One-way analysisAnalyze genotypes in single environment trials using fixed- or mixed-effect models |
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Genotype analysis by fixed-effect models |
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Genotype analysis by mixed-effect models |
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Several types of residual plots |
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Several types of residual plots |
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Predict method for gamem fits |
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Print an object of class gamem |
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AMMIFunctions for AMMI analysis |
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Cross-validation |
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Cross-validation procedure |
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Cross-validation procedure |
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Fit models |
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AMMI-based stability indexes |
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Missing value imputation |
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Additive Main effects and Multiplicative Interaction |
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Weighted Average of Absolute Scores |
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Weighted Average of Absolute Scores |
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Plot models |
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Plot the RMSPD of a cross-validation procedure |
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Several types of residual plots |
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Several types of residual plots |
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Predict models |
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Predict the means of a waas object |
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Predict the means of a performs_ammi object |
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Print models |
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Print an object of class AMMI_indexes |
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Print an object of class performs_ammi |
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Print an object of class waas |
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Print an object of class waas_means |
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BLUPAnalyze genotypes in single- or multi-environment trials using mixed-effect models with variance components and genetic parameter estimation. |
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Cross-validation procedure |
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Fit models |
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Genotype-environment analysis by mixed-effect models |
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Stability indexes based on a mixed-effect model |
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Weighted Average of Absolute Scores |
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Weighting between stability and mean performance |
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Plot models |
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Plot the BLUPs for genotypes |
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Plot the eigenvalues |
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Plot scores in different graphical interpretations |
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Plot WAASBY values for genotype ranking |
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Plot heat maps with genotype ranking |
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Several types of residual plots |
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Predict models |
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Predict method for waasb fits |
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Print models |
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Print an object of class waasb |
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GGEFunctions for GGE, GT, and GYT biplot analysis |
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Genotype plus genotype-by-environment model |
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Genotype by trait biplot |
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Genotype by yield*trait biplot |
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Create GGE, GT or GYT biplots |
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Predict a two-way table based on GGE model |
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Selection indexesIndexes for simultaneous selection for mean performance and stability |
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Computes the coincidence index of genotype selection |
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Multi-trait selection index |
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Multi-trait stability index |
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Genotype-Ideotype Distance Index |
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Multi-trait selection index |
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Plot the multi-trait genotype-ideotype distance index |
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Print an object of class mgidi
Print a |
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Plot the multi-trait stability index |
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Plot the Smith-Hazel index |
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Print an object of class coincidence |
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Print an object of class mtsi |
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Print an object of class sh |
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Smith-Hazel index |
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Genotype-environment interactionVisualize genotype-environment interaction patterns, rank genotypes within environments, compute genotype, environment, and genotype-environment effects; cluster environments, and compute parametric and non-parametric stability indexes |
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Initial approaches |
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Within-environment analysis of variance |
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Joint analysis of variance |
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Cluster genotypes or environments |
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Details for genotype-environment trials |
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Genotype-environment effects |
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Genotype-environment means |
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Graphical analysis of genotype-vs-environment interaction |
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Genotype-environment winners |
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Check if a data set is balanced |
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Parametric methods |
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Annicchiarico's genotypic confidence index |
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Correlation between stability indexes |
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Stability analysis based on Wricke's model |
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Dissimilarity between environments |
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Stability analysis and environment stratification |
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Eberhart and Russell's regression model |
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Statistics for genotype-vs-environment interaction |
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Geometric adaptability index |
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Several types of residual plots |
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Plot an object of class env_dissimilarity |
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Plot an object of class ge_cluster |
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Plot an object of class ge_effects |
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Plot the ge_factanal model |
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Plot an object of class ge_reg |
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Print an object of class Annicchiarico |
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Print an object of class anova_ind |
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Print an object of class anova_joint |
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Print an object of class ecovalence |
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Print an object of class env_dissimilarity |
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Print an object of class ge_factanal |
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Print an object of class ge_reg |
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Print an object of class ge_stats |
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Print an object of class Shukla |
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Print an object of class Schmildt |
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Schmildt's genotypic confidence index |
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Non-parametric methods |
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Fox's stability function |
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Huehn's stability statistics |
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Print an object of class Fox |
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Print an object ofclass |
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Print an object ofclass |
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Print an object ofclass |
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Shukla's stability variance parameter |
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Lin e Binns' superiority index |
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Thennarasu's stability statistics |
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BiometryUseful functions for biometric models |
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Correlation coefficient |
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Coerce to an object of class lpcor |
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Computes Pearson's correlation matrix with p-values |
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Visualization of a correlation matrix |
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Confidence interval for correlation coefficient |
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Sample size planning for a desired Pearson's correlation confidence interval |
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Generate correlated variables |
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Variance-covariance matrices for designed experiments |
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Coerce to an object of class lpcor |
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Linear and Partial Correlation Coefficients |
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Mantel test for a set of correlation matrices |
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Plot the confidence interval for correlation |
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Create a correlation heat map |
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Plot an object of class correlated_vars |
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Print an object of class corr_coef |
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Print the partial correlation coefficients |
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Canonical correlation coefficient |
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Canonical correlation analysis |
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Plots an object of class can_cor |
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Print an object of class can_cor |
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Clustering analysis |
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Clustering analysis |
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Mahalanobis Distance |
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Mahalanobis distance from designed experiments |
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Plot an object of class clustering |
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Path analysis |
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Collinearity Diagnostics |
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Select a set of predictors with minimal multicollinearity |
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Path coefficients with minimal multicollinearity |
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Print an object of class colindiag |
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Print an object of class path_coeff |
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Plot two-way dataCreate bar or line plots for two-way data quickly |
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Fast way to create bar plots |
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Fast way to create line plots |
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Plot the response surface model |
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Response surface model |
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DescriptiveUseful functions for computing descriptive statistics |
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Descriptive statistics |
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Find possible outliers in a dataset |
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Check for common errors in multi-environment trial data |
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Utilities for handling with NA and zero values |
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Useful functions for computing descriptive statistics |
Data manipulationUtilities for handling with columns, rows, numbers, strings, and matrices. |
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Copy-Paste |
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Utilities for data Copy-Pasta |
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Numbers and strings |
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Utilities for handling with numbers and strings |
Columns and rows |
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Utilities for handling with rows and columns |
Matrices |
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Utilities for handling with matrices |
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Two-way table to a 'long' format |
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Make a two-way table |
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Reorder a correlation matrix |
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Pseudoinverse of a square matrix |
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Select helpers |
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Select helper |
Other useful functions |
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Utilities for handling with classes |
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Arrange multiple ggplot2 graphics in a single image window |
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Split a data frame by factors |
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Bind cross-validation objects |
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Pairwise combinations of variables |
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Alternative to dplyr::do for doing anything |
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Get data from a model easily |
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Multi-Environment Trial Analysis |
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Combines data.frames by row filling missing values |
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Rescale a variable to have specified minimum and maximum values |
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Several types of residual plots |
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Generate significance stars from p-values |
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Encode variables to a factor |
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Personalized theme for ggplot2-based graphics |
Tukey Honest Significant Differences |
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DatasetsData for reproducible examples |
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Data from an alpha lattice design |
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Single maize trial |
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Multi-environment trial of oat |
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Multi-environment trial of maize |
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Data for examples |
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Data for examples |