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sticsrpacks

Easily Install and Load 'SticsRPacks' packages

https://github.com/sticsrpacks/sticsrpacks

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    Found codemeta.json file
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Last synced: 6 months ago · JSON representation ·

Repository

Easily Install and Load 'SticsRPacks' packages

Basic Info
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 3
  • Open Issues: 6
  • Releases: 13
Created over 6 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.Rmd 

---
output: github_document
---


```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# SticsRPacks 


[![R build status](https://github.com/SticsRPacks/SticsRPacks/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/SticsRPacks/SticsRPacks/actions/workflows/check-standard.yaml)
[![DOI](https://zenodo.org/badge/223148621.svg)](https://zenodo.org/badge/latestdoi/223148621)


## 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](https://github.com/tidyverse/tidyverse).

## 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:
```{r eval = FALSE}
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](https://github.com/SticsRPacks/documentation/blob/master/github_install.md).

 * otherwise, please follow the instructions given [here](https://github.com/SticsRPacks/SticsRPacks/issues/1#event-2864068985).


## Usage

`library(SticsRPacks)` will load the core SticsRPacks packages: 

* [SticsRFiles](https://github.com/SticsRPacks/SticsRFiles), for files manipulation.  
* [SticsOnR](https://github.com/SticsRPacks/SticsOnR), for STICS simulation management.  
* [CroPlotR](https://github.com/SticsRPacks/CroPlotR), for plotting and statistics.  
* [CroptimizR](https://github.com/SticsRPacks/CroptimizR), for parameter optimization.  

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

```{r example}
library(SticsRPacks)
```

You can see conflicts created later with `SticsRPacks_conflicts()`:

```{r conflicts}
library(MASS)
SticsRPacks_conflicts()
```

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

```{r update, eval = FALSE}
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! It can be run locally or online.**

### Preparing a local tutorial run
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 the `.Renviron` file located in your home directory:
  * `C:\Users\[username]\Documents` for windows
  * `/home/[username]` for linux
  * `/Users/[username]` for MacOS)
Create or modify this file or use `usethis::edit_r_environ()` to do so, 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.

### Using the tutorial online
In this case the tutorial can be used without installing SticsRPacks by using a virtual environment running a RStudio server in which all the needed applications and libraries are pre-installed.

It can be accessed just by clicking [here](https://mybinder.org/v2/git/https%3A%2F%2Fforge.inrae.fr%2Fstics-formation%2Fsticsrpacks-binder.git/v0.9.0?urlpath=rstudio), thanks to [@eric.casellas](https://forge.inrae.fr/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](https://github.com/SticsRPacks/SticsRPacks/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](https://github.com/SticsRPacks/.github/blob/master/CODE_OF_CONDUCT.md). 
By contributing to this project, you agree to abide by its terms.

Owner

  • Name: SticsRPacks
  • Login: SticsRPacks
  • Kind: organization

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "SticsRPacks" in publications use:'
type: software
license: LGPL-3.0-or-later
title: 'SticsRPacks: Easily Install and Load `SticsRPacks` Packages'
version: 0.9.0
abstract: A set of packages that work in harmony because they share common data representations
  and "API" design. This package is designed to make it easy to install and load multiple
  `SticsRPacks` packages in a single step. Learn more about `SticsRPacks` at <https://sticsrpacks.github.io/SticsRPacks/>.
authors:
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- family-names: Lecharpentier
  given-names: Patrice
  email: patrice.lecharpentier@inrae.fr
  orcid: https://orcid.org/0000-0002-4044-4322
- family-names: Giner
  given-names: Michel
  email: michel.giner@cirad.fr
  orcid: https://orcid.org/0000-0002-9310-2377
repository-code: https://github.com/SticsRPacks/SticsRPacks
url: https://doi.org/10.5281/zenodo.4442330
date-released: '2025-07-31'
contact:
- family-names: Vezy
  given-names: Remi
  email: remi.vezy@cirad.fr
  orcid: https://orcid.org/0000-0002-0808-1461
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  notes: Depends
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  - family-names: Wickham
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    email: hadley@posit.co
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  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.purrr
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  abstract: 'cli: Helpers for Developing Command Line Interfaces'
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    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.crayon
- type: software
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  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
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  notes: Imports
  url: https://tibble.tidyverse.org/
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  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
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    email: hadley@rstudio.com
  year: '2025'
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  url: https://rlang.r-lib.org
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  authors:
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    given-names: Lionel
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  year: '2025'
- type: software
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  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
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  notes: Imports
  url: https://doi.org/10.5281/zenodo.4442330
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  url: https://astamm.github.io/nloptr/
  repository: https://CRAN.R-project.org/package=nloptr
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  url: https://github.com/bertcarnell/lhs
  repository: https://CRAN.R-project.org/package=lhs
  authors:
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  repository: https://CRAN.R-project.org/package=tictoc
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  repository: https://CRAN.R-project.org/package=lifecycle
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Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • CroPlotR * imports
  • CroptimizR * imports
  • SticsOnR * imports
  • SticsRFiles * imports
  • cli * imports
  • crayon * imports
  • dplyr * imports
  • grDevices * imports
  • learnr * imports
  • magrittr * imports
  • purrr * imports
  • remotes * imports
  • rlang * imports
  • rstudioapi * imports
  • tibble * imports
  • utils * imports
  • knitr * suggests
  • testthat * suggests
.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite