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metan (version 1.7.0)

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) , Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) , joint Regression Analysis by Eberhart & Russel (1966) (), ecovalence by Wricke (1965), genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method , 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) , geometric adaptability index described by Shahbazi (2019) . 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

1.7.0

License

GPL-3

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Repository

https://github.com/TiagoOlivoto/metan

Maintainer

Tiago Olivoto

Last Published

July 18th, 2020

Functions in metan (1.7.0)

Annicchiarico's genotypic confidence index

Schmildt's genotypic confidence index

Smith-Hazel index

Shukla's stability variance parameter

AMMI-based stability indexes

Resende_indexes

Stability indexes based on a mixed-effect model

Thennarasu's stability statistics

Fox's stability function

Huehn's stability statistics

coincidence_index

Computes the coincidence index of genotype selection

Arrange multiple ggplot2 graphics in a single image window

Descriptive statistics

Pairwise combinations of variables

Joint analysis of variance

Single maize trial

Confidence interval for correlation coefficient

Collinearity Diagnostics

Within-environment analysis of variance

Data from an alpha lattice design

Fast way to create bar plots

Coerce to an object of class lpcor

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

Cross-validation procedure

Multi-environment trial of oat

Bind cross-validation objects

Cross-validation procedure

Correlation between stability indexes

Multi-environment trial of maize

Cluster genotypes or environments

Clustering analysis

Canonical correlation analysis

Genotype-environment winners

Alternative to dplyr::do for doing anything

Details for genotype-environment trials

Get data from a model easily

Genotype analysis by fixed-effect models

Genotype plus genotype-by-environment model

Genotype-environment means

Genotype by trait biplot

Computes Pearson's correlation matrix with p-values

Variance-covariance matrices for designed experiments

Cross-validation procedure

Data for examples

Coerce to an object of class lpcor

Graphical analysis of genotype-vs-environment interaction

Multi-trait selection index

Visualization of a correlation matrix

Stability analysis based on Wricke's model

Find possible outliers in a dataset

Genotype-environment effects

Mahalanobis distance from designed experiments

Eberhart and Russell's regression model

Stability analysis and environment stratification

Geometric adaptability index

Genotype analysis by mixed-effect models

env_dissimilarity

Dissimilarity between environments

Two-way table to a 'long' format

Data for examples

plot.anova_joint

Several types of residual plots

Make a two-way table

Plots an object of class can_cor

Genotype-environment analysis by mixed-effect models

is_balanced_trial

Check if a data set is balanced

Statistics for genotype-vs-environment interaction

Fast way to create line plots

Check for common errors in multi-environment trial data

Genotype-Ideotype Distance Index

Multi-Environment Trial Analysis

impute_missing_val

Missing value imputation

Mantel test for a set of correlation matrices

plot.clustering

Plot an object of class clustering

Multi-trait stability index

Create a correlation heat map

Linear and Partial Correlation Coefficients

Additive Main effects and Multiplicative Interaction

Mahalanobis Distance

plot.cvalidation

Plot the RMSPD of a cross-validation procedure

Several types of residual plots

plot.env_dissimilarity

Plot an object of class env_dissimilarity

Plot the Smith-Hazel index

Multi-trait selection index

Plot the multi-trait genotype-ideotype distance index

Path coefficients with minimal multicollinearity

Several types of residual plots

Plot the response surface model

plot.performs_ammi

Several types of residual plots

plot.ge_effects

Plot an object of class ge_effects

Plot WAASBY values for genotype ranking

Plot the BLUPs for genotypes

plot.ge_factanal

Plot the ge_factanal model

Plot the confidence interval for correlation

Predict method for gamem fits

Predict a two-way table based on GGE model

Several types of residual plots

Plot the multi-trait stability index

Plot the eigenvalues

print.Thennarasu

Print an object ofclass Thennarasu

Predict the means of a waas object

print.anova_ind

Print an object of class anova_ind

Predict method for waasb fits

plot.ge_cluster

Plot an object of class ge_cluster

non_collinear_vars

Select a set of predictors with minimal multicollinearity

Plot an object of class ge_reg

Print an object of class Shukla

Print an object of class Schmildt

print.corr_coef

Print an object of class corr_coef

Plot heat maps with genotype ranking

Several types of residual plots

print.AMMI_indexes

Print an object of class AMMI_indexes

Print an object of class gamem

print.env_dissimilarity

Print an object of class env_dissimilarity

print.ecovalence

Print an object of class ecovalence

predict.performs_ammi

Predict the means of a performs_ammi object

print.Annicchiarico

Print an object of class Annicchiarico

Plot scores in different graphical interpretations

Print an object of class Fox

Objects exported from other packages

Print an object ofclass Huehn

Reorder a correlation matrix

print.path_coeff

Print an object of class path_coeff

Print an object of class can_cor

print.anova_joint

Print an object of class anova_joint

Split a data frame by factors

Combines data.frames by row filling missing values

Print an object of class waasb

Print an object of class ge_stats

Generate significance stars from p-values

utils_rows_cols

Utilities for handling with rows and columns

print.colindiag

Print an object of class colindiag

Print an object of class ge_reg

Create GGE biplots

print.ge_factanal

Print an object of class ge_factanal

print.coincidence

Print an object of class coincidence

print.performs_ammi

Print an object of class performs_ammi

Print the partial correlation coefficients

Weighted Average of Absolute Scores

Encode variables to a factor

Tidy eval helpers

Print an object of class sh

Useful functions for computing descriptive statistics

print.superiority

Print an object ofclass superiority

Several types of residual plots

Rescale a variable to have specified minimum and maximum values

Utilities for data Copy-Pasta

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 mtsi

Utilities for handling with matrices

Weighted Average of Absolute Scores

Lin e Binns' superiority index

Personalized theme for ggplot2-based graphics

Utilities for handling with NA values

Utilities for handling with numbers and strings

Weighted Average of Absolute Scores

Weighting between stability and mean performance

Print an object of class waas

print.waas_means

Print an object of class waas_means

Response surface model

Pseudoinverse of a square matrix

Tukey Honest Significant Differences

Utilities for handling with classes