inst/doc/overview.R

In biotools: Tools for Biometry and Applied Statistics in Agricultural Science

## ----eval = FALSE--------------------------------------------------------
#  install.packages("biotools")
#  devtools::install_github("arsilva87/biotools")

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library(biotools)

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data(maize)
head(maize)   # firts 6 rows

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M <- lm(cbind(NKPR, ED, CD) ~ family, data = maize)
anova(M, test = "Wilks")

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mvpaircomp(M, "family", test = "Wilks", adjust = "bonferroni")

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res <- residuals(M)
boxM(data = res, grouping = maize$family)

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s <- singh(data = maize[, 1:3], cov = cov(res))
s
plot(s)

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d <- D2.dist(data = maize[, 1:3], cov = cov(res))
range(d)

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toc <- tocher(d, algorithm = "sequential")
toc

## ----digits=3------------------------------------------------------------
print(toc$distClust, digits = 2)

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cop <- cophenetic(toc)  # cophenetic matrix
cor(d, cop)             # cophenetic correlation coefficient

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mantelTest(d, cop, nperm = 900)

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D2.disc(data = maize[, 1:3], 
        grouping = maize$family, 
        pooled.cov = cov(res))