SticsRFiles

Read and modify STICS input/output files:

https://github.com/sticsrpacks/sticsrfiles

Science Score: 54.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (22.3%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Read and modify STICS input/output files:

Basic Info

Host: GitHub
Owner: SticsRPacks
License: lgpl-3.0
Language: R
Default Branch: main
Homepage: https://sticsrpacks.github.io/SticsRFiles
Size: 6.86 MB

Statistics

Stars: 4
Watchers: 3
Forks: 3
Open Issues: 42
Releases: 0

Created almost 7 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Code of conduct Citation

README.Rmd

---
title: SticsRFiles
output: 
  github_document:
   html_preview: true     
        
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
 

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R-CMD-check](https://github.com/SticsRPacks/SticsRFiles/actions/workflows/check-standard.yaml/badge.svg?branch=main)](https://github.com/SticsRPacks/SticsRFiles/actions/workflows/check-standard.yaml)
[![Codecov test coverage](https://codecov.io/gh/SticsRPacks/SticsRFiles/branch/master/graph/badge.svg)](https://app.codecov.io/gh/SticsRPacks/SticsRFiles?branch=master)
[![DOI](https://zenodo.org/badge/187986787.svg)](https://zenodo.org/badge/latestdoi/187986787)
![](https://www.r-pkg.org/badges/version-ago/SticsRFiles)



The goal of `SticsRFiles` is to perform manipulations of the [STICS](https://stics.inrae.fr/eng/)  model files either on XML files (used by the JavaSTICS GUI) or on text files used by the model fortran executable.

The basic functionalities allows to read parameters names and values through XML queries and replace parameters values in files. A starting guide is available on the [Get started page](https://sticsrpacks.github.io/SticsRFiles/articles/SticsRFiles.html).

Advanced functionalities are dedicated to produce XML parameter files using a mailing process like from XML templates and Excel sheets containing multiple simulations contexts. A JavaSTICS workspace is generated and directly usable from the JavaSTICS interface (GUI or command line), or with an R JavaSTICS interface provided by the [SticsOnR](https://sticsrpacks.github.io/SticsOnR/) package.

If you want to be notified when a new release of this package is made, you can tick the Releases box in the "Watch / Unwatch => Custom" menu at the top right of [this page](https://github.com/SticsRPacks/SticsRFiles).


## Prerequisites and technical tips

> Some information about software requirements and operating system constraints are given in the `SticsOnR` package documentation [here](https://sticsrpacks.github.io/SticsOnR/).

## Installation

---

_**Warning:**_ *If during the installation process, packages updates are suggested.*

* First, abort the installation.
* Second, update the installed packages, except the `XML` package.
* Finally, install the `SticsRFiles` package.

---

### Recommended installation: `SticsRPacks`

The best way to install the packages from `SticsRPacks`, from which `SticsRFiles` is part of, is by installing the `[SticsRPacks]` package. The package can be installed from [GitHub](https://github.com/) using either the `devtools` package, or the more lightweight the `remotes` package: 

* With `devtools`

```{r eval=FALSE}
devtools::install_github("SticsRPacks/SticsRPacks")
```

* With `remotes`

```{r eval=FALSE}
remotes::install_github("SticsRPacks/SticsRPacks")
```

The package will install the packages for you at the latest release version. 

### Direct installation from the CRAN or [GitHub](https://github.com/)

* From the CRAN    
```{r eval=FALSE}
install.packages("SticsRFiles")
```
* From GitHub     
```{r eval=FALSE}
devtools::install_github("SticsRPacks/SticsRFiles@*release")

or

remotes::install_github("SticsRPacks/SticsRFiles@*release")
```

Normally, all the package dependencies will be installed for CRAN packages.

## Examples

### Files manipulations
* A description of how to use the functions for manipulating XML input files is detailed 
[here](https://sticsrpacks.github.io/SticsRFiles/articles/Manipulating_Stics_XML_files.html)

* A description of how to use the functions for manipulating text input files is available [here](https://sticsrpacks.github.io/SticsRFiles/articles/Manipulating_Stics_text_files).

### Files generation
* A description of useful functions for generating XML input files from usms parameters data stored in Excel files sheets or CSV files is available [here](https://sticsrpacks.github.io/SticsRFiles/articles/Generating_Stics_XML_files.html).

* A description of functions for generating text input files from XML one of usms parameters is available [here](https://sticsrpacks.github.io/SticsRFiles/articles/Generating_Stics_text_files.html).

## 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/SticsRFiles/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("SticsRFiles")` from R otherwise.

## Code of conduct

Please note that this project is released with a [Contributor Code of Conduct](https://github.com/SticsRPacks/SticsRFiles/blob/master/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.

The package is under intensive development, so you can fill an issue or request us a feature [here](https://github.com/SticsRPacks/SticsRFiles/issues) at any time.

Owner

Name: SticsRPacks
Login: SticsRPacks
Kind: organization

Repositories: 7
Profile: https://github.com/SticsRPacks

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 "SticsRFiles" in publications use:'
type: software
license: LGPL-3.0-or-later
title: 'SticsRFiles: Read and Modify ''STICS'' Input/Output Files'
version: 1.6.0
doi: 10.32614/CRAN.package.SticsRFiles
abstract: Manipulating input and output files of the 'STICS' crop model. Files are
  either 'JavaSTICS' XML files or text files used by the model 'fortran' executable.
  Most basic functionalities are reading or writing parameter names and values in
  both XML or text input files, and getting data from output files. Advanced functionalities
  include XML files generation from XML templates and/or spreadsheets, or text files
  generation from XML files by using 'xslt' transformation.
authors:
- family-names: Lecharpentier
  given-names: Patrice
  email: patrice.lecharpentier@inrae.fr
  orcid: https://orcid.org/0000-0002-4044-4322
- family-names: Vezy
  given-names: Remi
  email: remi.vezy@cirad.fr
  orcid: https://orcid.org/0000-0002-0808-1461
- family-names: Buis
  given-names: Samuel
  email: samuel.buis@inrae.fr
  orcid: https://orcid.org/0000-0002-8676-5447
- family-names: Giner
  given-names: Michel
  email: michel.giner@cirad.fr
  orcid: https://orcid.org/0000-0002-9310-2377
- family-names: Flutre
  given-names: Timothee
  email: timothee.flutre@inrae.fr
  orcid: https://orcid.org/0000-0003-4489-4782
repository: https://CRAN.R-project.org/package=SticsRFiles
repository-code: https://github.com/SticsRPacks/SticsRFiles
url: https://doi.org/10.5281/zenodo.4443206
date-released: '2025-06-03'
contact:
- family-names: Lecharpentier
  given-names: Patrice
  email: patrice.lecharpentier@inrae.fr
  orcid: https://orcid.org/0000-0002-4044-4322
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.0.0'
- type: software
  title: cli
  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
  url: https://cli.r-lib.org
  repository: https://CRAN.R-project.org/package=cli
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: gabor@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.cli
- type: software
  title: crayon
  abstract: 'crayon: Colored Terminal Output'
  notes: Imports
  url: https://r-lib.github.io/crayon/
  repository: https://CRAN.R-project.org/package=crayon
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.crayon
- type: software
  title: curl
  abstract: 'curl: A Modern and Flexible Web Client for R'
  notes: Imports
  url: https://jeroen.r-universe.dev/curl
  repository: https://CRAN.R-project.org/package=curl
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2025'
  doi: 10.32614/CRAN.package.curl
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
  authors:
  - family-names: Barrett
    given-names: Tyson
    email: t.barrett88@gmail.com
    orcid: https://orcid.org/0000-0002-2137-1391
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  - family-names: Gorecki
    given-names: Jan
  - family-names: Chirico
    given-names: Michael
    orcid: https://orcid.org/0000-0003-0787-087X
  - family-names: Hocking
    given-names: Toby
    orcid: https://orcid.org/0000-0002-3146-0865
  - family-names: Schwendinger
    given-names: Benjamin
    orcid: https://orcid.org/0000-0003-3315-8114
  - family-names: Krylov
    given-names: Ivan
    email: ikrylov@disroot.org
    orcid: https://orcid.org/0000-0002-0172-3812
  year: '2025'
  doi: 10.32614/CRAN.package.data.table
- type: software
  title: dplyr
  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
  version: '>= 1.0.0'
- type: software
  title: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Imports
  url: https://lubridate.tidyverse.org
  repository: https://CRAN.R-project.org/package=lubridate
  authors:
  - family-names: Spinu
    given-names: Vitalie
    email: spinuvit@gmail.com
  - family-names: Grolemund
    given-names: Garrett
  - family-names: Wickham
    given-names: Hadley
  year: '2025'
  doi: 10.32614/CRAN.package.lubridate
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: rstudioapi
  abstract: 'rstudioapi: Safely Access the RStudio API'
  notes: Imports
  url: https://rstudio.github.io/rstudioapi/
  repository: https://CRAN.R-project.org/package=rstudioapi
  authors:
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Ritchie
    given-names: Gary
    email: gary@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rstudioapi
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.tibble
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2025'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: tidyselect
  abstract: 'tidyselect: Select from a Set of Strings'
  notes: Imports
  url: https://tidyselect.r-lib.org
  repository: https://CRAN.R-project.org/package=tidyselect
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.tidyselect
- type: software
  title: tools
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: XML
  abstract: 'XML: Tools for Parsing and Generating XML Within R and S-Plus'
  notes: Imports
  url: https://www.omegahat.net/RSXML/
  repository: https://CRAN.R-project.org/package=XML
  authors:
  - family-names: Temple Lang
    given-names: Duncan
    email: duncan@r-project.org
    orcid: https://orcid.org/0000-0003-0159-1546
  year: '2025'
  doi: 10.32614/CRAN.package.XML
- type: software
  title: xml2
  abstract: 'xml2: Parse XML'
  notes: Imports
  url: https://xml2.r-lib.org
  repository: https://CRAN.R-project.org/package=xml2
  authors:
  - family-names: Wickham
    given-names: Hadley
  - family-names: Hester
    given-names: Jim
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.xml2
- type: software
  title: xslt
  abstract: 'xslt: Extensible Style-Sheet Language Transformations'
  notes: Imports
  url: https://ropensci.r-universe.dev/xslt
  repository: https://CRAN.R-project.org/package=xslt
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2025'
  doi: 10.32614/CRAN.package.xslt
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.covr
- type: software
  title: formatR
  abstract: 'formatR: Format R Code Automatically'
  notes: Suggests
  url: https://github.com/yihui/formatR
  repository: https://CRAN.R-project.org/package=formatR
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.formatR
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: learnr
  abstract: 'learnr: Interactive Tutorials for R'
  notes: Suggests
  url: https://rstudio.github.io/learnr/
  repository: https://CRAN.R-project.org/package=learnr
  authors:
  - family-names: Aden-Buie
    given-names: Garrick
    email: garrick@posit.co
    orcid: https://orcid.org/0000-0002-7111-0077
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Rossell Hayes
    given-names: Alexander
    email: alex.rossellhayes@posit.co
    orcid: https://orcid.org/0000-0001-9412-0457
  year: '2025'
  doi: 10.32614/CRAN.package.learnr
- type: software
  title: readxl
  abstract: 'readxl: Read Excel Files'
  notes: Suggests
  url: https://readxl.tidyverse.org
  repository: https://CRAN.R-project.org/package=readxl
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.readxl
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://ropensci.r-universe.dev/spelling
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.spelling
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat

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Last Year

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Average time to close issues: about 1 month
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Merged pull requests: 44
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Average time to close issues: about 2 months
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Total dependent packages: 0
Total dependent repositories: 6
Total versions: 6
Total maintainers: 1

cran.r-project.org: SticsRFiles

Read and Modify 'STICS' Input/Output Files

Homepage: https://github.com/SticsRPacks/SticsRFiles
Documentation: http://cran.r-project.org/web/packages/SticsRFiles/SticsRFiles.pdf
License: LGPL (≥ 3)
Latest release: 1.6.0
published 9 months ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 6
Downloads: 348 Last month

Rankings

Dependent repos count: 12.1%

Forks count: 14.3%

Average: 25.3%

Dependent packages count: 27.9%

Stargazers count: 28.0%

Downloads: 44.4%

Maintainers (1)

patrice.lecharpentier@inrae.fr

Last synced: 6 months ago

Dependencies

.github/workflows/check-standard.yaml actions

actions/checkout v3 composite
peter-evans/repository-dispatch v2 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/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 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

DESCRIPTION cran

R >= 3.6.0 depends
XML * imports
cli * imports
crayon * imports
curl * imports
data.table * imports
dplyr >= 1.0.0 imports
lifecycle * imports
lubridate * imports
methods * imports
rlang * imports
rstudioapi * imports
stringr * imports
tibble * imports
tidyr * imports
tools * imports
utils * imports
xml2 * imports
xslt * imports
covr * suggests
formatR * suggests
knitr * suggests
learnr * suggests
readxl * suggests
rmarkdown * suggests
spelling * suggests
testthat * suggests

ecosyste.ms

Data

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