# Some demos of functions presented in
# Kozak M, Wnuk A, Krzanowski WJ (2010) 'A simple R function for inspecting multivariate data',
# Communications in Biometry and Crop Science 5(1), 34-40.

source("http://agrobiol.sggw.waw.pl/~cbcs/articles/5_1_6/functions_www.R")

# The simplest call to symb.mv function:
data(iris)
symb.mv(iris[, 1:4])

# NAs:
iris[20, 2] <- NA
symb.mv(iris[, 1:4])

# Using the grouping.variables argument to include goruping variables:
data(iris)
symb.mv(iris[, 1:4], grouping.variables = data.frame(Species = iris$Species))
symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 
    2)))

# Ordering by sums of scaled values:
symb.mv(iris[, 1:4], grouping.variables = data.frame(Species = iris$Species), 
    ord.method = "sum")

# Let's add the information on the species to row names:
data(iris)
rownames(iris) <- paste(substr(iris$Species, 1, 2), 
    rownames(iris), sep = "_")
iris.symb <- symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 
    2)))
iris.symb[1:10, ]
iris.symb[rownames(iris.symb) == "vi_123", ]
iris.symb[rownames(iris.symb) %in% c("se_1", "se_50", 
    "se_123"), ]

# Note: there is no 'se_123 row', so only two are printed

# Utilizing the cutoff value:
data(iris)
symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 2)), cutoff = 5)

symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 2)), cutoff = 10) # Notice the warning
# But:
iris[1, 1] <- 100
symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 2)), cutoff = 10) # Also an error, but one case left and is printed. 

# Writing into text file:
data(iris)
setwd(tempdir())
iris.symb <- symb.mv(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 
    2)))
write.table(iris.symb, "iris_symb.txt", quote = F, 
    row.names = F, sep = "\t")
file.show("iris_symb.txt")

# Or

a <- symb.mv(iris[, 1:4], grouping.variable = data.frame(species = iris$Species, 
    row = rownames(iris)))
a <- a[, c(6, 1:5)]
write.table(a, "iris_symb.txt", quote = F, row.names = F, 
    sep = "\t")
file.show("iris_symb.txt")

# Independently for species:
symb.mv(iris[iris$Species == "versicolor", 1:4])
symb.mv(iris[iris$Species == "setosa", 1:4])
symb.mv(iris[iris$Species == "virginica", 1:4])

# Now example on producing plastic film from Krzanowski (1998, p. 381) (see also ?summary.manova)
#  Krzanowski, W.J. (1988) Principles of Multivariate Analysis. A User's Perspective. Oxford.

tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 
    6.1, 6.3, 6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7, 7.2, 7.5, 7.6)
gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10, 9.9, 
    9.5, 9.4, 9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
opacity <- c(4.4, 6.4, 3, 4.1, 0.8, 5.7, 2, 3.9, 1.9, 
    5.7, 2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
Y <- cbind(tear, gloss, opacity)
rate <- factor(gl(2, 10), labels = c("Low", "High"))
additive <- factor(gl(2, 5, length = 20), labels = c("Low", 
    "High"))

symb.mv(Y, grouping.variables = data.frame(rate, additive))
symb.mv(Y, grouping.variables = data.frame(rate = abbreviate(rate, 
    1), add = abbreviate(additive, 1)))

# Now writing to a 'symb.html' html page with the symb.mv.www function:

library(hwriter)
setwd(tempdir()) # or any other directory
symb.mv.www(iris[, 1:4], grouping.variables = data.frame(Sp = abbreviate(iris$Species, 
    2)))
symb.mv.www(Y, grouping.variables = data.frame(rate = abbreviate(rate, 
    1), add = abbreviate(additive, 1)))
symb.mv.www(Y, grouping.variables = data.frame(rate = abbreviate(rate, 
    1), add = abbreviate(additive, 1)), ord.method = "sum") 
symb.mv.www(Y, cols.for.order = 1, grouping.variables = data.frame(rate = abbreviate(rate, 
    1), add = abbreviate(additive, 1)), ord.method = "sum")