Files in cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)

.Rbuildignore

DESCRIPTION

LICENSE

NAMESPACE

R/DL_reg_1.R R/DL_reg_2.R R/DL_reg_3.R R/ale_plots.R R/analysis_predictions_best_genotypes.R R/apply_PCA.R R/apply_pcs_G_Add.R R/clustering_env_data.R R/compute_EC.R R/compute_EC_gdd.R R/compute_EC_monthly.R R/compute_EC_user_defined_intervals.R R/create_METData.R R/dtw_distance.R R/etp_functions.R R/fit_DL_reg_1.R R/fit_DL_reg_2.R R/fit_DL_reg_3.R R/fit_cv_split.R R/fit_rf_reg_1.R R/fit_rf_reg_2.R R/fit_rf_reg_3.R R/fit_split.R R/fit_stacking_reg_1.R R/fit_stacking_reg_2.R R/fit_stacking_reg_3.R R/fit_xgb_reg_1.R R/fit_xgb_reg_2.R R/fit_xgb_reg_3.R R/gdd_information.R R/get_ECs.R R/get_elevation.R R/get_solar_radiation.R R/get_splits_processed_with_method.R R/get_weather_soil_data.R R/get_wind_data.R R/marker_effect_per_env_EN.R R/marker_effect_per_env_FarmCPU.R R/miscellaneous.R R/negation_function.R R/permutation_based_vip.R R/plot_results_cv.R R/plot_results_vip_functions.R R/predict_cv0.R R/predict_cv00.R R/predict_cv00_5folds.R R/predict_cv1.R R/predict_cv2.R R/predict_trait_MET.R R/predict_trait_MET_cv.R R/qc_raw_weather_data.R R/rf_reg_1.R R/rf_reg_2.R R/rf_reg_3.R R/select_markers.R R/snp_based_haploblocks.R R/stacking_reg_1.R R/stacking_reg_2.R R/stacking_reg_3.R R/summary.METData.R R/utils-ggplot2.R R/utils-pipe.R R/utils-purrr.R R/vapor_pressure.R R/variable_importance.R R/xgb_reg_1.R R/xgb_reg_2.R R/xgb_reg_3.R README.Rmd README.md

_pkgdown.yml

data/GDD_barley.rda

data/GDD_barley_haun_stages.rda

data/GDD_maize1300.rda

data/GDD_maize1500.rda

data/GDD_maize1700.rda

data/GDD_maize1900.rda

data/GDD_wheat1.rda

data/GDD_wheat2.rda

data/climate_variables_indica.rda

data/climate_variables_japonica.rda

data/geno_G2F.rda

data/geno_indica.rda

data/geno_japonica.rda

data/info_environments_G2F.rda

data/info_environments_indica.rda

data/info_environments_japonica.rda

data/intervals_growth_manual_G2F.rda

data/map_G2F.rda

data/map_indica.rda

data/map_japonica.rda

data/pheno_G2F.rda

data/pheno_indica.rda

data/pheno_japonica.rda

data/soil_G2F.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/climate_variables_only_clusters_environments_4.png

docs/articles/index.html

docs/articles/metalearner_cv0.png

docs/articles/model_interpretation.html

docs/articles/model_interpretation_files/header-attrs-2.11/header-attrs.js

docs/articles/model_interpretation_files/header-attrs-2.6/header-attrs.js

docs/articles/plot_elbow_method.png

docs/articles/plot_sil_score.png

docs/articles/vignette_cv_stacking_indica.html

docs/articles/vignette_cv_stacking_indica_files/header-attrs-2.11/header-attrs.js

docs/articles/vignette_cv_stacking_indica_files/header-attrs-2.6/header-attrs.js

docs/articles/vignette_cv_xgb_indica.html

docs/articles/vignette_cv_xgb_indica_files/header-attrs-2.11/header-attrs.js

docs/articles/vignette_cv_xgb_indica_files/header-attrs-2.6/header-attrs.js

docs/articles/vignette_getweatherdata.html

docs/articles/vignette_getweatherdata_files/header-attrs-2.11/header-attrs.js

docs/articles/vignette_getweatherdata_files/header-attrs-2.6/header-attrs.js

docs/articles/vignette_models_package.html

docs/articles/vignette_models_package_files/header-attrs-2.11/header-attrs.js

docs/articles/vignette_stacking.html

docs/articles/vignette_stacking_files/header-attrs-2.11/header-attrs.js

docs/articles/vignette_stacking_files/header-attrs-2.6/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/ALE_plot_split.html

docs/reference/DL_reg_1.html

docs/reference/DL_reg_2.html

docs/reference/DL_reg_3.html

docs/reference/NA

docs/reference/Rplot001.png

docs/reference/add_METData_to_predict.html

docs/reference/add_new_METData.html

docs/reference/analysis_predictions.html

docs/reference/analysis_predictions_best_genotypes.html

docs/reference/apply_pca.html

docs/reference/apply_pcs_G_Add.html

docs/reference/climate_variables_indica.html

docs/reference/climate_variables_japonica.html

docs/reference/clustering_env_data.html

docs/reference/clustering_weather_data.html

docs/reference/compute_EC_fixed_length_window.html

docs/reference/compute_EC_fixed_number_windows.html

docs/reference/compute_EC_gdd.html

docs/reference/compute_EC_user_defined_intervals.html

docs/reference/create_METData.html

docs/reference/daylength.html

docs/reference/env_data_indica.html

docs/reference/feature_interaction_split.html

docs/reference/fit_cv_split.html

docs/reference/fit_predict_model.html

docs/reference/fit_split.html

docs/reference/gdd_information.html

docs/reference/geno_G2F.html

docs/reference/geno_indica.html

docs/reference/geno_japonica.html

docs/reference/get.ea.html

docs/reference/get.ea.no.RH.html

docs/reference/get.ea.with.rhmax.html

docs/reference/get.ea.with.rhmean.html

docs/reference/get.es.html

docs/reference/get.esmn.html

docs/reference/get.esmx.html

docs/reference/get_ECs.html

docs/reference/get_daily_tables_per_env.html

docs/reference/get_elevation.html

docs/reference/get_soil_per_env.html

docs/reference/get_solar_radiation.html

docs/reference/get_splits_processed_with_method.html

docs/reference/get_wind_data.html

docs/reference/index.html

docs/reference/info_environments_G2F.html

docs/reference/info_environments_indica.html

docs/reference/info_environments_japonica.html

docs/reference/intervals_growth_manual_G2F.html

docs/reference/map_G2F.html

docs/reference/map_indica.html

docs/reference/map_japonica.html

docs/reference/marker_effect_per_env_EN.html

docs/reference/marker_effect_per_env_FarmCPU.html

docs/reference/penman_monteith_reference_et0.html

docs/reference/permutation_based_vip.html

docs/reference/pheno_G2F.html

docs/reference/pheno_indica.html

docs/reference/pheno_japonica.html

docs/reference/pipe.html

docs/reference/plot_results_cv.html

docs/reference/plot_results_vip.html

docs/reference/plot_results_vip_cv.html

docs/reference/predict_cv0.html

docs/reference/predict_cv00.html

docs/reference/predict_cv1.html

docs/reference/predict_cv2.html

docs/reference/predict_trait_MET.html

docs/reference/predict_trait_MET_cv.html

docs/reference/print.summary.METData.html

docs/reference/qc_raw_weather_data.html

docs/reference/rf_reg_1.html

docs/reference/rf_reg_2.html

docs/reference/rf_reg_3.html

docs/reference/sat_vap_pressure.html

docs/reference/select_markers.html

docs/reference/soil_G2F.html

docs/reference/stacking_reg_1.html

docs/reference/stacking_reg_2.html

docs/reference/stacking_reg_3.html

docs/reference/summary.METData.html

docs/reference/vapor_pressure_deficit.html

docs/reference/variable_importance_split.html

docs/reference/xgb_reg_1.html

docs/reference/xgb_reg_2.html

docs/reference/xgb_reg_3.html

inst/REFERENCES.bib

man/ALE_plot_split.Rd man/DL_reg_1.Rd man/DL_reg_2.Rd man/DL_reg_3.Rd man/analysis_predictions.Rd man/apply_pca.Rd man/apply_pcs_G_Add.Rd man/climate_variables_indica.Rd man/climate_variables_japonica.Rd man/clustering_env_data.Rd man/compute_EC_fixed_length_window.Rd man/compute_EC_fixed_number_windows.Rd man/compute_EC_gdd.Rd man/compute_EC_monthly.Rd man/compute_EC_user_defined_intervals.Rd man/create_METData.Rd man/daylength.Rd man/dtw_distance.Rd man/fit_cv_split.Rd man/fit_split.Rd man/gdd_information.Rd man/geno_G2F.Rd man/geno_indica.Rd man/geno_japonica.Rd man/get.ea.Rd man/get.ea.no.RH.Rd man/get.ea.with.rhmax.Rd man/get.ea.with.rhmean.Rd man/get.es.Rd man/get.esmn.Rd man/get.esmx.Rd man/get_ECs.Rd man/get_daily_tables_per_env.Rd man/get_elevation.Rd man/get_soil_per_env.Rd man/get_solar_radiation.Rd man/get_splits_processed_with_method.Rd man/get_wind_data.Rd man/info_environments_G2F.Rd man/info_environments_indica.Rd man/info_environments_japonica.Rd man/intervals_growth_manual_G2F.Rd man/map_G2F.Rd man/map_indica.Rd man/map_japonica.Rd man/marker_effect_per_env_EN.Rd man/marker_effect_per_env_FarmCPU.Rd man/penman_monteith_reference_et0.Rd man/permutation_based_vip.Rd man/pheno_G2F.Rd man/pheno_indica.Rd man/pheno_japonica.Rd man/pipe.Rd man/plot_results_cv.Rd man/plot_results_vip.Rd man/plot_results_vip_cv.Rd man/predict_cv0.Rd man/predict_cv00.Rd man/predict_cv00_5folds.Rd man/predict_cv1.Rd man/predict_cv2.Rd man/predict_trait_MET.Rd man/predict_trait_MET_cv.Rd man/print.summary.METData.Rd man/qc_raw_weather_data.Rd man/rf_reg_1.Rd man/rf_reg_2.Rd man/rf_reg_3.Rd man/sat_vap_pressure.Rd man/select_markers.Rd man/soil_G2F.Rd man/stacking_reg_1.Rd man/stacking_reg_2.Rd man/stacking_reg_3.Rd man/summary.METData.Rd man/variable_importance_split.Rd man/xgb_reg_1.Rd man/xgb_reg_2.Rd man/xgb_reg_3.Rd scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw1.Rmd

scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw1.sh

scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw2.Rmd

scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw2.sh

scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw3.Rmd

scripts_publication/bglr_g2f_fw/BGLR_G_E_W_GW_fw3.sh

scripts_publication/bglr_rice_data_indica/BGLR_G_E_W_GW_GC.Rmd scripts_publication/bglr_rice_data_indica/BGLR_G_E_W_GW_GY.Rmd scripts_publication/bglr_rice_data_indica/BGLR_G_E_W_GW_PHR.Rmd

scripts_publication/bglr_rice_data_indica/rice_bglr_GC.sh

scripts_publication/bglr_rice_data_indica/rice_bglr_GY.sh

scripts_publication/bglr_rice_data_indica/rice_bglr_PHR.sh

scripts_publication/bglr_rice_data_japonica/BGLR_G_E_W_GW_GC.Rmd scripts_publication/bglr_rice_data_japonica/BGLR_G_E_W_GW_GY.Rmd scripts_publication/bglr_rice_data_japonica/BGLR_G_E_W_GW_PHR.Rmd

scripts_publication/bglr_rice_data_japonica/rice_bglr_GC.sh

scripts_publication/bglr_rice_data_japonica/rice_bglr_GY.sh

scripts_publication/bglr_rice_data_japonica/rice_bglr_PHR.sh

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_1.R

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_1.sh

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_2.R

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_2.sh

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_3.R

scripts_publication/learnmet_analyses_g2f/script_forward_g2f_stacking_3.sh

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_1.R

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_1.sh

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_2.R

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_2.sh

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_3.R

scripts_publication/learnmet_analyses_g2f/script_forward_xgbreg_g2f_3.sh

scripts_publication/results_benchmarking_revisions_paper2.xlsx

vignettes/REFERENCES.bib

vignettes/climate_variables_only_clusters_environments_4.png

vignettes/daily_weather_tables_nasapower.RDS

vignettes/met_cv.RDS

vignettes/metalearner_cv0.png

vignettes/model_interpretation.Rmd

vignettes/plot_elbow_method.png

vignettes/plot_sil_score.png

vignettes/vignette_cv_stacking_indica.Rmd vignettes/vignette_cv_xgb_indica.Rmd vignettes/vignette_getweatherdata.Rmd vignettes/vignette_models_package.Rmd

vignettes/xgboost_cv0.png

cjubin/learnMET documentation built on Nov. 4, 2024, 6:23 p.m.

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cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)

Files in cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)

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cjubin/learnMET Predictions with Machine Learning methods in Multi Environment Trials (MET)

Files in cjubin/learnMET Predictions with Machine Learning methods in Multi Environment Trials (MET)

R Package Documentation

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cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)

Files in cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)