Nothing
## ----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))
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