Package: metan 1.18.0

metan: 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>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, 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>. 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.

Authors:Tiago Olivoto [aut, cre, cph]

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NEWS

# Install 'metan' in R:

install.packages('metan', repos = c('https://tiagoolivoto.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tiagoolivoto/metan/issues

Datasets:

data_alpha - Data from an alpha lattice design
data_g - Single maize trial
data_ge - Multi-environment trial of oat
data_ge2 - Multi-environment trial of maize
int.effects - Data for examples
meansGxE - Data for examples

On CRAN:

ammi ammi-model biplots gge hmrpgv mgidi mtsi rpgv stability waas waasb

278 exports 32 stars 6.14 score 71 dependencies 85 mentions 1.1k scripts 2.2k downloads

Last updated 4 months agofrom:0ab3870def. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 29 2024
R-4.5-win	WARNING	Aug 29 2024
R-4.5-linux	WARNING	Aug 29 2024
R-4.4-win	WARNING	Aug 29 2024
R-4.4-mac	WARNING	Aug 29 2024
R-4.3-win	WARNING	Aug 29 2024
R-4.3-mac	WARNING	Aug 29 2024

Exports::=.data %>%acv add_class add_cols add_prefix add_row_id add_rows add_seq_block add_suffix all_lower_case all_pairs all_title_case all_upper_case alpha_color ammi_indexes AMMI_indexes Annicchiarico anova_ind anova_joint arrange_ggplot as_character as_factor as_integer as_label as_logical as_name as_numeric as.lpcor as.split_factors av_dev ave_dev bind_cv blup_indexes can_corr ci_mean_t ci_mean_z clip_read clip_write clustering coincidence_index colindiag colnames_to_lower colnames_to_title colnames_to_upper column_exists column_to_first column_to_last column_to_rownames comb_vars concatenate contains corr_ci corr_coef corr_focus corr_plot corr_ss corr_stab_ind correlated_vars covcor_design cv cv_ammi cv_ammif cv_blup cv_by desc_stat desc_wider df_to_selegen_54 difference_var doo ecovalence ends_with enquo enquos env_dissimilarity env_stratification everything extract_number extract_string fai_blup fill_na find_outliers find_text_in_num first_upper_case Fox freq_hist freq_table g_simula gafem gai gamem gamem_met ge_acv ge_cluster ge_details ge_effects ge_factanal ge_means ge_plot ge_polar ge_reg ge_simula ge_stats ge_winners get_corvars get_covmat get_dist get_level_size get_levels get_levels_comb get_model_data get_wd_here gge ggplot_color gmd gmean group_by gtb gytb has_class has_na has_text_in_num has_zero hmean hmgv hmrpgv Huehn impute_missing_val inspect intersect_var is_balanced_trial is.lpcor is.split_factors kurt last_col lower_case_only lpcor mahala mahala_design make_long make_lower_tri make_lower_upper make_mat make_sym make_upper_tri mantel_test matches max_by mean_by means_by mgidi min_by mps mtmps mtsi mutate n_by n_missing n_unique n_valid network_plot non_collinear_vars num_range one_of open_wd open_wd_here pairs_mantel path_coeff path_coeff_mat path_coeff_seq performs_ammi plaisted_peterson plot_bars plot_blup plot_ci plot_eigen plot_factbars plot_factlines plot_lines plot_scores plot_waasby progress prop_na pseudo_sigma random_na range_data rbind_fill_id recode_factor remove_class remove_cols remove_cols_all_na remove_cols_na remove_cols_zero remove_rownames remove_rows remove_rows_all_na remove_rows_na remove_rows_zero remove_space remove_strings rename reorder_cols reorder_cormat replace_na replace_number replace_string replace_zero resca residual_plots resp_surf round_cols row_col_mean row_col_sum rownames_to_column rpgv run_progress sample_random sample_systematic Schmildt sd_amo sd_by sd_pop sel_gen select select_cols select_cols_na select_cols_zero select_first_col select_last_col select_non_numeric_cols select_numeric_cols select_pred select_rows select_rows_na select_rows_zero sem sem_by set_class set_difference set_intersect set_union set_wd_here Shukla skew Smith_Hazel solve_svd split_factors stars_pval starts_with sum_by sum_dev sum_sq sum_sq_dev superiority theme_metan theme_metan_minimal Thennarasu tidy_colnames tidy_strings tidy_sym title_case_only transparent_color transpose_df tukey_hsd union_var upper_case_only var_amo var_by var_pop venn_plot waas waas_means waasb width_greater_than width_less_than width_of wsmp

Dependencies:backports bit bit64 boot broom broom.helpers cards cli clipr colorspace cpp11 crayon dplyr fansi farver forcats generics GGally ggforce ggplot2 ggrepel ggstats glue gtable haven hms isoband labeling labelled lattice lifecycle lme4 lmerTest magrittr MASS mathjaxr Matrix mgcv minqa munsell nlme nloptr numDeriv patchwork pillar pkgconfig plyr polyclip prettyunits progress purrr R6 RColorBrewer Rcpp RcppEigen readr rlang scales stringi stringr systemfonts tibble tidyr tidyselect tweenr tzdb utf8 vctrs viridisLite vroom withr

Multi-environment Trial Analysis

Tiago Olivoto

Rendered frommetan_start.Rmdusingknitr::rmarkdownon Aug 29 2024.

Last update: 2021-11-10
Started: 2020-02-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Multi-Environment Trial Analysis	metan-package
Adjusted Coefficient of Variation	acv
AMMI-based stability indexes	AMMI_indexes ammi_indexes
Annicchiarico's genotypic confidence index	Annicchiarico
Within-environment analysis of variance	anova_ind
Joint analysis of variance	anova_joint
Arrange separate ggplots into the same graphic	arrange_ggplot
Coerce to an object of class lpcor	as.lpcor
Fast way to create bar plots	barplots plot_bars plot_factbars
Bind cross-validation objects	bind_cv
Stability indexes based on a mixed-effect model	blup_indexes hmgv hmrpgv rpgv
Canonical correlation analysis	can_corr
Clustering analysis	clustering
Computes the coincidence index of genotype selection	coincidence_index
Collinearity Diagnostics	colindiag
Pairwise combinations of variables	comb_vars
Confidence interval for correlation coefficient	corr_ci
Linear and partial correlation coefficients	corr_coef
Focus on section of a correlation matrix	corr_focus
Visualization of a correlation matrix	corr_plot
Sample size planning for a desired Pearson's correlation confidence interval	corr_ss
Correlation between stability indexes	corr_stab_ind
Generate correlated variables	correlated_vars
Variance-covariance matrices for designed experiments	covcor_design
Cross-validation procedure	cv_ammi
Cross-validation procedure	cv_ammif
Cross-validation procedure	cv_blup
Data from an alpha lattice design	data_alpha
Single maize trial	data_g
Multi-environment trial of oat	data_ge
Multi-environment trial of maize	data_ge2
Simulate genotype and genotype-environment data	data_simula ge_simula g_simula
Descriptive statistics	desc_stat desc_wider
Alternative to dplyr::do for doing anything	doo
Stability analysis based on Wricke's model	ecovalence
Dissimilarity between environments	env_dissimilarity
Environment stratification	env_stratification
Multi-trait selection index	fai_blup
Find possible outliers in a dataset	find_outliers
Fox's stability function	Fox
Genotype analysis by fixed-effect models	gafem
Geometric adaptability index	gai
Genotype analysis by mixed-effect models	gamem
Genotype-environment analysis by mixed-effect models	gamem_met
Adjusted Coefficient of Variation as yield stability index	ge_acv
Cluster genotypes or environments	ge_cluster
Details for genotype-environment trials	ge_details
Genotype-environment effects	ge_effects
Stability analysis and environment stratification	ge_factanal
Genotype-environment means	ge_means
Graphical analysis of genotype-vs-environment interaction	ge_plot
Power Law Residuals as yield stability index	ge_polar
Eberhart and Russell's regression model	ge_reg
Parametric and non-parametric stability statistics	ge_stats
Genotype-environment winners	ge_winners
Generate normal, correlated variables	get_corvars
Generate a covariance matrix	get_covmat
Get a distance matrix	get_dist
Get data from a model easily	get_model_data gmd sel_gen
Genotype plus genotype-by-environment model	gge
Genotype by trait biplot	gtb
Genotype by yield*trait biplot	gytb
Huehn's stability statistics	Huehn
Missing value imputation	impute_missing_val
Check for common errors in multi-environment trial data	inspect
Data for examples	int.effects
Check if a data set is balanced	is_balanced_trial
Coerce to an object of class lpcor	is.lpcor
Fast way to create line plots	lineplots plot_factlines plot_lines
Linear and Partial Correlation Coefficients	lpcor
Mahalanobis Distance	mahala
Mahalanobis distance from designed experiments	mahala_design
Two-way table to a 'long' format	make_long
Make a two-way table	make_mat
Mantel test	mantel_test
Data for examples	meansGxE
Multitrait Genotype-Ideotype Distance Index	mgidi
Mean performance and stability in multi-environment trials	mps
Multi-trait mean performance and stability index	mtmps
Multi-trait stability index	mtsi
Network plot of a correlation matrix	network_plot
Select a set of predictors with minimal multicollinearity	non_collinear_vars
Mantel test for a set of correlation matrices	pairs_mantel
Path coefficients with minimal multicollinearity	path_coeff path_coeff_mat path_coeff_seq
Additive Main effects and Multiplicative Interaction	performs_ammi
Stability analysis based on Plaisted and Peterson (1959)	plaisted_peterson
Plot the BLUPs for genotypes	plot_blup
Plot the confidence interval for correlation	plot_ci
Plot the eigenvalues	plot_eigen
Plot scores in different graphical interpretations	plot_scores
Plot WAASBY values for genotype ranking	plot_waasby
Several types of residual plots	plot.anova_joint
Plots an object of class can_cor	plot.can_cor
Plot an object of class clustering	plot.clustering
Create a correlation heat map	plot.corr_coef
Plot an object of class correlated_vars	plot.correlated_vars
Plot the RMSPD of a cross-validation procedure	plot.cvalidation
Plot an object of class env_dissimilarity	plot.env_dissimilarity
Plot the env_stratification model	plot.env_stratification
Multi-trait selection index	plot.fai_blup
Several types of residual plots	plot.gafem
Several types of residual plots	plot.gamem
Plot an object of class ge_cluster	plot.ge_cluster
Plot an object of class ge_effects	plot.ge_effects
Plot the ge_factanal model	plot.ge_factanal
Plot an object of class ge_reg	plot.ge_reg
Create GGE, GT or GYT biplots	plot.gge
Plot the multi-trait genotype-ideotype distance index	plot.mgidi
Plot the multi-trait stability index	plot.mtmps
Plot the multi-trait stability index	plot.mtsi
Plots an object of class 'path_coeff'	plot.path_coeff
Several types of residual plots	plot.performs_ammi
Plot the response surface model	plot.resp_surf
Plot the Smith-Hazel index	plot.sh
Several types of residual plots	plot.waas
Several types of residual plots	plot.waasb
Plot heat maps with genotype ranking	plot.wsmp
Predict method for gamem fits	predict.gamem
Predict a two-way table based on GGE model	predict.gge
Predict the means of a performs_ammi object	predict.performs_ammi
Predict the means of a waas object	predict.waas
Predict method for waasb fits	predict.waasb
Print an object of class ammi_indexes	print.ammi_indexes
Print an object of class Annicchiarico	print.Annicchiarico
Print an object of class anova_ind	print.anova_ind
Print an object of class anova_joint	print.anova_joint
Print an object of class can_cor	print.can_cor
Print an object of class coincidence	print.coincidence
Print an object of class colindiag	print.colindiag
Print an object of class corr_coef	print.corr_coef
Print an object of class ecovalence	print.ecovalence
Print an object of class env_dissimilarity	print.env_dissimilarity
Print the env_stratification model	print.env_stratification
Print an object of class Fox	print.Fox
Print an object of class gamem	print.gamem
Print an object of class ge_factanal	print.ge_factanal
Print an object of class ge_reg	print.ge_reg
Print an object of class ge_stats	print.ge_stats
Print an object ofclass 'Huehn'	print.Huehn
Print the partial correlation coefficients	print.lpcor
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.mgidi
Print an object of class mtmps	print.mtmps
Print an object of class mtsi	print.mtsi
Print an object of class path_coeff	print.path_coeff
Print an object of class performs_ammi	print.performs_ammi
Print an object of class plaisted_peterson	print.plaisted_peterson
Print an object of class Schmildt	print.Schmildt
Print an object of class sh	print.sh
Print an object of class Shukla	print.Shukla
Print an object ofclass 'superiority'	print.superiority
Print an object ofclass 'Thennarasu'	print.Thennarasu
Print an object of class waas	print.waas
Print an object of class waas_means	print.waas_means
Print an object of class waasb	print.waasb
Reorder a correlation matrix	reorder_cormat
Rescale a variable to have specified minimum and maximum values	resca
Several types of residual plots	residual_plots
Response surface model	resp_surf
Schmildt's genotypic confidence index	Schmildt
Select helper	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
Selects a best subset of predictor variables.	select_pred
Shukla's stability variance parameter	Shukla
Smith-Hazel index	Smith_Hazel
Pseudoinverse of a square matrix	solve_svd
Split a data frame by factors	as.split_factors is.split_factors split_factors
Generate significance stars from p-values	stars_pval
Lin e Binns' superiority index	superiority
Personalized theme for ggplot2-based graphics	alpha_color ggplot_color themes theme_metan theme_metan_minimal transparent_color
Thennarasu's stability statistics	Thennarasu
Transpose a data frame	transpose_df
Tukey Honest Significant Differences	tukey_hsd
Encode variables to a specific format	as_character as_factor as_integer as_logical as_numeric utils_as
Helper function for binding rows	rbind_fill_id utils_bind
Utilities for handling with classes	add_class has_class remove_class set_class utils_class
Utilities for data Copy-Pasta	clip_read clip_write utils_data
Utilities for data organization	add_seq_block df_to_selegen_54 recode_factor utils_data_org
Utilities for handling with matrices	make_lower_tri make_lower_upper make_sym make_upper_tri tidy_sym utils_mat
Utilities for handling with NA and zero values	fill_na has_na has_zero prop_na random_na remove_cols_all_na remove_cols_na remove_cols_zero remove_rows_all_na remove_rows_na remove_rows_zero replace_na replace_zero select_cols_na select_cols_zero select_rows_na select_rows_zero utils_na_zero
Utilities for handling with numbers and strings	all_lower_case all_title_case all_upper_case extract_number extract_string find_text_in_num first_upper_case has_text_in_num remove_space remove_strings replace_number replace_string round_cols tidy_strings utils_num_str
Utilities for text progress bar in the terminal	progress run_progress utils_progress
Utilities for handling with rows and columns	add_cols add_prefix add_rows add_row_id add_suffix all_pairs colnames_to_lower colnames_to_title colnames_to_upper column_exists column_to_first column_to_last column_to_rownames concatenate get_levels get_levels_comb get_level_size remove_cols remove_rownames remove_rows reorder_cols rownames_to_column select_cols select_first_col select_last_col select_non_numeric_cols select_numeric_cols select_rows tidy_colnames utils_rows_cols
Random Sampling	sample_random sample_systematic utils_samples
Utilities for set operations for many sets	set_difference set_intersect set_union utils_sets
Useful functions for computing descriptive statistics	ave_dev av_dev ci_mean_t ci_mean_z cv cv_by freq_hist freq_table gmean hmean kurt max_by means_by mean_by min_by n_by n_missing n_unique n_valid pseudo_sigma range_data row_col_mean row_col_sum sd_amo sd_by sd_pop sem sem_by skew sum_by sum_dev sum_sq sum_sq_dev utils_stats var_amo var_by var_pop
Set and get the Working Directory quicky	get_wd_here open_wd open_wd_here set_wd_here utils_wd
Draw Venn diagrams	venn_plot
Weighted Average of Absolute Scores	waas
Weighted Average of Absolute Scores	waas_means
Weighted Average of Absolute Scores	waasb
Weighting between stability and mean performance	wsmp