{ "_id": "6a2727f324555f66ed52ba9b", "Type": "Package", "Package": "metan", "Title": "Multi Environment Trials Analysis", "Version": "1.20.0", "Authors@R": "person(\"Tiago\", \"Olivoto\", , \"tiagoolivoto@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-0241-9636\"))", "Maintainer": "Tiago Olivoto ", "Description": "Performs stability analysis of multi-environment trial\ndata using parametric and non-parametric methods. Parametric\nmethods includes Additive Main Effects and Multiplicative\nInteraction (AMMI) analysis by Gauch (2013)\n, Ecovalence by Wricke (1965),\nGenotype plus Genotype-Environment (GGE) biplot analysis by Yan\n& Kang (2003) , geometric\nadaptability index by Mohammadi & Amri (2008)\n, joint regression analysis by\nEberhart & Russel (1966)\n, genotypic\nconfidence index by Annicchiarico (1992), Murakami & Cruz's\n(2004) method, power law residuals (POLAR) statistics by Doring\net al. (2015) , scale-adjusted\ncoefficient of variation by Doring & Reckling (2018)\n, stability variance by Shukla\n(1972) , weighted average of absolute\nscores by Olivoto et al. (2019a)\n, and multi-trait stability\nindex by Olivoto et al. (2019b)\n. Non-parametric methods\nincludes superiority index by Lin & Binns (1988)\n, nonparametric measures of phenotypic\nstability by Huehn (1990) , TOP third\nstatistic by Fox et al. (1990) .\nFunctions for computing biometrical analysis such as path\nanalysis, canonical correlation, partial correlation,\nclustering analysis, and tools for inspecting, manipulating,\nsummarizing and plotting typical multi-environment trial data\nare also provided.", "License": "GPL-3", "URL": "https://github.com/nepem-ufsc/metan,\nhttps://nepem-ufsc.github.io/metan/", "BugReports": "https://github.com/nepem-ufsc/metan/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "LazyLoad": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev make\nlibicu-dev libssl-dev", "Repository": "https://nepem-ufsc.r-universe.dev", "Date/Publication": "2026-06-08 15:49:54 UTC", "RemoteUrl": "https://github.com/nepem-ufsc/metan", "RemoteRef": "HEAD", "RemoteSha": "e8974c60888d9788ec57f5d70b9e68e566c32b2c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-08 20:30:55 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}, { "page": "covcor_design", "title": "Variance-covariance matrices for designed experiments", "topics": [ "covcor_design" ] }, { "page": "cv_ammi", "title": "Cross-validation procedure", "topics": [ "cv_ammi" ] }, { "page": "cv_ammif", "title": "Cross-validation procedure", "topics": [ "cv_ammif" ] }, { "page": "cv_blup", "title": "Cross-validation procedure", "topics": [ "cv_blup" ] }, { "page": "data_alpha", "title": "Data from an alpha lattice design", "topics": [ "data_alpha" ] }, { "page": "data_g", "title": "Single maize trial", "topics": [ "data_g" ] }, { "page": "data_ge", "title": "Multi-environment trial of oat", "topics": [ "data_ge" ] }, { "page": "data_ge2", "title": "Multi-environment trial of maize", "topics": [ "data_ge2" ] }, { "page": "data_simula", "title": "Simulate genotype and genotype-environment data", "topics": [ "data_simula", "ge_simula", "g_simula" ] }, { "page": "desc_stat", "title": "Descriptive statistics", "topics": [ "desc_stat", "desc_wider" ] }, { 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environments", "topics": [ "ge_cluster" ] }, { "page": "ge_details", "title": "Details for genotype-environment trials", "topics": [ "ge_details" ] }, { "page": "ge_effects", "title": "Genotype-environment effects", "topics": [ "ge_effects" ] }, { "page": "ge_factanal", "title": "Stability analysis and environment stratification", "topics": [ "ge_factanal" ] }, { "page": "ge_means", "title": "Genotype-environment means", "topics": [ "ge_means" ] }, { "page": "ge_plot", "title": "Graphical analysis of genotype-vs-environment interaction", "topics": [ "ge_plot" ] }, { "page": "ge_polar", "title": "Power Law Residuals as yield stability index", "topics": [ "ge_polar" ] }, { "page": "ge_stats", "title": "Parametric and non-parametric stability statistics", "topics": [ "ge_stats" ] }, { "page": "ge_winners", "title": "Genotype-environment winners", "topics": [ "ge_winners" ] }, { "page": "get_climate", "title": "Fetch and Process NASA POWER Agro-Climatology API Queries", "topics": [ "get_climate" ] }, { "page": "get_corvars", "title": "Generate normal, correlated variables", "topics": [ "get_corvars" ] }, { "page": "get_covmat", "title": "Generate a covariance matrix", "topics": [ "get_covmat" ] }, { "page": "get_dist", "title": "Get a distance matrix", "topics": [ "get_dist" ] }, { "page": "get_model_data", "title": "Get data from a model easily", "topics": [ "get_model_data", "gmd", "sel_gen" ] }, { "page": "gge", "title": "Genotype plus genotype-by-environment model", "topics": [ "gge" ] }, { "page": "gtb", "title": "Genotype by trait biplot", "topics": [ "gtb" ] }, { "page": "gytb", "title": "Genotype by yield*trait biplot", "topics": [ "gytb" ] }, { "page": "Huehn", "title": "Huehn's stability statistics", "topics": [ "Huehn" ] }, { "page": "impute_missing_val", "title": "Missing value imputation", "topics": [ "impute_missing_val" ] }, { "page": "inspect", "title": "Check for common errors in multi-environment trial data", "topics": [ "inspect" ] }, { "page": "int.effects", "title": "Data for examples", "topics": [ "int.effects" ] }, { "page": "is_balanced_trial", "title": "Check if a data set is balanced", "topics": [ "is_balanced_trial" ] }, { "page": "is.lpcor", "title": "Coerce to an object of class lpcor", "topics": [ "is.lpcor" ] }, { "page": "lin_binns", "title": "Lin e Binns' superiority index", "topics": [ "lin_binns" ] }, { "page": "lineplots", "title": "Fast way to create line plots", "topics": [ "lineplots", "plot_factlines", "plot_lines" ] }, { "page": "lpcor", "title": "Linear and Partial Correlation Coefficients", "topics": [ "lpcor" ] }, { "page": "mahala", "title": "Mahalanobis Distance", "topics": [ "mahala" ] }, { "page": "mahala_design", "title": "Mahalanobis distance from designed experiments", "topics": [ "mahala_design" ] }, { "page": "make_long", "title": "Two-way table to a 'long' format", "topics": [ "make_long" ] }, { "page": "make_mat", "title": "Make a two-way table", "topics": [ "make_mat" ] }, { "page": "mantel_test", "title": "Mantel test", "topics": [ "mantel_test" ] }, { "page": "meansGxE", "title": "Data for examples", "topics": [ "meansGxE" ] }, { "page": "metan", "title": "Multi-Environment Trial Analysis", "topics": [ "metan" ] }, { "page": "mgidi", "title": "Multitrait Genotype-Ideotype Distance Index", "topics": [ "mgidi" ] }, { "page": "mps", "title": "Mean performance and stability in multi-environment trials", "topics": [ "mps" ] }, { "page": "mtmps", "title": "Multi-trait mean performance and stability index", "topics": [ "mtmps" ] }, { "page": "mtsi", "title": "Multi-trait stability index", "topics": [ "mtsi" ] }, { "page": "network_plot", "title": "Network plot of a correlation matrix", "topics": [ "network_plot" ] }, { "page": "non_collinear_vars", "title": "Select a set of predictors with minimal multicollinearity", "topics": [ "non_collinear_vars" ] }, { "page": "pairs_mantel", "title": "Mantel test for a set of correlation matrices", "topics": [ "pairs_mantel" ] }, { "page": "path_coeff", "title": "Path coefficients with minimal multicollinearity", "topics": [ "path_coeff", "path_coeff_mat", "path_coeff_seq" ] }, { "page": "performs_ammi", "title": "Additive Main effects and Multiplicative Interaction", "topics": [ "performs_ammi" ] }, { "page": "plaisted_peterson", "title": "Stability analysis based on Plaisted and Peterson (1959)", "topics": [ "plaisted_peterson" ] }, { "page": "plot_blup", "title": "Plot the BLUPs for genotypes", "topics": [ "plot_blup" ] }, { "page": "plot_ci", "title": "Plot the confidence interval for correlation", "topics": [ "plot_ci" ] }, { "page": "plot_eigen", "title": "Plot the eigenvalues", "topics": [ "plot_eigen" ] }, { "page": "plot_scores", "title": "Plot scores in different graphical interpretations", "topics": [ "plot_scores" ] }, { "page": "plot_waasby", "title": "Plot WAASBY values for genotype ranking", "topics": [ "plot_waasby" ] }, { "page": "plot.anova_joint", "title": "Several types of residual plots", "topics": [ "plot.anova_joint" ] }, { "page": "plot.can_cor", "title": "Plots an object of class can_cor", "topics": [ "plot.can_cor" ] }, { "page": "plot.clustering", "title": "Plot an object of class clustering", "topics": [ "plot.clustering" ] }, { "page": "plot.corr_coef", "title": "Create a correlation heat map", "topics": [ "plot.corr_coef" ] }, { "page": "plot.correlated_vars", "title": "Plot an object of class correlated_vars", "topics": [ "plot.correlated_vars" ] }, { "page": "plot.cvalidation", "title": "Plot the RMSPD of a cross-validation procedure", "topics": [ "plot.cvalidation" ] }, { "page": "plot.eberhart_russell", "title": "Plot an object of class eberhart_russell", "topics": [ "plot.eberhart_russell" ] }, { "page": "plot.env_dissimilarity", "title": "Plot an object of class env_dissimilarity", "topics": [ "plot.env_dissimilarity" ] }, { "page": "plot.env_stratification", "title": "Plot the env_stratification model", "topics": [ "plot.env_stratification" ] }, { "page": "plot.fai_blup", "title": "Multi-trait selection index", "topics": [ "plot.fai_blup" ] }, { "page": "plot.FW", "title": "Plot Method for Finlay-Wilkinson Multi-Trait Objects", "topics": [ "plot.FW" ] }, { "page": "plot.gafem", "title": "Several types of residual plots", "topics": [ "plot.gafem" ] }, { "page": "plot.gamem", "title": "Several types of residual plots", "topics": [ "plot.gamem" ] }, { "page": "plot.ge_cluster", "title": "Plot an object of class ge_cluster", "topics": [ "plot.ge_cluster" ] }, { "page": "plot.ge_effects", "title": "Plot an object of class ge_effects", "topics": [ "plot.ge_effects" ] }, { "page": "plot.ge_factanal", "title": "Plot the ge_factanal model", "topics": [ "plot.ge_factanal" ] }, { "page": "plot.gge", "title": "Create GGE, GT or GYT biplots", "topics": [ "plot.gge" ] }, { "page": "plot.mgidi", "title": "Plot the multi-trait genotype-ideotype distance index", "topics": [ "plot.mgidi" ] }, { "page": "plot.mtmps", "title": "Plot the multi-trait stability index", "topics": [ "plot.mtmps" ] }, { "page": "plot.mtsi", "title": "Plot the multi-trait stability index", "topics": [ "plot.mtsi" ] }, { "page": "plot.path_coeff", "title": "Plots an object of class 'path_coeff'", "topics": [ "plot.path_coeff" ] }, { "page": "plot.performs_ammi", "title": "Several types of residual plots", "topics": [ "plot.performs_ammi" ] }, { "page": "plot.resp_surf", "title": "Plot the response surface model", "topics": [ "plot.resp_surf" ] }, { "page": "plot.sh", "title": "Plot the Smith-Hazel index", "topics": [ "plot.sh" ] }, { "page": "plot.waas", "title": "Several types of residual plots", "topics": [ "plot.waas" ] }, { "page": "plot.waasb", "title": "Several types of residual plots", "topics": [ "plot.waasb" ] }, { "page": "plot.wsmp", "title": "Plot heat maps with genotype ranking", "topics": [ "plot.wsmp" ] }, { "page": "predict.gamem", "title": "Predict method for gamem fits", "topics": [ "predict.gamem" ] }, { "page": "predict.gge", "title": "Predict a two-way table based on GGE model", "topics": [ "predict.gge" ] }, { "page": "predict.performs_ammi", "title": "Predict the means of a performs_ammi object", "topics": [ "predict.performs_ammi" ] }, { "page": "predict.waas", "title": "Predict the means of a waas object", "topics": [ "predict.waas" ] }, { "page": "predict.waasb", "title": "Predict method for waasb fits", "topics": [ "predict.waasb" ] }, { "page": "print.AMMI_indexes", "title": "Print an object of class ammi_indexes", "topics": [ "print.ammi_indexes" ] }, { "page": "print.Annicchiarico", "title": "Print an object of class Annicchiarico", "topics": [ "print.Annicchiarico" ] }, { "page": "print.anova_ind", "title": "Print an object of class anova_ind", "topics": [ "print.anova_ind" ] }, { "page": "print.anova_joint", "title": "Print an object of class anova_joint", "topics": [ "print.anova_joint" ] }, { "page": "print.can_cor", "title": "Print an object of class can_cor", "topics": [ "print.can_cor" ] }, { "page": "print.coincidence", "title": "Print an object of class coincidence", "topics": [ "print.coincidence" ] }, { "page": "print.colindiag", "title": "Print an object of class colindiag", "topics": [ "print.colindiag" ] }, { "page": "print.corr_coef", "title": "Print an object of class corr_coef", "topics": [ "print.corr_coef" ] }, { "page": "print.eberhart_russell", "title": "Print an object of class eberhart_russell", "topics": [ "print.eberhart_russell" ] }, { "page": "print.ecovalence", "title": "Print an object of class ecovalence", "topics": [ "print.ecovalence" ] }, { "page": "print.env_dissimilarity", "title": "Print an object of class env_dissimilarity", "topics": [ "print.env_dissimilarity" ] }, { "page": "print.env_stratification", "title": "Print the env_stratification model", "topics": [ "print.env_stratification" ] }, { "page": "print.Fox", "title": "Print an object of class Fox", "topics": [ "print.Fox" ] }, { "page": "print.gamem", "title": "Print an object of class gamem", "topics": [ "print.gamem" ] }, { "page": "print.ge_factanal", "title": "Print an object of class ge_factanal", "topics": [ "print.ge_factanal" ] }, { "page": "print.ge_stats", "title": "Print an object of class ge_stats", "topics": [ "print.ge_stats" ] }, { "page": "print.Huehn", "title": "Print an object ofclass 'Huehn'", "topics": [ "print.Huehn" ] }, { "page": "print.lin_binns", "title": "Print an object of class 'lin_binns'", "topics": [ "print.lin_binns" ] }, { "page": "print.lpcor", "title": "Print the partial correlation coefficients", "topics": [ "print.lpcor" ] }, { "page": "print.mgidi", "title": "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.", "topics": [ "print.mgidi" ] }, { "page": "print.mtmps", "title": "Print an object of class mtmps", "topics": [ "print.mtmps" ] }, { "page": "print.mtsi", "title": "Print an object of class mtsi", "topics": [ "print.mtsi" ] }, { "page": "print.path_coeff", "title": "Print an object of class path_coeff", "topics": [ "print.path_coeff" ] }, { "page": "print.performs_ammi", "title": "Print an object of class performs_ammi", "topics": [ "print.performs_ammi" ] }, { "page": "print.plaisted_peterson", "title": "Print an object of class plaisted_peterson", "topics": [ "print.plaisted_peterson" ] }, { "page": "print.Schmildt", "title": "Print an object of class Schmildt", "topics": [ "print.Schmildt" ] }, { "page": "print.sh", "title": "Print an object of class sh", "topics": [ "print.sh" ] }, { "page": "print.Shukla", "title": "Print an object of class Shukla", "topics": [ "print.Shukla" ] }, { "page": "print.Thennarasu", "title": "Print an object ofclass 'Thennarasu'", "topics": [ "print.Thennarasu" ] }, { "page": "print.waas", "title": "Print an object of class waas", "topics": [ "print.waas" ] }, { "page": "print.waas_means", "title": "Print an object of class waas_means", "topics": [ "print.waas_means" ] }, { "page": "print.waasb", "title": "Print an object of class waasb", "topics": [ "print.waasb" ] }, { "page": "reorder_cormat", "title": "Reorder a correlation matrix", "topics": [ "reorder_cormat" ] }, { "page": "resca", "title": "Rescale a variable to have specified minimum and maximum values", "topics": [ "resca" ] }, { "page": "residual_plots", "title": "Several types of residual plots", "topics": [ "residual_plots" ] }, { "page": "resp_surf", "title": "Response surface model", "topics": [ "resp_surf" ] }, { "page": "Schmildt", "title": "Schmildt's genotypic confidence index", "topics": [ "Schmildt" ] }, { "page": "Select_helper", "title": "Select helper", "topics": [ "difference_var", "intersect_var", "lower_case_only", "Select_helper", "title_case_only", "union_var", "upper_case_only", "width_greater_than", "width_less_than", "width_of" ] }, { "page": "select_pred", "title": "Selects a best subset of predictor variables.", "topics": [ "select_pred" ] }, { "page": "Shukla", "title": "Shukla's stability variance parameter", "topics": [ "Shukla" ] }, { "page": "Smith_Hazel", "title": "Smith-Hazel index", "topics": [ "Smith_Hazel" ] }, { "page": "solve_svd", "title": "Pseudoinverse of a square matrix", "topics": [ "solve_svd" ] }, { "page": "split_factors", "title": "Split a data frame by factors", "topics": [ "as.split_factors", "is.split_factors", "split_factors" ] }, { "page": "stars_pval", "title": "Generate significance stars from p-values", "topics": [ "stars_pval" ] }, { "page": "themes", "title": "Personalized theme for ggplot2-based graphics", "topics": [ "alpha_color", "ggplot_color", "themes", "theme_metan", "theme_metan_minimal", "transparent_color" ] }, { "page": "Thennarasu", "title": "Thennarasu's stability statistics", "topics": [ "Thennarasu" ] }, { "page": "transpose_df", "title": "Transpose a data frame", "topics": [ "transpose_df" ] }, { "page": "tukey_hsd", "title": "Tukey Honest Significant Differences", "topics": [ "tukey_hsd" ] }, { "page": "utils_as", "title": "Encode variables to a specific format", "topics": [ "as_character", "as_factor", "as_integer", "as_logical", "as_numeric", "utils_as" ] }, { "page": "utils_bind", "title": "Helper function for binding rows", "topics": [ "rbind_fill_id", "utils_bind" ] }, { "page": "utils_class", "title": "Utilities for handling with classes", "topics": [ "add_class", "has_class", "remove_class", "set_class", "utils_class" ] }, { "page": "utils_data", "title": "Utilities for data Copy-Pasta", "topics": [ "clip_read", "clip_write", "utils_data" ] }, { "page": "utils_data_org", "title": "Utilities for data organization", "topics": [ "add_seq_block", "df_to_selegen_54", "recode_factor", 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