Learn R Programming

⚠️There's a newer version (1.19.0) of this package.Take me there.

metan (version 1.17.0)

Multi Environment Trials Analysis

Description

Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) , Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) , geometric adaptability index by Mohammadi & Amri (2008) , joint regression analysis by Eberhart & Russel (1966) , genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) , scale-adjusted coefficient of variation by Doring & Reckling (2018) , stability variance by Shukla (1972) , weighted average of absolute scores by Olivoto et al. (2019a) , and multi-trait stability index by Olivoto et al. (2019b) . Non-parametric methods includes superiority index by Lin & Binns (1988) , nonparametric measures of phenotypic stability by Huehn (1990) , TOP third statistic by Fox et al. (1990) . Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.

Copy Link

Version

Install

install.packages('metan')

Monthly Downloads

2,686

Version

1.17.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/TiagoOlivoto/metan

Maintainer

Tiago Olivoto

Last Published

June 10th, 2022

Functions in metan (1.17.0)

Adjusted Coefficient of Variation

Smith-Hazel index

Shukla's stability variance parameter

Thennarasu's stability statistics

AMMI-based stability indexes

Schmildt's genotypic confidence index

Annicchiarico's genotypic confidence index

Huehn's stability statistics

Fox's stability function

Arrange separate ggplots into the same graphic

Joint analysis of variance

Within-environment analysis of variance

Fast way to create bar plots

Bind cross-validation objects

Coerce to an object of class lpcor

Correlation between stability indexes

correlated_vars

Generate correlated variables

Pairwise combinations of variables

Collinearity Diagnostics

Visualization of a correlation matrix

Sample size planning for a desired Pearson's correlation confidence interval

Computes Pearson's correlation matrix with p-values

Confidence interval for correlation coefficient

Alternative to dplyr::do for doing anything

Stability analysis based on Wricke's model

Canonical correlation analysis

Stability indexes based on a mixed-effect model

Variance-covariance matrices for designed experiments

Single maize trial

Cross-validation procedure

Adjusted Coefficient of Variation as yield stability index

Data from an alpha lattice design

Simulate genotype and genotype-environment data

Descriptive statistics

Clustering analysis

Cluster genotypes or environments

Cross-validation procedure

coincidence_index

Computes the coincidence index of genotype selection

Find possible outliers in a dataset

Multi-trait selection index

Cross-validation procedure

Eberhart and Russell's regression model

Genotype analysis by fixed-effect models

Genotype-environment winners

Geometric adaptability index

Stability analysis and environment stratification

env_dissimilarity

Dissimilarity between environments

Generate normal, correlated variables

is_balanced_trial

Check if a data set is balanced

Coerce to an object of class lpcor

Data for examples

Multi-environment trial of maize

Multi-environment trial of oat

Parametric and non-parametric stability statistics

Details for genotype-environment trials

env_stratification

Environment stratification

Genotype-environment effects

Genotype-environment means

Linear and Partial Correlation Coefficients

impute_missing_val

Missing value imputation

Check for common errors in multi-environment trial data

Genotype by yield*trait biplot

Genotype by trait biplot

Data for examples

Fast way to create line plots

plot.anova_joint

Several types of residual plots

Mahalanobis Distance

Get data from a model easily

Generate a covariance matrix

Power Law Residuals as yield stability index

Genotype analysis by mixed-effect models

Genotype-environment analysis by mixed-effect models

Graphical analysis of genotype-vs-environment interaction

Make a two-way table

Multi-Environment Trial Analysis

Plots an object of class can_cor

Genotype plus genotype-by-environment model

Get a distance matrix

Plot the multi-trait stability index

Additive Main effects and Multiplicative Interaction

plot.cvalidation

Plot the RMSPD of a cross-validation procedure

Path coefficients with minimal multicollinearity

plot.clustering

Plot an object of class clustering

Mahalanobis distance from designed experiments

plot.ge_factanal

Plot the ge_factanal model

Plot an object of class ge_reg

Plot the multi-trait stability index

print.env_dissimilarity

Print an object of class env_dissimilarity

Print an object of class ge_stats

print.ecovalence

Print an object of class ecovalence

Plot heat maps with genotype ranking

Plot the BLUPs for genotypes

plot.path_coeff

Plots an object of class path_coeff

plot.env_dissimilarity

Plot an object of class env_dissimilarity

Multi-trait mean performance and stability index

Print the partial correlation coefficients

Print an object of class Fox

plot.performs_ammi

Several types of residual plots

print.anova_ind

Print an object of class anova_ind

Print an object of class mtsi

Print an object ofclass Huehn

print.anova_joint

Print an object of class anova_joint

Plot scores in different graphical interpretations

Print an object of class waas

Generate significance stars from p-values

Split a data frame by factors

print.superiority

Print an object ofclass superiority

Utilities for data Copy-Pasta

Two-way table to a 'long' format

Multitrait Genotype-Ideotype Distance Index

Utilities for data organization

Weighted Average of Absolute Scores

Weighting between stability and mean performance

print.Thennarasu

Print an object ofclass Thennarasu

Mean performance and stability in multi-environment trials

Plot WAASBY values for genotype ranking

Predict method for waasb fits

print.Annicchiarico

Print an object of class Annicchiarico

Multi-trait stability index

non_collinear_vars

Select a set of predictors with minimal multicollinearity

Several types of residual plots

Mantel test for a set of correlation matrices

Several types of residual plots

Create a correlation heat map

print.path_coeff

Print an object of class path_coeff

print.waas_means

Print an object of class waas_means

Tidy eval helpers

Print an object of class waasb

Transpose a data frame

Tukey Honest Significant Differences

plot.correlated_vars

Plot an object of class correlated_vars

Objects exported from other packages

print.ammi_indexes

Print an object of class ammi_indexes

Reorder a correlation matrix

plot.ge_cluster

Plot an object of class ge_cluster

Encode variables to a specific format

Plot the confidence interval for correlation

plot.ge_effects

Plot an object of class ge_effects

predict.performs_ammi

Predict the means of a performs_ammi object

Plot the eigenvalues

Predict the means of a waas object

print.corr_coef

Print an object of class corr_coef

print.colindiag

Print an object of class colindiag

print.env_stratification

Print the env_stratification model

Print an object of class gamem

Several types of residual plots

Several types of residual plots

Several types of residual plots

Pseudoinverse of a square matrix

Set the Working Directory quicky

Rescale a variable to have specified minimum and maximum values

Selects a best subset of predictor variables.

Utilities for handling with numbers and strings

Response surface model

utils_rows_cols

Utilities for handling with rows and columns

Utilities for text progress bar in the terminal

Utilities for set operations for many sets

plot.env_stratification

Plot the env_stratification model

Utilities for handling with matrices

Utilities for handling with NA and zero values

Multi-trait selection index

Predict method for gamem fits

Print an object of class can_cor

print.ge_factanal

Print an object of class ge_factanal

Predict a two-way table based on GGE model

print.coincidence

Print an object of class coincidence

Plot the multi-trait genotype-ideotype distance index

Create GGE, GT or GYT biplots

Plot the response surface model

Plot the Smith-Hazel index

Print an object of class Shukla

Print an object of class Schmildt

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 an object of class mtmps

Print an object of class ge_reg

print.performs_ammi

Print an object of class performs_ammi

Helper function for binding rows

Utilities for handling with classes

Draw Venn diagrams

Useful functions for computing descriptive statistics

Weighted Average of Absolute Scores

Lin e Binns' superiority index

Print an object of class sh

Personalized theme for ggplot2-based graphics

Weighted Average of Absolute Scores