shipunov (version 1.0)

PlotBest.mdist: Plots dotchart with best distance method, use multiple non-base distances

Description

Plots dotchart with best distance method, use multiple non-base distances

Usage

PlotBest.mdist(data, distances=c("manhattan", "euclidean", "canberra", "clark",
 "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "binomial",
 "chao", "cao", "mahalanobis", "cor.pearson", "cor.spearman", "cor.kendall",
 "gower_dist", "daisy.gower", "smirnov"), dim=2, binary.only=FALSE, plot=TRUE, ...)

Arguments

data

Data frame with values

distances

Distances to use

dim

Number of dimensions

binary.only

Use binary only distances?

plot

Plot?

...

Arguments to 'vegdist()'

Value

Numeric vector with correlation values (equal to the number of distances involved)

Details

Plots the "best" distance method, uses many non-base distances from diverse packages. Uses correlation between multidimentional scaling of distance object and PCA of data. Does not include "mountford" and "raup" from vegdist() as they are very special. Two dimensions are default, change it with "dim" option.

See Also

PlotBest.dist

Examples

# NOT RUN {
PlotBest.mdist(iris[, -5], scale.pca=TRUE)
mo <- read.table("http://ashipunov.info/shipunov/open/moldino.txt", h=TRUE, sep="\t",
 row.names=1)
m1 <- t((mo > 0) * 1)
PlotBest.mdist(m1, binary.only=TRUE)
# }