## ----eval = FALSE------------------------------------------------------------- # install.packages("biotools") # devtools::install_github("arsilva87/biotools") ## ----------------------------------------------------------------------------- library(biotools) ## ----------------------------------------------------------------------------- data(maize) head(maize) # firts 6 rows ## ----------------------------------------------------------------------------- M <- lm(cbind(NKPR, ED, CD) ~ family, data = maize) anova(M, test = "Wilks") ## ----------------------------------------------------------------------------- mvpaircomp(M, "family", test = "Wilks", adjust = "bonferroni") ## ----------------------------------------------------------------------------- res <- residuals(M) boxM(data = res, grouping = maize$family) ## ----------------------------------------------------------------------------- s <- singh(data = maize[, 1:3], cov = cov(res)) s plot(s) ## ----------------------------------------------------------------------------- d <- D2.dist(data = maize[, 1:3], cov = cov(res)) range(d) ## ----------------------------------------------------------------------------- toc <- tocher(d, algorithm = "sequential") toc ## ----digits=3----------------------------------------------------------------- print(toc$distClust, digits = 2) ## ----------------------------------------------------------------------------- cop <- cophenetic(toc) # cophenetic matrix cor(d, cop) # cophenetic correlation coefficient ## ----------------------------------------------------------------------------- mantelTest(d, cop, nperm = 900) ## ----------------------------------------------------------------------------- D2.disc(data = maize[, 1:3], grouping = maize$family, pooled.cov = cov(res))