Multi Environment Trials Analysis


[Up] [Top]

Documentation for package ‘metan’ version 1.7.0

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