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metan (version 1.10.0)

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

3,307

Version

1.10.0

License

GPL-3

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Repository

https://github.com/TiagoOlivoto/metan

Maintainer

Tiago Olivoto

Last Published

October 24th, 2020

Functions in metan (1.10.0)

Schmildt's genotypic confidence index

Shukla's stability variance parameter

Smith-Hazel index

Huehn's stability statistics

AMMI-based stability indexes

Resende_indexes

Stability indexes based on a mixed-effect model

Thennarasu's stability statistics

Fox's stability function

Joint analysis of variance

Bind cross-validation objects

Arrange multiple ggplot2 graphics in a single image window

Annicchiarico's genotypic confidence index

Clustering analysis

coincidence_index

Computes the coincidence index of genotype selection

correlated_vars

Generate correlated variables

Correlation between stability indexes

Stability analysis based on Wricke's model

Collinearity Diagnostics

Canonical correlation analysis

Pairwise combinations of variables

env_dissimilarity

Dissimilarity between environments

Within-environment analysis of variance

Adjusted Coefficient of Variation

Multi-environment trial of oat

Graphical analysis of genotype-vs-environment interaction

Multi-environment trial of maize

Genotype-environment means

Fast way to create bar plots

Coerce to an object of class lpcor

Visualization of a correlation matrix

Coerce to an object of class lpcor

Descriptive statistics

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

Variance-covariance matrices for designed experiments

Cluster genotypes or environments

Geometric adaptability index

Alternative to dplyr::do for doing anything

Genotype analysis by mixed-effect models

is_balanced_trial

Check if a data set is balanced

Make a two-way table

Two-way table to a 'long' format

Details for genotype-environment trials

Get a distance matrix

Get data from a model easily

Plots an object of class can_cor

plot.anova_joint

Several types of residual plots

Fast way to create line plots

Cross-validation procedure

Genotype analysis by fixed-effect models

Find possible outliers in a dataset

env_stratification

Environment stratification

Cross-validation procedure

Cross-validation procedure

Statistics for genotype-vs-environment interaction

Genotype-environment winners

Computes Pearson's correlation matrix with p-values

Confidence interval for correlation coefficient

Multi-trait selection index

Data for examples

Genotype-environment effects

Stability analysis and environment stratification

Data from an alpha lattice design

Single maize trial

impute_missing_val

Missing value imputation

Genotype by yield*trait biplot

Power Law Residuals as yield stability index

Eberhart and Russell's regression model

Genotype-Ideotype Distance Index

Multi-Environment Trial Analysis

Check for common errors in multi-environment trial data

Mantel test for a set of correlation matrices

Linear and Partial Correlation Coefficients

Multi-trait stability index

Genotype-environment analysis by mixed-effect models

Adjusted Coefficient of Variation as yield stability index

Path coefficients with minimal multicollinearity

Generate normal, correlated variables

Generate a covariance matrix

Genotype by trait biplot

Several types of residual plots

Genotype plus genotype-by-environment model

plot.ge_cluster

Plot an object of class ge_cluster

Additive Main effects and Multiplicative Interaction

Plot the Smith-Hazel index

Several types of residual plots

Data for examples

plot.env_dissimilarity

Plot an object of class env_dissimilarity

Several types of residual plots

Plot the confidence interval for correlation

Multi-trait selection index

Plot the BLUPs for genotypes

Mahalanobis Distance

Mahalanobis distance from designed experiments

Create a correlation heat map

plot.clustering

Plot an object of class clustering

plot.correlated_vars

Plot an object of class correlated_vars

plot.cvalidation

Plot the RMSPD of a cross-validation procedure

plot.env_stratification

Plot the env_stratification model

Predict the means of a waas object

Plot the multi-trait genotype-ideotype distance index

non_collinear_vars

Select a set of predictors with minimal multicollinearity

plot.ge_factanal

Plot the ge_factanal model

Plot an object of class ge_reg

plot.ge_effects

Plot an object of class ge_effects

plot.performs_ammi

Several types of residual plots

Several types of residual plots

print.Thennarasu

Print an object ofclass Thennarasu

print.anova_ind

Print an object of class anova_ind

Plot the response surface model

Plot WAASBY values for genotype ranking

Predict method for gamem fits

print.Annicchiarico

Print an object of class Annicchiarico

print.AMMI_indexes

Print an object of class AMMI_indexes

Create GGE, GT or GYT biplots

Predict method for waasb fits

Print an object of class ge_reg

Print an object of class gamem

print.anova_joint

Print an object of class anova_joint

print.corr_coef

Print an object of class corr_coef

Print an object of class can_cor

print.ecovalence

Print an object of class ecovalence

Print an object of class ge_stats

print.superiority

Print an object ofclass superiority

print.performs_ammi

Print an object of class performs_ammi

print.colindiag

Print an object of class colindiag

print.coincidence

Print an object of class coincidence

Print an object of class waas

Plot the multi-trait stability index

Print the partial correlation coefficients

Print an object of class sh

Print an object of class mtsi

print.path_coeff

Print an object of class path_coeff

print.ge_factanal

Print an object of class ge_factanal

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.

Predict a two-way table based on GGE model

predict.performs_ammi

Predict the means of a performs_ammi object

Plot heat maps with genotype ranking

Several types of residual plots

Plot scores in different graphical interpretations

Plot the eigenvalues

Split a data frame by factors

Pseudoinverse of a square matrix

Utilities for data Copy-Pasta

Selects a best subset of predictor variables.

Utilities for handling with classes

Generate significance stars from p-values

Response surface model

Print an object of class Schmildt

Print an object of class Shukla

Rescale a variable to have specified minimum and maximum values

Tukey Honest Significant Differences

Reorder a correlation matrix

Utilities for handling with NA and zero values

Utilities for handling with matrices

Encode variables to a specific format

Print an object of class waasb

Combines data.frames by row filling missing values

print.env_stratification

Print the env_stratification model

Print an object ofclass Huehn

print.waas_means

Print an object of class waas_means

Print an object of class Fox

print.env_dissimilarity

Print an object of class env_dissimilarity

utils_rows_cols

Utilities for handling with rows and columns

Utilities for handling with numbers and strings

Lin e Binns' superiority index

Useful functions for computing descriptive statistics

Objects exported from other packages

Tidy eval helpers

Weighted Average of Absolute Scores

Personalized theme for ggplot2-based graphics

Weighting between stability and mean performance

Weighted Average of Absolute Scores

Weighted Average of Absolute Scores

Transpose a data frame