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metan (version 1.16.0)

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.

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Install

install.packages('metan')

Monthly Downloads

3,082

Version

1.16.0

License

GPL-3

Issues

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Repository

https://github.com/TiagoOlivoto/metan

Maintainer

Tiago Olivoto

Last Published

November 10th, 2021

Functions in metan (1.16.0)

Smith-Hazel index

Within-environment analysis of variance

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

Cross-validation procedure

Joint analysis of variance

Cross-validation procedure

Visualization of a correlation matrix

Schmildt's genotypic confidence index

Huehn's stability statistics

Clustering analysis

Adjusted Coefficient of Variation as yield stability index

coincidence_index

Computes the coincidence index of genotype selection

Cluster genotypes or environments

Stability indexes based on a mixed-effect model

Shukla's stability variance parameter

Confidence interval for correlation coefficient

is_balanced_trial

Check if a data set is balanced

Stability analysis and environment stratification

Genotype-environment means

Collinearity Diagnostics

Pairwise combinations of variables

Canonical correlation analysis

Computes Pearson's correlation matrix with p-values

Correlation between stability indexes

Multi-trait selection index

correlated_vars

Generate correlated variables

Fast way to create line plots

Create a correlation heat map

Multitrait Genotype-Ideotype Distance Index

plot.correlated_vars

Plot an object of class correlated_vars

Mean performance and stability in multi-environment trials

AMMI-based stability indexes

Find possible outliers in a dataset

Adjusted Coefficient of Variation

Check for common errors in multi-environment trial data

impute_missing_val

Missing value imputation

Data from an alpha lattice design

Genotype-environment winners

Multi-environment trial of maize

Multi-environment trial of oat

Single maize trial

Plot the multi-trait stability index

Descriptive statistics

Coerce to an object of class lpcor

Fox's stability function

Annicchiarico's genotypic confidence index

Arrange separate ggplots into the same graphic

Simulate genotype and genotype-environment data

Data for examples

Plot the multi-trait stability index

Fast way to create bar plots

Genotype analysis by mixed-effect models

Multi-Environment Trial Analysis

Genotype by trait biplot

Generate normal, correlated variables

Genotype by yield*trait biplot

Predict method for gamem fits

Plot WAASBY values for genotype ranking

Print an object ofclass Huehn

Make a two-way table

Genotype-environment analysis by mixed-effect models

Genotype analysis by fixed-effect models

Multi-trait mean performance and stability index

Geometric adaptability index

Graphical analysis of genotype-vs-environment interaction

Parametric and non-parametric stability statistics

Eberhart and Russell's regression model

Data for examples

Bind cross-validation objects

Coerce to an object of class lpcor

Multi-trait stability index

Variance-covariance matrices for designed experiments

Cross-validation procedure

Alternative to dplyr::do for doing anything

plot.anova_joint

Several types of residual plots

Power Law Residuals as yield stability index

print.anova_ind

Print an object of class anova_ind

Print an object of class Schmildt

print.ammi_indexes

Print an object of class ammi_indexes

Stability analysis based on Wricke's model

Print an object of class gamem

env_dissimilarity

Dissimilarity between environments

Genotype plus genotype-by-environment model

Get data from a model easily

Linear and Partial Correlation Coefficients

non_collinear_vars

Select a set of predictors with minimal multicollinearity

Mantel test for a set of correlation matrices

Plot the response surface model

Plots an object of class can_cor

plot.clustering

Plot an object of class clustering

plot.performs_ammi

Several types of residual plots

Mahalanobis Distance

Details for genotype-environment trials

env_stratification

Environment stratification

Genotype-environment effects

Generate a covariance matrix

Plot the eigenvalues

Get a distance matrix

print.ge_factanal

Print an object of class ge_factanal

Print an object of class waas

print.waas_means

Print an object of class waas_means

Plot scores in different graphical interpretations

plot.cvalidation

Plot the RMSPD of a cross-validation procedure

Utilities for text progress bar in the terminal

Utilities for handling with numbers and strings

print.Annicchiarico

Print an object of class Annicchiarico

Mahalanobis distance from designed experiments

print.anova_joint

Print an object of class anova_joint

Several types of residual plots

Several types of residual plots

Several types of residual plots

Print an object of class Fox

Plot an object of class ge_reg

plot.env_dissimilarity

Plot an object of class env_dissimilarity

plot.ge_factanal

Plot the ge_factanal model

Print the partial correlation coefficients

Plot heat maps with genotype ranking

Print an object of class can_cor

Print an object of class mtmps

Print an object of class mtsi

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.

Draw Venn diagrams

Transpose a data frame

Useful functions for computing descriptive statistics

Tidy eval helpers

Two-way table to a 'long' format

Additive Main effects and Multiplicative Interaction

Multi-trait selection index

plot.env_stratification

Plot the env_stratification model

Path coefficients with minimal multicollinearity

Print an object of class waasb

Objects exported from other packages

Create GGE, GT or GYT biplots

Plot the multi-trait genotype-ideotype distance index

Split a data frame by factors

Plot the confidence interval for correlation

Plot the BLUPs for genotypes

Generate significance stars from p-values

plot.ge_cluster

Plot an object of class ge_cluster

plot.ge_effects

Plot an object of class ge_effects

Plot the Smith-Hazel index

print.Thennarasu

Print an object ofclass Thennarasu

Print an object of class Shukla

Several types of residual plots

Predict the means of a waas object

Helper function for binding rows

Predict a two-way table based on GGE model

predict.performs_ammi

Predict the means of a performs_ammi object

print.coincidence

Print an object of class coincidence

Predict method for waasb fits

print.env_dissimilarity

Print an object of class env_dissimilarity

Print an object of class sh

print.colindiag

Print an object of class colindiag

print.ecovalence

Print an object of class ecovalence

print.corr_coef

Print an object of class corr_coef

Weighted Average of Absolute Scores

Utilities for handling with classes

Weighting between stability and mean performance

print.env_stratification

Print the env_stratification model

Print an object of class ge_reg

print.superiority

Print an object ofclass superiority

Lin e Binns' superiority index

Personalized theme for ggplot2-based graphics

Several types of residual plots

Print an object of class ge_stats

Response surface model

Utilities for data Copy-Pasta

Selects a best subset of predictor variables.

Utilities for data organization

Weighted Average of Absolute Scores

print.path_coeff

Print an object of class path_coeff

print.performs_ammi

Print an object of class performs_ammi

Weighted Average of Absolute Scores

Pseudoinverse of a square matrix

Reorder a correlation matrix

Rescale a variable to have specified minimum and maximum values

Utilities for handling with matrices

Utilities for handling with NA and zero values

Tukey Honest Significant Differences

Encode variables to a specific format

utils_rows_cols

Utilities for handling with rows and columns

Utilities for set operations for many sets

Thennarasu's stability statistics