PatentSafeR

The goal of PatentSafeR is to make it quick and easy to submit your experimental work to the PatentSafe ELN from Amphora Research Systems.

Installation

Install PatentSafeR from CRAN as normal.

Requirements

You will need to have pandoc installed on your computer. This is used to convert your R Markdown file to a PDF.

You will also need a LaTeX distribution installed.

On a Mac with Homebrew installed you can do this with:

brew install pandoc
brew install --cask mactex

Note you will need to restart your R environment after installing mactex to pick up the new binaries.

On Ubuntu:

sudo apt-get update
sudo apt-get install texlive-latex-recommended texlive-latex-extra

Example

To submit the current directory to PatentSafe, assuming you have a file Report.Rmd which is your write up.

PatentSafeR::submit_this_project(".")

Credentials

Store in your .Renviron file

• PATENTSAFE_URL - Your PatentSafe server URL
• PATENTSAFE_USERID - Your PatentSafe user ID

To set the environment variables, use usethis::edit_r_environ()

e.g.

PATENTSAFE_URL=test.morescience.com
PATENTSAFE_USERID=clarusc

Development

Devcontainer

To get an R Session in the included Dev Container, "R: Create R Terminal".

To check the Package, use devtools::check()

To generate documentation use devtools::document()

Quick Examples for use in Development

To test you can use the folllowing. Note that system.file("extdata", "test.pdf", package = "PatentSafeR") is a way to get to the inst/extdata directory and wouldn't be needed normally)

devtools::load_all()
PatentSafeR::submit_pdf(system.file("extdata", "test.pdf", package = "PatentSafeR"))
PatentSafeR::submit_rmd(system.file("extdata", "Writeup.Rmd", package = "PatentSafeR"))
PatentSafeR::submit_rmd(system.file("extdata", "Writeup.Rmd", package = "PatentSafeR"), metadata = list(key1 = "value1", key2 = "value2", key3 = "value3"))
PatentSafeR::submit_this_project(directory = system.file("extdata", package = "PatentSafeR"), report_filename = system.file("extdata", "Writeup.Rmd", package = "PatentSafeR"), url = "test.morescience.com", author_id = "simonc")

When shipping, remember to increment the version number.

Installing the Development Version

You can install the development version of PatentSafeR from GitHub with:

# install.packages("devtools")
devtools::install_github("amphora/PatentSafeR")

Releasing

Do `usethis::use_release_issue(version = x.x.x.x)