To create package documentation

1. On Linux (sc) cd to the project directory
2. run roxygen2::roxygenize(). This will create the Rd files in the man directory of the main package directory
3. on Linux, cd to the diretory above the package directory
4. run R CMD Rd2pdf <packagename>


adding to the remote bitbucket ...

git config --global user.name "Richard Judson"
git config --global user.email "judson.richard@epa.gov"

cd existing-project
git init
git add --all
git commit -m "Initial Commit"
git remote add origin ssh://git@ncct-bitbucket.epa.gov:7999/tcplfit2/tcplfit2.git
git push -u origin master

To pull from the git repository ...
git pull origin master

Pointing to pdflatex ...

Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/Program Files/MiKTeX 2.9/miktex/bin/x64/",sep=";"))

Running documentation - this builds the file tcplFit2_manual.pdf
roxygen2::roxygenise()

Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:/Program Files/MiKTeX 2.9/miktex/bin/x64", sep=.Platform$path.sep))
Sys.setenv(R_PAPERSIZE="letter")
system("R CMD Rd2pdf . --title=tcplfit2 tcplfit2 --output=./tcplfit2_manual.pdf --force --no-clean --internals")

Getting ready to submit to cran
Note that libraries need to be in C:/program files/R and not in the local version
rm(list=ls())
devtools::install()
devtools::check()

Creating a vignette ...
usethis::use_vignette("tcplfit2-vignette")
Open the Rmd file and run knitr

Creating a word version of the vignette
library(rmarkdown)
file <- "vignettes/tcplfit2-vignette.Rmd"
render(file,output_format="word_document")

To install this package from git ...
devtools::install_git("http://ncct-bitbucket.epa.gov/scm/tcplFit2/tcplFit2")