SticsRPacks/CroptimizR
A Package to Estimate Parameters of Crop Models

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SticsRPacks/CroptimizR: A Package to Estimate Parameters of Crop Models
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Files in SticsRPacks/CroptimizR
A Package to Estimate Parameters of Crop Models

.Rbuildignore
.gitattributes
.github/.gitignore
.github/dependabot.yml
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.github/workflows/style.yaml
.github/workflows/test-coverage.yaml
.github/workflows/update-citation-cff.yaml
.gitignore
.vscode/settings.json
CITATION.cff
CODE_OF_CONDUCT.md
CroptimizR.Rproj
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/FwdRegAgMIP.R R/bayesian_functions.R R/compute_eq_const.R R/estim_param.R R/filter_obs.R R/frequentist_functions.R R/get_params_per_sit.R R/get_reserved_keywords.R R/information_criteria.R R/intersect_sim_obs.R R/is_data.R R/likelihoods.R R/ls_criteria.R R/main_crit.R R/obsSim_consistency.R R/optim_switch.R R/param_info_functions.R R/sample_params.R R/test_wrapper.R R/wrap_BayesianTools.R R/wrap_nloptr.R R/wrap_optim.R R/zzz.R README.Rmd README.md
_pkgdown.yml
codecov.yml
cran-comments.md
inst/WORDLIST
inst/extdata/ResAgmipPheno_2rep4it/V10.0/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V10.0/param_selection_steps.csv
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_1/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_1/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_1/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_1/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_2/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_2/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_2/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_2/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_3/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_3/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_3/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_3/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_4/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_4/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_4/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V10.0/results_all_steps/step_4/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V9.0/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V9.0/param_selection_steps.csv
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_1/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_1/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_1/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_1/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_2/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_2/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_2/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_2/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_3/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_3/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_3/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_3/optim_results.Rdata
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_4/EstimatedVSinit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_4/ValuesVSit.pdf inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_4/ValuesVSit_2D.pdf
inst/extdata/ResAgmipPheno_2rep4it/V9.0/results_all_steps/step_4/optim_results.Rdata
inst/extdata/ResSimpleCase2rep4it/optim_results.Rdata
inst/extdata/ResSpecVarDREAM_4it/optim_results.Rdata
inst/extdata/ResSpecVar_2rep4it/V10.0/optim_results.Rdata
inst/extdata/ResSpecVar_2rep4it/V9.0/optim_results.Rdata
man/AIC.Rd man/AICc.Rd man/BIC.Rd man/Likelihoods.Rd man/check_obsSim_consistency.Rd man/complete_init_values.Rd man/compute_eq_const.Rd man/estim_param.Rd
man/figures/logo.png
man/filter_obs.Rd man/filter_param_info.Rd man/get_init_values.Rd man/get_params_bounds.Rd man/get_params_init_values.Rd man/get_params_names.Rd man/get_params_per_sit.Rd man/get_reserved_keywords.Rd man/intersect_sim_obs.Rd man/is.data.Rd man/is.obs.Rd man/is.sim.Rd man/is_sim_inf_or_na.Rd man/ls_criteria.Rd man/main_crit.Rd man/make_obsSim_consistent.Rd man/optim_switch.Rd man/plot_bayesian.Rd man/plot_estimVSinit.Rd man/plot_frequentist.Rd man/plot_valuesVSit.Rd man/plot_valuesVSit_2D.Rd man/post_treat_FwdRegAgMIP.Rd man/post_treat_frequentist.Rd man/sample_params.Rd man/save_results_FwdRegAgMIP.Rd man/select_param_FwdRegAgMIP.Rd man/set_init_values.Rd man/summary_FwdRegAgMIP.Rd man/summary_bayesian.Rd man/summary_frequentist.Rd man/test_wrapper.Rd man/wrap_BayesianTools.Rd man/wrap_nloptr.Rd man/wrap_optim.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
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pkgdown/favicon/favicon.ico
tests/spelling.R tests/testthat.R tests/testthat/test-compute_eq_const.R tests/testthat/test-filter_obs.R tests/testthat/test-filter_params.R tests/testthat/test-get_params.R tests/testthat/test-information_crit.R tests/testthat/test-init_values_functions.R tests/testthat/test-intersect_sim_obs.R tests/testthat/test-isdata.R tests/testthat/test-likelihood.R tests/testthat/test-ls_criteria.R tests/testthat/test-obsSim_consistency.R tests/testthat/test-optim_switch.R tests/testthat/test-sample_params.R tests/testthat/test-test_wrapper.R vignettes/AgMIP_Calibration_Phenology_protocol.Rmd vignettes/ApsimX_parameter_estimation_simple_case.Rmd vignettes/Available_parameter_estimation_algorithms.Rmd vignettes/CroptimizR.Rmd vignettes/Designing_a_model_wrapper.Rmd
vignettes/GettingStarted/main_scheme.png
vignettes/GettingStarted/obs.csv
vignettes/GettingStarted/obs_file.png
vignettes/Parameter_estimation_DREAM.Rmd vignettes/Parameter_estimation_Specific_and_Varietal.Rmd vignettes/Parameter_estimation_simple_case.Rmd
vignettes/ResultsAgmipPhenology/all_situations.png
vignettes/ResultsAgmipPhenology/obs_list.Rdata
vignettes/ResultsAgmipPhenology/optim_results.Rdata
vignettes/ResultsAgmipPhenology/param_selection_steps.csv
vignettes/ResultsAgmipPhenology/results_all_steps/step_1/EstimatedVSinit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_1/ValuesVSit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_1/ValuesVSit_2D.pdf
vignettes/ResultsAgmipPhenology/results_all_steps/step_1/optim_results.Rdata
vignettes/ResultsAgmipPhenology/results_all_steps/step_2/EstimatedVSinit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_2/ValuesVSit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_2/ValuesVSit_2D.pdf
vignettes/ResultsAgmipPhenology/results_all_steps/step_2/optim_results.Rdata
vignettes/ResultsAgmipPhenology/results_all_steps/step_3/EstimatedVSinit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_3/ValuesVSit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_3/ValuesVSit_2D.pdf
vignettes/ResultsAgmipPhenology/results_all_steps/step_3/optim_results.Rdata
vignettes/ResultsAgmipPhenology/results_all_steps/step_4/EstimatedVSinit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_4/ValuesVSit.pdf vignettes/ResultsAgmipPhenology/results_all_steps/step_4/ValuesVSit_2D.pdf
vignettes/ResultsAgmipPhenology/results_all_steps/step_4/optim_results.Rdata
vignettes/ResultsAgmipPhenology/stats.Rdata
vignettes/ResultsSimpleCase/EstimatedVSinit.pdf
vignettes/ResultsSimpleCase/critVSit.PNG
vignettes/ResultsSimpleCase/dlaimaxVSdurvieF.PNG
vignettes/ResultsSimpleCase/dlaimaxVSit.PNG
vignettes/ResultsSimpleCase/durvieFVSit.PNG
vignettes/ResultsSimpleCase/estimInit_dlaimax.PNG
vignettes/ResultsSimpleCase/estimInit_durvieF.PNG
vignettes/ResultsSimpleCase/optim_results.Rdata
vignettes/ResultsSimpleCase/sim_obs_plots.png
vignettes/ResultsSimpleCaseApsim/EstimatedVSinit.pdf
vignettes/ResultsSimpleCaseApsim/estimInit_ExtinctionCoeff.png
vignettes/ResultsSimpleCaseApsim/estimInit_RUE.png
vignettes/ResultsSimpleCaseApsim/optim_results.Rdata
vignettes/ResultsSimpleCaseApsim/sim_obs_plots.png
vignettes/ResultsSimpleCaseDREAM/N10000/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N10000/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N10000/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N10000/log.txt
vignettes/ResultsSimpleCaseDREAM/N10000/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N10000/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/N1500/EstimatedVSinit.pdf vignettes/ResultsSimpleCaseDREAM/N1500/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500/log.txt
vignettes/ResultsSimpleCaseDREAM/N1500/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/log.txt
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/1stLaunch/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/log.txt
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/2ndLaunch/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/log.txt
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_5chains/3rdLaunch/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/iterAndDensityPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/log.txt
vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/N1500_pcrUpdateTRUE/optim_results.Rdata
vignettes/ResultsSimpleCaseDREAM/correlationPlots.pdf vignettes/ResultsSimpleCaseDREAM/gelmanDiagPlots.pdf vignettes/ResultsSimpleCaseDREAM/iterAndDensityPlots.pdf vignettes/ResultsSimpleCaseDREAM/marginalPlots.pdf
vignettes/ResultsSimpleCaseDREAM/optim_results.Rdata
vignettes/ResultsSpecificVarietal/EstimatedVSinit.pdf
vignettes/ResultsSpecificVarietal/estimInit_dlaimax.PNG
vignettes/ResultsSpecificVarietal/estimInit_durvieF_var1.PNG
vignettes/ResultsSpecificVarietal/estimInit_durvieF_var2.PNG
vignettes/ResultsSpecificVarietal/optim_results.Rdata
vignettes/ResultsSpecificVarietal/sim_obs.png
vignettes/ResultsSpecificVarietalDREAM/N10000/Gelman_dlaimax.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/Gelman_durvieF1.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/Gelman_durvieF2.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/correlationPlots.pdf
vignettes/ResultsSpecificVarietalDREAM/N10000/correlation_plot.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/densities_dlaimax.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/densities_durvieF1.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/densities_durvieF2.PNG
vignettes/ResultsSpecificVarietalDREAM/N10000/gelmanDiagPlots.pdf vignettes/ResultsSpecificVarietalDREAM/N10000/iterAndDensityPlots.pdf
vignettes/ResultsSpecificVarietalDREAM/N10000/log.txt
vignettes/ResultsSpecificVarietalDREAM/N10000/marginalPlots.pdf
vignettes/ResultsSpecificVarietalDREAM/N10000/optim_results.Rdata
vignettes/bibliography.bib
SticsRPacks/CroptimizR documentation built on Dec. 16, 2024, 11:54 a.m.

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