metan v1.2.1

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Multi Environment Trials Analysis

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) <doi:10.2135/cropsci2013.04.0241>, Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, joint Regression Analysis by Eberhart & Russel (1966) (<doi:10.2135/cropsci1966.0011183X000600010011x>), ecovalence by Wricke (1965), genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method <doi:10.12702/1984-7033.v04n01a02>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <https://link.springer.com/article/10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>, geometric adaptability index described by Shahbazi (2019) <doi:10.1016/j.scienta.2019.04.047>. 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.

Functions in metan

Name Description
Thennarasu Thennarasu's stability statistics
Fox Fox's stability function
colindiag Collinearity Diagnostics
cv_ammi Cross-validation procedure
covcor_design Variance-covariance matrices for designed experiments
Huehn Huehn's stability statistics
arrange_ggplot Arrange multiple ggplot2 graphics in a single image window
clustering Clustering analysis
cv_ammif Cross-validation procedure
anova_joint Joint analysis of variance
cv_blup Cross-validation procedure
AMMI_indexes AMMI-based stability indexes
desc_wider Descriptive statistics from long to wide
corr_plot Visualization of a correlation matrix
Shukla Shukla's stability variance parameter
corr_ci Confidence interval for correlation coefficient
Select_helper Select helper
comb_vars Pairwise combinations of variables
desc_stat Descriptive statistics
corr_coef Computes Pearson's correlation matrix with p-values
bind_cv Bind cross-validation objects
can_corr Canonical correlation analysis
data_ge2 Multi-environment trial of maize
ge_factanal Stability analysis and environment stratification
lpcor Linear and Partial Correlation Coefficients
pairs_mantel Mantel test for a set of correlation matrices
is.split_factors Check if an object is of class split_factors
ge_effects Genotype-environment effects
data_ge Multi-environment trial of oat
mtsi Multi-trait stability index
Annicchiarico Annicchiarico's genotypic confidence index
fai_blup Multi-trait selection index
plot.cvalidation Plot the RMSPD of a cross-validation procedure
data_g Single maize trial
as.split_factors Coerce to an object of class split_factors
gai Geometric adaptability index
as.lpcor Coerce to an object of class lpcor
data_alpha Data from an alpha lattice design
corr_stab_ind Correlation between stability indexes
corr_ss Sample size planning for a desired Pearson's correlation confidence interval
ge_means Genotype-environment means
ge_plot Graphical analysis of genotype-vs-environment interaction
plot.env_dissimilarity Plot an object of class env_dissimilarity
gamem Genotype analysis by mixed-effect models
ge_reg Eberhart and Russell's regression model
ge_stats Statistics for genotype-vs-environment interaction
gge Genotype plus genotype-by-environment model
find_outliers Find possible outliers in a dataset
plot.waasb Several types of residual plots
plot_blup Plot the BLUPs for genotypes
plot.wsmp Plot heat maps with genotype ranking
ge_cluster Cluster genotypes or environments
make_mat Make a two-way table
make_sym Make a symmetric matrix on a triangular matrix
gm_mean Geometric mean
plot.clustering Plot an object of class clustering
plot.corr_coef Create a correlation heat map
plot.ge_effects Plot an object of class ge_effects
predict.gge Predict a two-way table based on GGE model
plot.ge_factanal Plot the ge_factanal model
predict.performs_ammi Predict the means of a performs_ammi object
ecovalence Stability analysis based on Wricke's model
ge_details Details for genotype-environment trials
print.Schmildt Print an object of class Schmildt
env_dissimilarity Dissimilarity between environments
ge_winners Genotype-environment winners
mahala Mahalanobis Distance
meansGxE Data for examples
plot.fai_blup Multi-trait selection index
mahala_design Mahalanobis distance from designed experiments
make_upper_tri Make an upper triangular matrix
plot.ge_cluster Plot an object of class ge_cluster
get_model_data Get data from a model easily
plot_ci Plot the confidence interval for correlation
hm_mean Harmonic mean
plot.ge_reg Plot an object of class ge_reg
%>% Pipe operator
make_lower_tri Make a lower triangular matrix
make_long Two-way table to a 'long' format
print.corr_coef Print an object of class corr_coef
print.can_cor Print an object of class can_cor
inspect Check for common erros in multi-environment trial data
plot.gge Create GGE biplots
plot_scores Plot scores in different graphical interpretations
int.effects Data for examples
print.Shukla Print an object of class Shukla
path_coeff Path coefficients with minimal multicollinearity
means_by Means by one or more factors
metan-package Multi-Environment Trial Analysis
performs_ammi Additive Main effects and Multiplicative Interaction
is.lpcor Coerce to an object of class lpcor
print.superiority Print an object ofclass superiority
print.performs_ammi Print an object of class performs_ammi
print.waasb Print an object of class waasb
plot.can_cor Plots an object of class can_cor
plot.mtsi Plot the multi-trait stability index
print.Annicchiarico Print an object of class Annicchiarico
plot_waasby Plot WAASBY values for genotype ranking
plot_eigen Plot the eigenvalues
predict.waas Predict the means of a waas object
print.ge_reg Print an object of class ge_reg
reexports Objects exported from other packages
print.AMMI_indexes Print an object of class AMMI_indexes
plot.performs_ammi Several types of residual plots
plot_factbars Fast way to create a bar plot
print.ge_stats Print an object of class ge_stats
print.gamem Print an object of class gamem
remove_na_values Remove NA values
waas_means Weighted Average of Absolute Scores
waas Weighted Average of Absolute Scores
rbind_fill Combines data.frames by row filling missing values
theme_metan Personalized theme for ggplot2-based graphics
superiority Lin e Binns' superiority index
print.Fox Print an object of class Fox
print.path_coeff Print an object of class path_coeff
print.mtsi Print an object of class mtsi
sem Standard Error of the Mean
resp_surf Response surface model
print.ge_factanal Print an object of class ge_factanal
solve_svd Pseudoinverse of a square matrix
plot.waas Several types of residual plots
plot.resp_surf Plot the response surface model
split_factors Split a data frame by factors
waasb Weighted Average of Absolute Scores
plot_lines Fast way to create a line plot
plot_factlines Fast way to create a line plot
print.anova_ind Print an object of class anova_ind
print.ecovalence Print an object of class ecovalence
print.anova_joint Print an object of class anova_joint
print.waas Print an object of class waas
utils_num_str Utilities for handling with numbers and strings
print.waas_means Print an object of class waas_means
utils_rows_cols Utilities for handling with rows and columns
wsmp Weighting between stability and mean performance
print.env_dissimilarity Print an object of class env_dissimilarity
reorder_cormat Reorder a correlation matrix
tidyeval Tidy eval helpers
resca Rescale a variable to have specified minimum and maximum values
to_factor Encode variables to a factor
Schmildt Schmildt's genotypic confidence index
Resende_indexes Stability indexes based on a mixed-effect model
anova_ind Within-environment analysis of variance
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Vignettes of metan

Name
ammi.RData
cvali.RData
indexes.RData
metan.RData
metanref.bib
plots_corr.RData
validation.png
vignettes_metan.Rmd
wratio.RData
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Details

Type Package
License GPL-3
URL https://github.com/TiagoOlivoto/metan
BugReports https://github.com/TiagoOlivoto/metan/issues
VignetteBuilder knitr
Encoding UTF-8
Language en-US
LazyData true
RoxygenNote 7.0.2
NeedsCompilation no
Packaged 2020-01-10 17:23:25 UTC; tiago
Repository CRAN
Date/Publication 2020-01-14 10:20:02 UTC

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