R: Multi Environment Trials Analysis

# Multi Environment Trials Analysis

## Documentation for package ‘metan’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H I K L M N O P R S T U V W

## -- 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
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
metan | Multi-Environment Trial Analysis
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
plaisted_peterson | Stability analysis based on Plaisted and Peterson (1959)
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.plaisted_peterson | Print an object of class plaisted_peterson
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