SticsRPacks

Overview

SticsRPacks is a set of packages that work in harmony because they share common data representations and API design. The SticsRPacks package is designed to make it easy to install and load core packages from SticsRPacks in a single command.

If you’d like to learn how to use the SticsRPacks packages, the best place to start are the vignettes that come along the packages, and also available from each websites (Article sections).

This package is heavily inspired from the tidyverse package.

Installation

The installation requires the devtools package. If it is not yet installed, run first install.packages("devtools").

Then, you can install the SticsRPacks packages by running:

devtools::install_github("SticsRPacks/SticsRPacks@*release")

Troubleshooting

It the installation does not work:

  • In case you have messages such as:

    • “cannot remove prior installation of package ‘*****’”

    or

    • API rate limit exceeded for ****

    please refer to here.

  • otherwise, please follow the instructions given here.

Usage

library(SticsRPacks) will load the core SticsRPacks packages:

You also get a condensed summary of conflicts with other packages you have loaded:

library(SticsRPacks)
#> ── Attaching packages ───────────────────────────────────── SticsRPacks 0.6.2 ──
#> ✔ SticsRFiles 1.2.0     ✔ SticsOnR    1.2.0
#> ✔ CroptimizR  0.6.1     ✔ CroPlotR    0.9.0
#> ── Conflicts ──────────────────────────────────────── SticsRPacks_conflicts() ──
#> ✖ CroptimizR::AIC()    masks stats::AIC()
#> ✖ CroptimizR::BIC()    masks stats::BIC()
#> ✖ methods::body<-()    masks base::body<-()
#> ✖ methods::kronecker() masks base::kronecker()

You can see conflicts created later with SticsRPacks_conflicts():

library(MASS)
SticsRPacks_conflicts()
#> ── Conflicts ──────────────────────────────────────── SticsRPacks_conflicts() ──
#> ✖ CroptimizR::AIC()    masks stats::AIC()
#> ✖ CroptimizR::BIC()    masks stats::BIC()
#> ✖ methods::body<-()    masks base::body<-()
#> ✖ methods::kronecker() masks base::kronecker()

And you can check that all SticsRPacks packages are up-to-date with SticsRPacks_update():

SticsRPacks_update()
#> The following packages are out of date:
#>  * SticsRFiles (0.4.0 -> 0.4.1)
#>  * CroptimizR (0.4.1 -> 0.5)
#> Update now?
#> 
#> 1: Yes
#> 2: No

Tutorial

A tutorial is provided to learn how to use the main features of the SticsRPacks packages!

To run it you need to install the learnr package.

If you have a version of STICS more recent or equal to 9.2.0 installed on your computer, it is recommended that you use this version to carry out the exercises of the tutorial.

For this, an environment variable javastics_path must be set to the path of the corresponding JavaSTICS folder. This can be done:

  • in your R session, each time before running the tutorial, by executing the following command: Sys.setenv(javastics_path="path_to_JavaSTICS"), where path_to_JavaSTICS should be replaced by the absolute path of the corresponding JavaSTICS folder.

or

  • by defining this environment variable in your .Renviron file: edit this file (located in your Home directory, can be edited also using usethis::edit_r_environ()), and add a new line javastics_path="path_to_JavaSTICS". In this case, your R session must then be restarted (in RStudio: menu Session-> Restart R).

Then, if you have RStudio version 1.3 or greater, click on the Tutorial pane on the right of the RStudio window (close to Environment, History, … panes), scroll to see Tutorial for SticsRPacks and click on the button Start Tutorial.

Alternatively, e.g. if you have an older version of RStudio or if you don’t have the Tutorial pane for any reason, you can run the tutorial by running the command: learnr::run_tutorial("SticsRpacks", package="SticsRPacks")

The first time it is started, the tutorial takes a few minutes to initialize in order to download all the materials and run the solutions. Subsequent runs do not need this steps, the tutorial will thus start almost immediately from the second run.

NEWS: the tutorial can now be done online, without installing SticsRPacks: just by clicking here, thanks to @eric.casellas.

Getting help

If you have any question or suggestion or if you want to report a bug, please do it via the GitHub issues.

Thanks for that, this would greatly help us to improve this package.

Citation

If you have used this package for a study that led to a publication or report, please cite us. You can either use the citation tool from Github if you used the last version, or use citation("SticsRPacks") from R otherwise.

Code of Conduct

Please note that the SticsRPacks project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.