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metan (version 1.12.0)

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

1.12.0

License

GPL-3

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Repository

https://github.com/TiagoOlivoto/metan

Maintainer

Tiago Olivoto

Last Published

January 27th, 2021

Functions in metan (1.12.0)

coincidence_index

Computes the coincidence index of genotype selection

Clustering analysis

Smith-Hazel index

Thennarasu's stability statistics

Variance-covariance matrices for designed experiments

Cross-validation procedure

Joint analysis of variance

Cross-validation procedure

Simulate genotype and genotype-environment data

Annicchiarico's genotypic confidence index

AMMI-based stability indexes

Arrange separate ggplots into the same graphic

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

Data from an alpha lattice design

Visualization of a correlation matrix

Multi-trait selection index

Geometric adaptability index

Descriptive statistics

Genotype analysis by fixed-effect models

Single maize trial

Find possible outliers in a dataset

Fast way to create bar plots

Coerce to an object of class lpcor

Shukla's stability variance parameter

Collinearity Diagnostics

Pairwise combinations of variables

Bind cross-validation objects

Canonical correlation analysis

Cross-validation procedure

Details for genotype-environment trials

Graphical analysis of genotype-vs-environment interaction

Fox's stability function

Huehn's stability statistics

Within-environment analysis of variance

Confidence interval for correlation coefficient

Adjusted Coefficient of Variation

Computes Pearson's correlation matrix with p-values

Genotype-environment effects

Generate a covariance matrix

Get a distance matrix

Mahalanobis distance from designed experiments

Correlation between stability indexes

Alternative to dplyr::do for doing anything

Genotype-environment analysis by mixed-effect models

Get data from a model easily

Genotype analysis by mixed-effect models

Adjusted Coefficient of Variation as yield stability index

Stability analysis based on Wricke's model

Genotype plus genotype-by-environment model

Multi-environment trial of oat

Stability analysis and environment stratification

Cluster genotypes or environments

Genotype-environment means

Multi-environment trial of maize

Path coefficients with minimal multicollinearity

Two-way table to a 'long' format

Additive Main effects and Multiplicative Interaction

plot.cvalidation

Plot the RMSPD of a cross-validation procedure

Plot the response surface model

plot.env_dissimilarity

Plot an object of class env_dissimilarity

Coerce to an object of class lpcor

Data for examples

env_stratification

Environment stratification

correlated_vars

Generate correlated variables

env_dissimilarity

Dissimilarity between environments

plot.anova_joint

Several types of residual plots

Make a two-way table

Genotype-environment winners

Genotype by trait biplot

Generate normal, correlated variables

Predict the means of a waas object

Plot the Smith-Hazel index

predict.performs_ammi

Predict the means of a performs_ammi object

Power Law Residuals as yield stability index

impute_missing_val

Missing value imputation

Check for common errors in multi-environment trial data

Data for examples

Genotype by yield*trait biplot

Multi-Environment Trial Analysis

non_collinear_vars

Select a set of predictors with minimal multicollinearity

plot.ge_cluster

Plot an object of class ge_cluster

Mantel test for a set of correlation matrices

plot.env_stratification

Plot the env_stratification model

Plots an object of class can_cor

Fast way to create line plots

is_balanced_trial

Check if a data set is balanced

Multi-trait selection index

plot.clustering

Plot an object of class clustering

Create a correlation heat map

plot.ge_effects

Plot an object of class ge_effects

plot.correlated_vars

Plot an object of class correlated_vars

Several types of residual plots

Several types of residual plots

Print an object of class Fox

Print an object of class ge_reg

print.Annicchiarico

Print an object of class Annicchiarico

print.ge_factanal

Print an object of class ge_factanal

Eberhart and Russell's regression model

Statistics for genotype-vs-environment interaction

Plot the BLUPs for genotypes

Predict method for waasb fits

Plot heat maps with genotype ranking

Plot the multi-trait stability index

Linear and Partial Correlation Coefficients

Mahalanobis Distance

print.AMMI_indexes

Print an object of class AMMI_indexes

Multi-trait stability index

Genotype-Ideotype Distance Index

Several types of residual plots

print.env_dissimilarity

Print an object of class env_dissimilarity

Response surface model

print.path_coeff

Print an object of class path_coeff

print.performs_ammi

Print an object of class performs_ammi

print.ecovalence

Print an object of class ecovalence

Plot the confidence interval for correlation

Plot the eigenvalues

Selects a best subset of predictor variables.

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.

Several types of residual plots

Transpose a data frame

Plot an object of class ge_reg

Predict method for gamem fits

Predict a two-way table based on GGE model

plot.ge_factanal

Plot the ge_factanal model

plot.performs_ammi

Several types of residual plots

Print an object of class can_cor

print.coincidence

Print an object of class coincidence

print.waas_means

Print an object of class waas_means

Print an object of class waas

Print an object of class waasb

Print an object of class Shukla

Print an object of class ge_stats

print.Thennarasu

Print an object ofclass Thennarasu

Print the partial correlation coefficients

Print an object of class mtsi

Create GGE, GT or GYT biplots

Plot WAASBY values for genotype ranking

Plot scores in different graphical interpretations

Print an object ofclass Huehn

Tukey Honest Significant Differences

Pseudoinverse of a square matrix

Several types of residual plots

Rescale a variable to have specified minimum and maximum values

Weighted Average of Absolute Scores

Print an object of class Schmildt

Weighting between stability and mean performance

Generate significance stars from p-values

Plot the multi-trait genotype-ideotype distance index

Combines data.frames by row filling missing values

print.anova_ind

Print an object of class anova_ind

print.env_stratification

Print the env_stratification model

utils_rows_cols

Utilities for handling with rows and columns

Lin e Binns' superiority index

Utilities for set operations for many sets

Split a data frame by factors

print.anova_joint

Print an object of class anova_joint

print.corr_coef

Print an object of class corr_coef

print.superiority

Print an object ofclass superiority

print.colindiag

Print an object of class colindiag

Print an object of class sh

Print an object of class gamem

Personalized theme for ggplot2-based graphics

Useful functions for computing descriptive statistics

Tidy eval helpers

Reorder a correlation matrix

Objects exported from other packages

Encode variables to a specific format

Utilities for handling with numbers and strings

Utilities for handling with NA and zero values

Utilities for handling with matrices

Utilities for data Copy-Pasta

Draw Venn diagrams

Utilities for handling with classes

Weighted Average of Absolute Scores

Weighted Average of Absolute Scores

Resende_indexes

Stability indexes based on a mixed-effect model

Schmildt's genotypic confidence index