
+ * [Efficient and Robust Code](http://bioconductor.org/developers/how-to/efficient-code/) 
+ * [Query Web Resource](http://bioconductor.org/developers/how-to/web-query/)
+2. Bioconductor connection - reuse existing classes and structure - link to other packages
+ * [BiocViews](http://bioconductor.org/packages/release/BiocViews.html#___Software)
+3. Tests 
+ * [unitTest guidelines](http://bioconductor.org/developers/how-to/unitTesting-guidelines/)
+4. complete and detailed Vignettes and man pages with executable examples
+5. check time < 5min 
+6. package size < 4Mb
+7. All package guidelines can be found [here](http://bioconductor.org/developers/package-guidelines/)
+
+A clean build and check and BiocCheck is not a guarantee to acceptance. It will
+go through a formal view process. 
+
+### Submitting to Bioconductor
+Read the [Contributions Page](https://github.com/Bioconductor/Contributions) and 
+when ready to submit open a [New Issue](https://github.com/Bioconductor/Contributions/issues). The Title: should be the name of your package. Once the package is approved for building, 
+don't forget to set up the [webhook](https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook)