croptimizr

Estimate Crop Models' parameters

https://github.com/sticsrpacks/croptimizr

Science Score: 64.0%

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Keywords

crop-model parameter-estimation sensitivity-analysis uncertainty-analysis

Last synced: 6 months ago · JSON representation ·

Repository

Estimate Crop Models' parameters

Basic Info

Host: GitHub
Owner: SticsRPacks
License: lgpl-3.0
Language: R
Default Branch: main
Homepage: https://sticsrpacks.github.io/CroptimizR/
Size: 28.1 MB

Statistics

Stars: 28
Watchers: 4
Forks: 6
Open Issues: 6
Releases: 13

Topics

crop-model parameter-estimation sensitivity-analysis uncertainty-analysis

Created almost 7 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Code of conduct Citation

README.Rmd

---
title: CroptimizR
output: 
  github_document:
   html_preview: true     
        
---


  

```{r setup, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
options(tibble.print_min = 5, tibble.print_max = 5)
```
  
# CroptimizR: A Package to estimate parameters of Crop Models

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[![Codecov test coverage](https://codecov.io/gh/SticsRPacks/CroptimizR/branch/master/graph/badge.svg)](https://codecov.io/gh/SticsRPacks/CroptimizR?branch=master)
[![DOI](https://zenodo.org/badge/187874725.svg)](https://zenodo.org/badge/latestdoi/187874725)

The purpose of CroptimizR is to provide functions for estimating crop model parameters from observations of their simulated variables, a process often referred to as calibration. For that, it offers a generic framework for linking crop models with up-to-date and ad-hoc algorithms, as well as a choice of goodness-of-fit criteria and additional features adapted to the problem of crop model calibration. It facilitates the comparison of different types of methods on different models. It is used in this context in the [AgMIP Calibration project](https://agmip.org/crop-model-calibration-3/) on a dozen of crop models.

The [Get started page](https://sticsrpacks.github.io/CroptimizR/articles/CroptimizR.html) describes the main concepts and features of the package and details how to connect its own crop model to CroptimizR.

The list of functions accessible to the users is provided in the [Reference](https://sticsrpacks.github.io/CroptimizR/reference/index.html) tab.

**The package is still under active development, feel free to fill an issue or request a feature [here](https://github.com/SticsRPacks/CroptimizR/issues) at any time.** 

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/CroptimizR).

## Installation

Before installing the package, it is recommended to update all already installed R packages. This can be done using the command `update.packages()` or clicking on the Update button of the Packages panel of Rstudio. 

The latest released version of the package can be installed from [GitHub](https://github.com/) using:

``` r
devtools::install_github("SticsRPacks/CroptimizR@*release")
```
Or using the lightweight [remotes](https://github.com/r-lib/remotes#readme) package: 

``` r
# install.packages("remotes")
remotes::install_github("SticsRPacks/CroptimizR@*release")
```

## Examples

* A simple introductory example of model calibration using the Nelder-Mead simplex method on the STICS model is given in this [vignette](https://SticsRPacks.github.io/CroptimizR/articles/Parameter_estimation_simple_case.html).

* A more complex one with simultaneous estimation of specific and varietal plant parameters is given  [here](https://SticsRPacks.github.io/CroptimizR/articles/Parameter_estimation_Specific_and_Varietal.html).

* An example of application of the AgMIP phase III protocol, designed to calibrate phenology of crop models, as described in detail in Wallach et al (2022), is given [here](https://SticsRPacks.github.io/CroptimizR/articles/AgMIP_Calibration_Phenology_protocol.html).

* An example using the ApsimX model is detailed [here](https://SticsRPacks.github.io/CroptimizR/articles/ApsimX_parameter_estimation_simple_case.html).

* An example using the DREAM-zs Bayesian algorithm is detailed [here](https://SticsRPacks.github.io/CroptimizR/articles/Parameter_estimation_DREAM.html).


See [here](https://sticsrpacks.github.io/CroptimizR/reference/estim_param.html) for a detailed description of the input and output arguments of the estim_param function (or type `? estim_param` in an R console after having installed and loaded the CroptimizR package).

## 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/CroptimizR/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. To get the suggested citation, run `citation("CroptimizR")`.

## Code of conduct

Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.

Owner

Name: SticsRPacks
Login: SticsRPacks
Kind: organization

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

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "CroptimizR" in publications use:'
type: software
title: 'CroptimizR: A Package to Estimate Parameters of Crop Models'
version: 0.5.1
abstract: The purpose of CroptimizR is to provide functions for estimating crop model
  parameters from observations of their simulated variables. This process is often
  referred to as calibration. For that, it offers a generic framework for linking
  crop models with up-to-date and ad-hoc algorithms, as well as a choice of goodness-of-fit
  criteria and additional features adapted to the problem of crop model calibration.
  It facilitates the comparison of different types of methods on different models.
authors:
- family-names: Buis
  given-names: Samuel
  email: samuel.buis@inrae.fr
  orcid: https://orcid.org/0000-0002-8676-5447
- 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: Giner
  given-names: Michel
  email: michel.giner@cirad.fr
  orcid: https://orcid.org/0000-0002-9310-2377
repository-code: https://github.com/SticsRPacks/CroptimizR
url: https://doi.org/10.5281/zenodo.4066451
date-released: '2023-01-06'
contact:
- family-names: Buis
  given-names: Samuel
  email: samuel.buis@inrae.fr
  orcid: https://orcid.org/0000-0002-8676-5447
keywords:
- crop-model
- parameter-estimation
- sensitivity-analysis
- uncertainty-analysis
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  - family-names: Minunno
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  - family-names: Paul
    given-names: Stefan
  year: '2023'
- type: software
  title: crayon
  abstract: 'crayon: Colored Terminal Output'
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- type: software
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  abstract: 'doParallel: Foreach Parallel Adaptor for the ''parallel'' Package'
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  repository: https://CRAN.R-project.org/package=doParallel
  authors:
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    given-names: Microsoft
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  year: '2023'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
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  authors:
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    given-names: Hadley
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    orcid: https://orcid.org/0000-0003-4757-117X
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  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
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  year: '2023'
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  notes: Imports
  url: https://github.com/bertcarnell/lhs
  repository: https://CRAN.R-project.org/package=lhs
  authors:
  - family-names: Carnell
    given-names: Rob
    email: bertcarnell@gmail.com
  year: '2023'
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    given-names: Garrett
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  year: '2023'
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  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
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  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
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    email: hadley@rstudio.com
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  notes: Imports
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  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
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  - family-names: Wickham
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- type: software
  title: tictoc
  abstract: 'tictoc: Functions for Timing R Scripts, as Well as Implementations of
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  notes: Imports
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  repository: https://CRAN.R-project.org/package=tictoc
  authors:
  - family-names: Izrailev
    given-names: Sergei
  year: '2023'
- type: software
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  abstract: 'ApsimOnR: Running the Apsim model with parameters forcing'
  notes: Suggests
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- type: software
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  abstract: 'CroPlotR: A Package to Analyze Crop Model Simulations Outputs with Plots
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  notes: Suggests
  url: https://doi.org/10.5281/zenodo.4442330
  authors:
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  authors:
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  abstract: 'gridExtra: Miscellaneous Functions for "Grid" Graphics'
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    given-names: Baptiste
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  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
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  abstract: 'rmarkdown: Dynamic Documents for R'
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  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
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    given-names: JJ
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  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
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  authors:
  - family-names: Lecharpentier
    given-names: Patrice
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    orcid: https://orcid.org/0000-0002-4044-4322
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    given-names: Remi
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  - family-names: Buis
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  - family-names: Giner
    given-names: Michel
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  year: '2023'
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  abstract: 'SticsRFiles: Read and Modify STICS Input/Output Files'
  notes: Suggests
  url: https://doi.org/10.5281/zenodo.4443206
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  - family-names: Lecharpentier
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  - 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
  year: '2023'
- type: software
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  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: '2023'
  version: '>= 2.1.0'
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Suggests
  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: '2023'

GitHub Events

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Last Year

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Release event: 1
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Watch event: 6
Delete event: 14
Issue comment event: 11
Push event: 55
Pull request review event: 3
Pull request event: 37

Committers

Last synced: about 2 years ago

All Time

Total Commits: 629
Total Committers: 12
Avg Commits per committer: 52.417
Development Distribution Score (DDS): 0.475

Past Year

Commits: 47
Committers: 5
Avg Commits per committer: 9.4
Development Distribution Score (DDS): 0.489

Top Committers

Name	Email	Commits
Samuel Buis	s**s@i**r	330
Samuel Buis	s**s@i**r	84
remi.vezy	V****Y	50
Patrice Lecharpentier	p**r@i**r	43
Samuel Buis	s**s@i**l	42
Michel Giner	m**r@c**r	28
Patrice Lecharpentier	p**r@i**r	27
tvailhere	4****e	12
GinerM	4****M	6
sbuis	s**s@g**m	4
sbuis	s****s	2
hol430	d**h@c**u	1

Committer Domains (Top 20 + Academic)

inrae.fr: 2 inra.fr: 2 csiro.au: 1 cirad.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 20
Total pull requests: 34
Average time to close issues: 5 months
Average time to close pull requests: 3 days
Total issue authors: 10
Total pull request authors: 5
Average comments per issue: 1.05
Average comments per pull request: 0.09
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 6

Past Year

Issues: 10
Pull requests: 22
Average time to close issues: 3 days
Average time to close pull requests: 4 days
Issue authors: 4
Pull request authors: 3
Average comments per issue: 0.5
Average comments per pull request: 0.14
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 6

View more stats

Top Authors

Issue Authors

sbuis (7)
plecharpent (3)
hol430 (3)
flydephone (1)
mnqoliveira (1)
VEZY (1)
sylvainfa (1)
i-heis (1)
JodyBig (1)
htribouillois (1)

Pull Request Authors

sbuis (18)
VEZY (7)
dependabot[bot] (6)
plecharpent (2)
hol430 (1)

Top Labels

Issue Labels

invalid (1) bug (1)

Pull Request Labels

dependencies (6) github_actions (1)

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
BayesianTools * imports
crayon * imports
doParallel * imports
dplyr * imports
ggplot2 * imports
lhs * imports
lifecycle * imports
lubridate * imports
methods * imports
nloptr * imports
purrr * imports
rlang * imports
rstudioapi * imports
stringr * imports
tibble * imports
tictoc * imports
ApsimOnR * suggests
CroPlotR * suggests
SticsOnR * suggests
SticsRFiles * suggests
covr * suggests
devtools * suggests
gridExtra * suggests
knitr * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 2.1.0 suggests
tidyr * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

croptimizr

Science Score: 64.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies