Man pages for cjubin/learnMET
Predictions with Machine Learning methods in Multi Environment Trials (MET)
| ALE_plot_split | ALE plots feature-wise |
| analysis_predictions | Analysis of prediction results from 'predict_trait_MET()' by... |
| apply_pca | Data dimensionality reduction using PCA on a split object. |
| apply_pcs_G_Add | Data dimensionality reduction by modeling genetic effects... |
| climate_variables_indica | Multi-year trial data of rice |
| climate_variables_japonica | Multi-year trial data of rice |
| clustering_env_data | Clustering of environments solely based on environmental... |
| compute_EC_fixed_length_window | Compute ECs based on day-windows of fixed length. |
| compute_EC_fixed_number_windows | Compute ECs based on a fixed number of day-windows (fixed... |
| compute_EC_gdd | Compute ECs based on growth stages which are estimated based... |
| compute_EC_monthly | Compute ECs on a monthly basis. |
| compute_EC_user_defined_intervals | Compute ECs based on day-windows of fixed length. |
| create_METData | Create a multi-environment trials data object |
| daylength | Compute the day length given the altitude and day of year. |
| DL_reg_1 | Processing of a split object to get data ready to be used and... |
| DL_reg_2 | Processing of a split object to get data ready to be used and... |
| DL_reg_3 | Processing of a split object to get data ready to be used and... |
| dtw_distance | Compute the DTW distance using the dtwcluster R package &... |
| fit_cv_split | S3 method used to fit an object of class 'rf_reg_1',... |
| fit_split | S3 method used to fit an object of class 'rf_reg_1',... |
| gdd_information | Internal function of [compute_EC_gdd())] [compute_EC_gdd())]:... |
| geno_G2F | Maize experimental multi-environment data sets (Genomes to... |
| geno_indica | Multi-year trial data of rice |
| geno_japonica | Multi-year trial data of rice |
| get_daily_tables_per_env | Obtain daily climate data for an environment from NASA POWER... |
| get.ea | Formulas to compute vapour pressure deficit according to... |
| get.ea.no.RH | Formulas to compute vapour pressure deficit according to... |
| get.ea.with.rhmax | Formulas to compute vapour pressure deficit according to... |
| get.ea.with.rhmean | Formulas to compute vapour pressure deficit according to... |
| get_ECs | Compute environmental covariates for each environment of the... |
| get_elevation | Obtain elevation data for each field trial based on longitude... |
| get.es | Formulas to compute vapour pressure deficit according to... |
| get.esmn | Formulas to compute vapour pressure deficit according to... |
| get.esmx | Formulas to compute vapour pressure deficit according to... |
| get_soil_per_env | Obtain soil data for a given environment |
| get_solar_radiation | Obtain daily solar radiation for an IDenv with package... |
| get_splits_processed_with_method | Attribute a processing method for each list of training/test... |
| get_wind_data | Obtain daily wind data for an IDenv with package nasapower... |
| info_environments_G2F | Maize experimental multi-environment data sets (Genomes to... |
| info_environments_indica | Multi-year trial data of rice |
| info_environments_japonica | Multi-year trial data of rice |
| intervals_growth_manual_G2F | Maize experimental multi-environment data sets (Genomes to... |
| map_G2F | Maize experimental multi-environment data sets (Genomes to... |
| map_indica | Multi-year trial data of rice |
| map_japonica | Multi-year trial data of rice |
| marker_effect_per_env_EN | Compute marker effects per environment with Elastic Net |
| marker_effect_per_env_FarmCPU | Compute marker P-values for each environment with GWAS. |
| penman_monteith_reference_et0 | Calculates reference ET0 based on the Penman-Monteith model... |
| permutation_based_vip | Compute variable importance according to the machine learning... |
| pheno_G2F | Maize experimental multi-environment data sets (Genomes to... |
| pheno_indica | Multi-year trial data of rice |
| pheno_japonica | Multi-year trial data of rice |
| pipe | Pipe operator |
| plot_results_cv | Plot cross-validated results for the ML model and the trait... |
| plot_results_vip | Plot variable importance scores |
| plot_results_vip_cv | Plot variable importance scores |
| predict_cv0 | Get train/test splits of the phenotypic MET dataset based on... |
| predict_cv00 | Get train/test splits of the phenotypic MET dataset based on... |
| predict_cv00_5folds | Get train/test splits of the phenotypic MET dataset based on... |
| predict_cv1 | Get train/test splits of the phenotypic MET dataset based on... |
| predict_cv2 | Get train/test splits of the phenotypic MET dataset based on... |
| predict_trait_MET | Phenotypic prediction of unobserved data. |
| predict_trait_MET_cv | Cross-validation procedure for phenotypic prediction of crop... |
| print.summary.METData | Print the summary of an object of class METData |
| qc_raw_weather_data | Quality control on daily weather data |
| rf_reg_1 | Processing of a split object to get data ready to be used and... |
| rf_reg_2 | Processing of a split object to get data ready to be used and... |
| rf_reg_3 | Processing of a split object to get data ready to be used and... |
| sat_vap_pressure | Formulas to compute saturated vapor pressure deficit |
| select_markers | Selection of specific SNPs covariates. |
| soil_G2F | Maize experimental multi-environment data sets (Genomes to... |
| stacking_reg_1 | Processing of a split object to get data ready to be used and... |
| stacking_reg_2 | Processing of a split object to get data ready to be used and... |
| stacking_reg_3 | Processing of a split object to get data ready to be used and... |
| summary.METData | Summary of an object of class METData |
| variable_importance_split | Compute variable importance according to the machine learning... |
| xgb_reg_1 | Processing of a split object to get data ready to be used and... |
| xgb_reg_2 | Processing of a split object to get data ready to be used and... |
| xgb_reg_3 | Processing of a split object to get data ready to be used and... |
