# Multi Environment Trials Analysis

## Documentation for package ‘metan’ version 1.7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

metan-package | Multi-Environment Trial Analysis

## -- A --

add_class | Utilities for handling with classes
add_cols | Utilities for handling with rows and columns
add_rows | 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 multiple ggplot2 graphics in a single image window
as.lpcor | Coerce to an object of class lpcor
as.split_factors | Split a data frame by factors
av_dev | Useful functions for computing descriptive statistics

## -- B --

barplots | Fast way to create bar plots
bind_cv | Bind cross-validation objects

## -- C --

can_corr | Canonical correlation analysis
ci_mean | 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
comb_vars | Pairwise combinations of variables
concatenate | Utilities for handling with rows and columns
corr_ci | Confidence interval for correlation coefficient
corr_coef | Computes Pearson's correlation matrix with p-values
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
desc_stat | Descriptive statistics
desc_wider | Descriptive statistics
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
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
find_outliers | Find possible outliers in a dataset
find_text_in_num | Utilities for handling with numbers and strings
Fox | Fox's stability function
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_levels | 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
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_reg | Eberhart and Russell's regression model
ge_stats | Statistics for genotype-vs-environment interaction
ge_winners | Genotype-environment winners
gge | Genotype plus genotype-by-environment model
gmd | Get data from a model easily
gmean | Useful functions for computing descriptive statistics
gtb | Genotype by trait biplot

## -- H --

has_class | Utilities for handling with classes
has_na | Utilities for handling with NA values
has_text_in_num | Utilities for handling with numbers and strings
hmean | Useful functions for computing descriptive statistics
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_mat | Make a two-way table
make_sym | Utilities for handling with matrices
make_upper_tri | Utilities for handling with matrices
max_by | Useful functions for computing descriptive statistics
meansGxE | Data for examples
means_by | Useful functions for computing descriptive statistics
mgidi | Genotype-Ideotype Distance Index
min_by | Useful functions for computing descriptive statistics
mtsi | Multi-trait stability index

## -- N --

non_collinear_vars | Select a set of predictors with minimal multicollinearity
n_by | Useful functions for computing descriptive statistics

## -- P --

pairs_mantel | Mantel test for a set of correlation matrices
path_coeff | 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.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.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 biplots
plot.mgidi | Plot the multi-trait genotype-ideotype distance index
plot.mtsi | Plot the multi-trait stability index
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.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.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
pseudo_sigma | Useful functions for computing descriptive statistics

## -- R --

random_na | Utilities for handling with NA values
range_data | Useful functions for computing descriptive statistics
rbind_fill | Combines data.frames by row filling missing values
remove_class | Utilities for handling with classes
remove_cols | Utilities for handling with rows and columns
remove_cols_na | Utilities for handling with NA values
remove_rows | Utilities for handling with rows and columns
remove_rows_na | Utilities for handling with NA 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 values
replace_number | Utilities for handling with numbers and strings
replace_string | Utilities for handling with numbers and strings
resca | Rescale a variable to have specified minimum and maximum values
Resende_indexes | Stability indexes based on a mixed-effect model
residual_plots | Several types of residual plots
resp_surf | Response surface model
round_cols | Utilities for handling with numbers and strings

## -- S --

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 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_rows | Utilities for handling with rows and columns
select_rows_na | Utilities for handling with NA values
sem | Useful functions for computing descriptive statistics
sem_by | Useful functions for computing descriptive statistics
set_class | Utilities for handling with classes
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_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_strings | Utilities for handling with numbers and strings
tidy_sym | Utilities for handling with matrices
title_case_only | Select helper
to_factor | Encode variables to a factor
transparent_color | Personalized theme for ggplot2-based graphics
tukey_hsd | Tukey Honest Significant Differences

## -- U --

union_var | Select helper
upper_case_only | Select helper
utils_class | Utilities for handling with classes
utils_data | Utilities for data Copy-Pasta
utils_mat | Utilities for handling with matrices
utils_na | Utilities for handling with NA values
utils_num_str | Utilities for handling with numbers and strings
utils_rows_cols | Utilities for handling with rows and columns
utils_stats | Useful functions for computing descriptive statistics

## -- V --

valid_n | Useful functions for computing descriptive statistics
var_amo | Useful functions for computing descriptive statistics
var_pop | Useful functions for computing descriptive statistics

## -- 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