Multi Environment Trials Analysis
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Documentation for package ‘metan’ version 1.18.0
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A B C D E F G H I K L M N O P R S T U V W
| metan-package | Multi-Environment Trial Analysis |
-- A --
| acv | Adjusted Coefficient of Variation |
| add_class | Utilities for handling with classes |
| add_cols | Utilities for handling with rows and columns |
| add_prefix | Utilities for handling with rows and columns |
| add_rows | Utilities for handling with rows and columns |
| add_row_id | Utilities for handling with rows and columns |
| add_seq_block | Utilities for data organization |
| add_suffix | Utilities for handling with rows and columns |
| all_lower_case | Utilities for handling with numbers and strings |
| all_pairs | Utilities for handling with rows and columns |
| all_title_case | Utilities for handling with numbers and strings |
| all_upper_case | Utilities for handling with numbers and strings |
| alpha_color | Personalized theme for ggplot2-based graphics |
| AMMI_indexes | AMMI-based stability indexes |
| ammi_indexes | AMMI-based stability indexes |
| Annicchiarico | Annicchiarico's genotypic confidence index |
| anova_ind | Within-environment analysis of variance |
| anova_joint | Joint analysis of variance |
| arrange_ggplot | Arrange separate ggplots into the same graphic |
| as.lpcor | Coerce to an object of class lpcor |
| as.split_factors | Split a data frame by factors |
| as_character | Encode variables to a specific format |
| as_factor | Encode variables to a specific format |
| as_integer | Encode variables to a specific format |
| as_logical | Encode variables to a specific format |
| as_numeric | Encode variables to a specific format |
| ave_dev | Useful functions for computing descriptive statistics |
| av_dev | Useful functions for computing descriptive statistics |
-- B --
| barplots | Fast way to create bar plots |
| bind_cv | Bind cross-validation objects |
| blup_indexes | Stability indexes based on a mixed-effect model |
-- C --
| can_corr | Canonical correlation analysis |
| ci_mean_t | Useful functions for computing descriptive statistics |
| ci_mean_z | Useful functions for computing descriptive statistics |
| clip_read | Utilities for data Copy-Pasta |
| clip_write | Utilities for data Copy-Pasta |
| clustering | Clustering analysis |
| coincidence_index | Computes the coincidence index of genotype selection |
| colindiag | Collinearity Diagnostics |
| colnames_to_lower | Utilities for handling with rows and columns |
| colnames_to_title | Utilities for handling with rows and columns |
| colnames_to_upper | Utilities for handling with rows and columns |
| column_exists | Utilities for handling with rows and columns |
| column_to_first | Utilities for handling with rows and columns |
| column_to_last | Utilities for handling with rows and columns |
| column_to_rownames | Utilities for handling with rows and columns |
| comb_vars | Pairwise combinations of variables |
| concatenate | Utilities for handling with rows and columns |
| correlated_vars | Generate correlated variables |
| corr_ci | Confidence interval for correlation coefficient |
| corr_coef | Linear and partial correlation coefficients |
| corr_focus | Focus on section of a correlation matrix |
| corr_plot | Visualization of a correlation matrix |
| corr_ss | Sample size planning for a desired Pearson's correlation confidence interval |
| corr_stab_ind | Correlation between stability indexes |
| covcor_design | Variance-covariance matrices for designed experiments |
| cv | Useful functions for computing descriptive statistics |
| cv_ammi | Cross-validation procedure |
| cv_ammif | Cross-validation procedure |
| cv_blup | Cross-validation procedure |
| cv_by | Useful functions for computing descriptive statistics |
-- D --
| data_alpha | Data from an alpha lattice design |
| data_g | Single maize trial |
| data_ge | Multi-environment trial of oat |
| data_ge2 | Multi-environment trial of maize |
| data_simula | Simulate genotype and genotype-environment data |
| desc_stat | Descriptive statistics |
| desc_wider | Descriptive statistics |
| df_to_selegen_54 | Utilities for data organization |
| difference_var | Select helper |
| doo | Alternative to dplyr::do for doing anything |
-- E --
| ecovalence | Stability analysis based on Wricke's model |
| env_dissimilarity | Dissimilarity between environments |
| env_stratification | Environment stratification |
| extract_number | Utilities for handling with numbers and strings |
| extract_string | Utilities for handling with numbers and strings |
-- F --
| fai_blup | Multi-trait selection index |
| fill_na | Utilities for handling with NA and zero values |
| find_outliers | Find possible outliers in a dataset |
| find_text_in_num | Utilities for handling with numbers and strings |
| first_upper_case | Utilities for handling with numbers and strings |
| Fox | Fox's stability function |
| freq_hist | Useful functions for computing descriptive statistics |
| freq_table | Useful functions for computing descriptive statistics |
-- G --
| gafem | Genotype analysis by fixed-effect models |
| gai | Geometric adaptability index |
| gamem | Genotype analysis by mixed-effect models |
| gamem_met | Genotype-environment analysis by mixed-effect models |
| get_corvars | Generate normal, correlated variables |
| get_covmat | Generate a covariance matrix |
| get_dist | Get a distance matrix |
| get_levels | Utilities for handling with rows and columns |
| get_levels_comb | Utilities for handling with rows and columns |
| get_level_size | Utilities for handling with rows and columns |
| get_model_data | Get data from a model easily |
| get_wd_here | Set and get the Working Directory quicky |
| ge_acv | Adjusted Coefficient of Variation as yield stability index |
| ge_cluster | Cluster genotypes or environments |
| ge_details | Details for genotype-environment trials |
| ge_effects | Genotype-environment effects |
| ge_factanal | Stability analysis and environment stratification |
| ge_means | Genotype-environment means |
| ge_plot | Graphical analysis of genotype-vs-environment interaction |
| ge_polar | Power Law Residuals as yield stability index |
| ge_reg | Eberhart and Russell's regression model |
| ge_simula | Simulate genotype and genotype-environment data |
| ge_stats | Parametric and non-parametric stability statistics |
| ge_winners | Genotype-environment winners |
| gge | Genotype plus genotype-by-environment model |
| ggplot_color | Personalized theme for ggplot2-based graphics |
| gmd | Get data from a model easily |
| gmean | Useful functions for computing descriptive statistics |
| gtb | Genotype by trait biplot |
| gytb | Genotype by yield*trait biplot |
| g_simula | Simulate genotype and genotype-environment data |
-- H --
| has_class | Utilities for handling with classes |
| has_na | Utilities for handling with NA and zero values |
| has_text_in_num | Utilities for handling with numbers and strings |
| has_zero | Utilities for handling with NA and zero values |
| hmean | Useful functions for computing descriptive statistics |
| hmgv | Stability indexes based on a mixed-effect model |
| hmrpgv | Stability indexes based on a mixed-effect model |
| Huehn | Huehn's stability statistics |
-- I --
| impute_missing_val | Missing value imputation |
| inspect | Check for common errors in multi-environment trial data |
| int.effects | Data for examples |
| intersect_var | Select helper |
| is.lpcor | Coerce to an object of class lpcor |
| is.split_factors | Split a data frame by factors |
| is_balanced_trial | Check if a data set is balanced |
-- K --
| kurt | Useful functions for computing descriptive statistics |
-- L --
| lineplots | Fast way to create line plots |
| lower_case_only | Select helper |
| lpcor | Linear and Partial Correlation Coefficients |
-- M --
| mahala | Mahalanobis Distance |
| mahala_design | Mahalanobis distance from designed experiments |
| make_long | Two-way table to a 'long' format |
| make_lower_tri | Utilities for handling with matrices |
| make_lower_upper | Utilities for handling with matrices |
| make_mat | Make a two-way table |
| make_sym | Utilities for handling with matrices |
| make_upper_tri | Utilities for handling with matrices |
| mantel_test | Mantel test |
| max_by | Useful functions for computing descriptive statistics |
| meansGxE | Data for examples |
| means_by | Useful functions for computing descriptive statistics |
| mean_by | Useful functions for computing descriptive statistics |
| mgidi | Multitrait Genotype-Ideotype Distance Index |
| min_by | Useful functions for computing descriptive statistics |
| mps | Mean performance and stability in multi-environment trials |
| mtmps | Multi-trait mean performance and stability index |
| mtsi | Multi-trait stability index |
-- N --
| network_plot | Network plot of a correlation matrix |
| non_collinear_vars | Select a set of predictors with minimal multicollinearity |
| n_by | Useful functions for computing descriptive statistics |
| n_missing | Useful functions for computing descriptive statistics |
| n_unique | Useful functions for computing descriptive statistics |
| n_valid | Useful functions for computing descriptive statistics |
-- O --
| open_wd | Set and get the Working Directory quicky |
| open_wd_here | Set and get the Working Directory quicky |
-- P --
| pairs_mantel | Mantel test for a set of correlation matrices |
| path_coeff | Path coefficients with minimal multicollinearity |
| path_coeff_mat | Path coefficients with minimal multicollinearity |
| path_coeff_seq | Path coefficients with minimal multicollinearity |
| performs_ammi | Additive Main effects and Multiplicative Interaction |
| plot.anova_joint | Several types of residual plots |
| plot.can_cor | Plots an object of class can_cor |
| plot.clustering | Plot an object of class clustering |
| plot.correlated_vars | Plot an object of class correlated_vars |
| plot.corr_coef | Create a correlation heat map |
| plot.cvalidation | Plot the RMSPD of a cross-validation procedure |
| plot.env_dissimilarity | Plot an object of class env_dissimilarity |
| plot.env_stratification | Plot the env_stratification model |
| plot.fai_blup | Multi-trait selection index |
| plot.gafem | Several types of residual plots |
| plot.gamem | Several types of residual plots |
| plot.ge_cluster | Plot an object of class ge_cluster |
| plot.ge_effects | Plot an object of class ge_effects |
| plot.ge_factanal | Plot the ge_factanal model |
| plot.ge_reg | Plot an object of class ge_reg |
| plot.gge | Create GGE, GT or GYT biplots |
| plot.mgidi | Plot the multi-trait genotype-ideotype distance index |
| plot.mtmps | Plot the multi-trait stability index |
| plot.mtsi | Plot the multi-trait stability index |
| plot.path_coeff | Plots an object of class 'path_coeff' |
| plot.performs_ammi | Several types of residual plots |
| plot.resp_surf | Plot the response surface model |
| plot.sh | Plot the Smith-Hazel index |
| plot.waas | Several types of residual plots |
| plot.waasb | Several types of residual plots |
| plot.wsmp | Plot heat maps with genotype ranking |
| plot_bars | Fast way to create bar plots |
| plot_blup | Plot the BLUPs for genotypes |
| plot_ci | Plot the confidence interval for correlation |
| plot_eigen | Plot the eigenvalues |
| plot_factbars | Fast way to create bar plots |
| plot_factlines | Fast way to create line plots |
| plot_lines | Fast way to create line plots |
| plot_scores | Plot scores in different graphical interpretations |
| plot_waasby | Plot WAASBY values for genotype ranking |
| predict.gamem | Predict method for gamem fits |
| predict.gge | Predict a two-way table based on GGE model |
| predict.performs_ammi | Predict the means of a performs_ammi object |
| predict.waas | Predict the means of a waas object |
| predict.waasb | Predict method for waasb fits |
| print.ammi_indexes | Print an object of class ammi_indexes |
| print.Annicchiarico | Print an object of class Annicchiarico |
| print.anova_ind | Print an object of class anova_ind |
| print.anova_joint | Print an object of class anova_joint |
| print.can_cor | Print an object of class can_cor |
| print.coincidence | Print an object of class coincidence |
| print.colindiag | Print an object of class colindiag |
| print.corr_coef | Print an object of class corr_coef |
| print.ecovalence | Print an object of class ecovalence |
| print.env_dissimilarity | Print an object of class env_dissimilarity |
| print.env_stratification | Print the env_stratification model |
| print.Fox | Print an object of class Fox |
| print.gamem | Print an object of class gamem |
| print.ge_factanal | Print an object of class ge_factanal |
| print.ge_reg | Print an object of class ge_reg |
| print.ge_stats | Print an object of class ge_stats |
| print.Huehn | Print an object ofclass 'Huehn' |
| print.lpcor | Print the partial correlation coefficients |
| print.mgidi | Print an object of class mgidi Print a 'mgidi' object in two ways. By default, the results are shown in the R console. The results can also be exported to the directory. |
| print.mtmps | Print an object of class mtmps |
| print.mtsi | Print an object of class mtsi |
| print.path_coeff | Print an object of class path_coeff |
| print.performs_ammi | Print an object of class performs_ammi |
| print.Schmildt | Print an object of class Schmildt |
| print.sh | Print an object of class sh |
| print.Shukla | Print an object of class Shukla |
| print.superiority | Print an object ofclass 'superiority' |
| print.Thennarasu | Print an object ofclass 'Thennarasu' |
| print.waas | Print an object of class waas |
| print.waasb | Print an object of class waasb |
| print.waas_means | Print an object of class waas_means |
| progress | Utilities for text progress bar in the terminal |
| prop_na | Utilities for handling with NA and zero values |
| pseudo_sigma | Useful functions for computing descriptive statistics |
-- R --
| random_na | Utilities for handling with NA and zero values |
| range_data | Useful functions for computing descriptive statistics |
| rbind_fill_id | Helper function for binding rows |
| recode_factor | Utilities for data organization |
| remove_class | Utilities for handling with classes |
| remove_cols | Utilities for handling with rows and columns |
| remove_cols_all_na | Utilities for handling with NA and zero values |
| remove_cols_na | Utilities for handling with NA and zero values |
| remove_cols_zero | Utilities for handling with NA and zero values |
| remove_rownames | Utilities for handling with rows and columns |
| remove_rows | Utilities for handling with rows and columns |
| remove_rows_all_na | Utilities for handling with NA and zero values |
| remove_rows_na | Utilities for handling with NA and zero values |
| remove_rows_zero | Utilities for handling with NA and zero values |
| remove_space | Utilities for handling with numbers and strings |
| remove_strings | Utilities for handling with numbers and strings |
| reorder_cols | Utilities for handling with rows and columns |
| reorder_cormat | Reorder a correlation matrix |
| replace_na | Utilities for handling with NA and zero values |
| replace_number | Utilities for handling with numbers and strings |
| replace_string | Utilities for handling with numbers and strings |
| replace_zero | Utilities for handling with NA and zero values |
| resca | Rescale a variable to have specified minimum and maximum values |
| residual_plots | Several types of residual plots |
| resp_surf | Response surface model |
| round_cols | Utilities for handling with numbers and strings |
| rownames_to_column | Utilities for handling with rows and columns |
| row_col_mean | Useful functions for computing descriptive statistics |
| row_col_sum | Useful functions for computing descriptive statistics |
| rpgv | Stability indexes based on a mixed-effect model |
| run_progress | Utilities for text progress bar in the terminal |
-- S --
| sample_random | Random Sampling |
| sample_systematic | Random Sampling |
| Schmildt | Schmildt's genotypic confidence index |
| sd_amo | Useful functions for computing descriptive statistics |
| sd_by | Useful functions for computing descriptive statistics |
| sd_pop | Useful functions for computing descriptive statistics |
| select_cols | Utilities for handling with rows and columns |
| select_cols_na | Utilities for handling with NA and zero values |
| select_cols_zero | Utilities for handling with NA and zero values |
| select_first_col | Utilities for handling with rows and columns |
| Select_helper | Select helper |
| select_last_col | Utilities for handling with rows and columns |
| select_non_numeric_cols | Utilities for handling with rows and columns |
| select_numeric_cols | Utilities for handling with rows and columns |
| select_pred | Selects a best subset of predictor variables. |
| select_rows | Utilities for handling with rows and columns |
| select_rows_na | Utilities for handling with NA and zero values |
| select_rows_zero | Utilities for handling with NA and zero values |
| sel_gen | Get data from a model easily |
| sem | Useful functions for computing descriptive statistics |
| sem_by | Useful functions for computing descriptive statistics |
| set_class | Utilities for handling with classes |
| set_difference | Utilities for set operations for many sets |
| set_intersect | Utilities for set operations for many sets |
| set_union | Utilities for set operations for many sets |
| set_wd_here | Set and get the Working Directory quicky |
| Shukla | Shukla's stability variance parameter |
| skew | Useful functions for computing descriptive statistics |
| Smith_Hazel | Smith-Hazel index |
| solve_svd | Pseudoinverse of a square matrix |
| split_factors | Split a data frame by factors |
| stars_pval | Generate significance stars from p-values |
| sum_by | Useful functions for computing descriptive statistics |
| sum_dev | Useful functions for computing descriptive statistics |
| sum_sq | Useful functions for computing descriptive statistics |
| sum_sq_dev | Useful functions for computing descriptive statistics |
| superiority | Lin e Binns' superiority index |
-- T --
| themes | Personalized theme for ggplot2-based graphics |
| theme_metan | Personalized theme for ggplot2-based graphics |
| theme_metan_minimal | Personalized theme for ggplot2-based graphics |
| Thennarasu | Thennarasu's stability statistics |
| tidy_colnames | Utilities for handling with rows and columns |
| tidy_strings | Utilities for handling with numbers and strings |
| tidy_sym | Utilities for handling with matrices |
| title_case_only | Select helper |
| transparent_color | Personalized theme for ggplot2-based graphics |
| transpose_df | Transpose a data frame |
| tukey_hsd | Tukey Honest Significant Differences |
-- U --
| union_var | Select helper |
| upper_case_only | Select helper |
| utils_as | Encode variables to a specific format |
| utils_bind | Helper function for binding rows |
| utils_class | Utilities for handling with classes |
| utils_data | Utilities for data Copy-Pasta |
| utils_data_org | Utilities for data organization |
| utils_mat | Utilities for handling with matrices |
| utils_na_zero | Utilities for handling with NA and zero values |
| utils_num_str | Utilities for handling with numbers and strings |
| utils_progress | Utilities for text progress bar in the terminal |
| utils_rows_cols | Utilities for handling with rows and columns |
| utils_samples | Random Sampling |
| utils_sets | Utilities for set operations for many sets |
| utils_stats | Useful functions for computing descriptive statistics |
| utils_wd | Set and get the Working Directory quicky |
-- V --
| var_amo | Useful functions for computing descriptive statistics |
| var_by | Useful functions for computing descriptive statistics |
| var_pop | Useful functions for computing descriptive statistics |
| venn_plot | Draw Venn diagrams |
-- W --
| waas | Weighted Average of Absolute Scores |
| waasb | Weighted Average of Absolute Scores |
| waas_means | Weighted Average of Absolute Scores |
| width_greater_than | Select helper |
| width_less_than | Select helper |
| width_of | Select helper |
| wsmp | Weighting between stability and mean performance |