From 3c45061c8237b402e80ebcc74c4803470c644a97 Mon Sep 17 00:00:00 2001 From: sbuis Date: Fri, 6 Jan 2023 14:06:38 +0000 Subject: [PATCH] Update CITATION.cff --- CITATION.cff | 525 ++++++++++++++++++++++++++------------------------- 1 file changed, 265 insertions(+), 260 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 7df2933..f6efcfc 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,14 +1,19 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.2.2 +# CITATION file created with {cffr} R package, v0.4.0 # 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: 0.4.0 -abstract: CroptimizR provides facilities to estimate parameters of crop models. +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 @@ -26,45 +31,9 @@ authors: given-names: Michel email: michel.giner@cirad.fr orcid: https://orcid.org/0000-0002-9310-2377 -preferred-citation: - type: manual - title: 'CroptimizR: A Package to estimate parameters of Crop 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 - version: 0.4.0 - abstract: CroptimizR provides facilities to estimate parameters of crop models. - repository-code: https://github.com/SticsRPacks/CroptimizR - url: https://doi.org/10.5281/zenodo.4066451 - date-released: '2021-07-22' - 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 - year: '2021' repository-code: https://github.com/SticsRPacks/CroptimizR url: https://doi.org/10.5281/zenodo.4066451 -date-released: '2021-07-22' +date-released: '2023-01-06' contact: - family-names: Buis given-names: Samuel @@ -79,42 +48,21 @@ 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 location: name: Vienna, Austria - year: '2022' - url: https://www.R-project.org/ + year: '2023' institution: name: R Foundation for Statistical Computing version: '>= 3.6.0' -- type: software - title: nloptr - abstract: 'nloptr: R Interface to NLopt' - notes: Imports - authors: - - family-names: Ypma - given-names: Jelmer - email: uctpjyy@ucl.ac.uk - - family-names: Johnson - given-names: Steven G. - year: '2022' - url: https://CRAN.R-project.org/package=nloptr -- type: software - title: lhs - abstract: 'lhs: Latin Hypercube Samples' - notes: Imports - authors: - - family-names: Carnell - given-names: Rob - email: bertcarnell@gmail.com - year: '2022' - url: https://CRAN.R-project.org/package=lhs - type: software title: BayesianTools abstract: 'BayesianTools: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics' notes: Imports + url: https://github.com/florianhartig/BayesianTools authors: - family-names: Hartig given-names: Florian @@ -124,65 +72,36 @@ references: given-names: Francesco - family-names: Paul given-names: Stefan - year: '2022' - url: https://CRAN.R-project.org/package=BayesianTools -- type: software - title: coda - abstract: 'coda: Output Analysis and Diagnostics for MCMC' - notes: Imports - authors: - - family-names: Plummer - given-names: Martyn - email: martyn.plummer@gmail.com - - family-names: Best - given-names: Nicky - - family-names: Cowles - given-names: Kate - - family-names: Vines - given-names: Karen - - family-names: Sarkar - given-names: Deepayan - - family-names: Bates - given-names: Douglas - - family-names: Almond - given-names: Russell - - family-names: Magnusson - given-names: Arni - year: '2022' - url: https://CRAN.R-project.org/package=coda -- type: software - title: rstudioapi - abstract: 'rstudioapi: Safely Access the RStudio API' - notes: Imports - authors: - - family-names: Ushey - given-names: Kevin - email: kevin@rstudio.com - - family-names: Allaire - given-names: JJ - email: jj@rstudio.com - - family-names: Wickham - given-names: Hadley - email: hadley@rstudio.com - - family-names: Ritchie - given-names: Gary - email: gary@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=rstudioapi + year: '2023' - type: software title: crayon abstract: 'crayon: Colored Terminal Output' notes: Imports + url: https://github.com/r-lib/crayon#readme + repository: https://CRAN.R-project.org/package=crayon authors: - family-names: Csárdi given-names: Gábor email: csardi.gabor@gmail.com - year: '2022' - url: https://CRAN.R-project.org/package=crayon + year: '2023' +- type: software + title: doParallel + abstract: 'doParallel: Foreach Parallel Adaptor for the ''parallel'' Package' + notes: Imports + url: https://github.com/RevolutionAnalytics/doparallel + repository: https://CRAN.R-project.org/package=doParallel + authors: + - family-names: Corporation + given-names: Microsoft + - family-names: Weston + given-names: Steve + year: '2023' - 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 @@ -196,72 +115,13 @@ references: - family-names: Müller given-names: Kirill orcid: https://orcid.org/0000-0002-1416-3412 - year: '2022' - url: https://CRAN.R-project.org/package=dplyr -- type: software - title: lubridate - abstract: 'lubridate: Make Dealing with Dates a Little Easier' - notes: Imports - authors: - - family-names: Spinu - given-names: Vitalie - email: spinuvit@gmail.com - - family-names: Grolemund - given-names: Garrett - - family-names: Wickham - given-names: Hadley - year: '2022' - url: https://CRAN.R-project.org/package=lubridate -- type: software - title: rlang - abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features' - notes: Imports - authors: - - family-names: Henry - given-names: Lionel - email: lionel@rstudio.com - - family-names: Wickham - given-names: Hadley - email: hadley@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=rlang -- type: software - title: tictoc - abstract: 'tictoc: Functions for Timing R Scripts, as Well as Implementations of - Stack and List Structures' - notes: Imports - authors: - - family-names: Izrailev - given-names: Sergei - year: '2022' - url: https://CRAN.R-project.org/package=tictoc -- type: software - title: stringr - abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations' - notes: Imports - authors: - - family-names: Wickham - given-names: Hadley - email: hadley@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=stringr -- type: software - title: tibble - abstract: 'tibble: Simple Data Frames' - notes: Imports - authors: - - family-names: Müller - given-names: Kirill - email: krlmlr+r@mailbox.org - - family-names: Wickham - given-names: Hadley - email: hadley@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=tibble + year: '2023' - type: software title: ggplot2 abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics' notes: Imports + url: https://ggplot2.tidyverse.org + repository: https://CRAN.R-project.org/package=ggplot2 authors: - family-names: Wickham given-names: Hadley @@ -290,24 +150,24 @@ references: - family-names: Dunnington given-names: Dewey orcid: https://orcid.org/0000-0002-9415-4582 - year: '2022' - url: https://CRAN.R-project.org/package=ggplot2 + year: '2023' - type: software - title: methods - abstract: 'R: A Language and Environment for Statistical Computing' + title: lhs + abstract: 'lhs: Latin Hypercube Samples' notes: Imports + url: https://github.com/bertcarnell/lhs + repository: https://CRAN.R-project.org/package=lhs authors: - - name: R Core Team - location: - name: Vienna, Austria - year: '2022' - url: https://www.R-project.org/ - institution: - name: R Foundation for Statistical Computing + - family-names: Carnell + given-names: Rob + email: bertcarnell@gmail.com + year: '2023' - type: software title: lifecycle abstract: 'lifecycle: Manage the Life Cycle of your Package Functions' notes: Imports + url: https://lifecycle.r-lib.org/ + repository: https://CRAN.R-project.org/package=lifecycle authors: - family-names: Henry given-names: Lionel @@ -316,12 +176,67 @@ references: given-names: Hadley email: hadley@rstudio.com orcid: https://orcid.org/0000-0003-4757-117X - year: '2022' - url: https://CRAN.R-project.org/package=lifecycle + year: '2023' +- 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: '2023' +- type: software + title: methods + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: '2023' + institution: + name: R Foundation for Statistical Computing +- type: software + title: nloptr + abstract: 'nloptr: R Interface to NLopt' + notes: Imports + url: https://astamm.github.io/nloptr/index.html + repository: https://CRAN.R-project.org/package=nloptr + authors: + - family-names: Ypma + given-names: Jelmer + email: uctpjyy@ucl.ac.uk + - family-names: Johnson + given-names: Steven G. + year: '2023' - type: software title: purrr abstract: 'purrr: Functional Programming Tools' notes: Imports + url: https://purrr.tidyverse.org/ + repository: https://CRAN.R-project.org/package=purrr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + year: '2023' +- 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 @@ -329,44 +244,154 @@ references: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=purrr + year: '2023' - type: software - title: testthat - abstract: 'testthat: Unit Testing for R' - notes: Suggests + 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@rstudio.com + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + - family-names: Ritchie + given-names: Gary + email: gary@rstudio.com + year: '2023' +- type: software + title: stringr + abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations' + notes: Imports + url: https://stringr.tidyverse.org + repository: https://CRAN.R-project.org/package=stringr authors: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com - year: '2022' - url: https://CRAN.R-project.org/package=testthat - version: '>= 2.1.0' + year: '2023' +- 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: krlmlr+r@mailbox.org + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + year: '2023' +- type: software + title: tictoc + abstract: 'tictoc: Functions for Timing R Scripts, as Well as Implementations of + "Stack" and "List" Structures' + notes: Imports + url: https://github.com/jabiru/tictoc + repository: https://CRAN.R-project.org/package=tictoc + authors: + - family-names: Izrailev + given-names: Sergei + year: '2023' +- type: software + title: ApsimOnR + abstract: 'ApsimOnR: Running the Apsim model with parameters forcing' + notes: Suggests + url: https://github.com/ApsimOnR + authors: + - family-names: Holzworth + given-names: Drew + email: drew.holzworth@csiro.au + year: '2023' - 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: '2022' - url: https://CRAN.R-project.org/package=covr + year: '2023' +- type: software + title: CroPlotR + abstract: 'CroPlotR: A Package to Analyze Crop Model Simulations Outputs with Plots + and Statistics' + notes: Suggests + url: https://doi.org/10.5281/zenodo.4442330 + authors: + - 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: 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 + year: '2023' +- type: software + title: devtools + abstract: 'devtools: Tools to Make Developing R Packages Easier' + notes: Suggests + url: https://devtools.r-lib.org/ + repository: https://CRAN.R-project.org/package=devtools + authors: + - family-names: Wickham + given-names: Hadley + - family-names: Hester + given-names: Jim + - family-names: Chang + given-names: Winston + - family-names: Bryan + given-names: Jennifer + email: jenny@rstudio.com + orcid: https://orcid.org/0000-0002-6983-2759 + year: '2023' +- type: software + title: gridExtra + abstract: 'gridExtra: Miscellaneous Functions for "Grid" Graphics' + notes: Suggests + repository: https://CRAN.R-project.org/package=gridExtra + authors: + - family-names: Auguie + given-names: Baptiste + email: baptiste.auguie@gmail.com + year: '2023' - 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: '2022' - url: https://CRAN.R-project.org/package=knitr + year: '2023' - 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 @@ -400,12 +425,27 @@ references: given-names: Richard email: rich@rstudio.com orcid: https://orcid.org/0000-0003-3925-190X - year: '2022' - url: https://CRAN.R-project.org/package=rmarkdown + year: '2023' - type: software - title: SticsRFiles - abstract: 'SticsRFiles: Read And Modify STICS Input/Output Files' + title: spelling + abstract: 'spelling: Tools for Spell Checking in R' notes: Suggests + url: https://docs.ropensci.org/spelling/ + repository: https://CRAN.R-project.org/package=spelling + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroen@berkeley.edu + orcid: https://orcid.org/0000-0002-4035-0289 + - family-names: Hester + given-names: Jim + email: james.hester@rstudio.com + year: '2023' +- type: software + title: SticsOnR + abstract: 'SticsOnR: Manage STICS Simulations Running the Executable or JavaStics,' + notes: Suggests + url: https://doi.org/10.5281/zenodo.4443130 authors: - family-names: Lecharpentier given-names: Patrice @@ -423,11 +463,12 @@ references: given-names: Michel email: michel.giner@cirad.fr orcid: https://orcid.org/0000-0002-9310-2377 - year: '2022' + year: '2023' - type: software - title: SticsOnR - abstract: 'SticsOnR: Manage STICS Simulations Running the Executable or JavaStics,' + title: SticsRFiles + abstract: 'SticsRFiles: Read And Modify STICS Input/Output Files' notes: Suggests + url: https://doi.org/10.5281/zenodo.4443206 authors: - family-names: Lecharpentier given-names: Patrice @@ -445,65 +486,29 @@ references: given-names: Michel email: michel.giner@cirad.fr orcid: https://orcid.org/0000-0002-9310-2377 - year: '2022' -- type: software - title: gridExtra - abstract: 'gridExtra: Miscellaneous Functions for "Grid" Graphics' - notes: Suggests - authors: - - family-names: Auguie - given-names: Baptiste - email: baptiste.auguie@gmail.com - year: '2022' - url: https://CRAN.R-project.org/package=gridExtra -- type: software - title: doParallel - abstract: 'doParallel: Foreach Parallel Adaptor for the ''parallel'' Package' - notes: Suggests - authors: - - family-names: Corporation - given-names: Microsoft - - family-names: Weston - given-names: Steve - year: '2022' - url: https://CRAN.R-project.org/package=doParallel + year: '2023' - type: software - title: devtools - abstract: 'devtools: Tools to Make Developing R Packages Easier' + 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 - - family-names: Hester - given-names: Jim - - family-names: Chang - given-names: Winston - - family-names: Bryan - given-names: Jennifer - email: jenny@rstudio.com - orcid: https://orcid.org/0000-0002-6983-2759 - year: '2022' - url: https://CRAN.R-project.org/package=devtools + email: hadley@rstudio.com + year: '2023' + version: '>= 2.1.0' - type: software - title: CroPlotR - abstract: 'CroPlotR: A Package to Analyse Crop Model Simulations Outputs with Plots - and Statistics' + 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: 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: 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 - year: '2022' + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + - family-names: Girlich + given-names: Maximilian + year: '2023'