as.mixstock.data: class for marker data from sources and mixed stocks

In mixstock: functions for mixed stock analysis

Description

This class provides a standard structure for information on markers (e.g. mitochondrial DNA samples) from a variety of different sources (e.g. sources) and from (a) mixed population(s) that draw(s) from those sources.

Usage

as.mixstock.data(object,nmix=1,sourcesize)
## S3 method for class 'mixstock.data'
plot(x,prop = TRUE, legend = TRUE, colors = rainbow(x$H), 
    leg.space = 0.3, leg.ncol, leg.cex=1, mix.off = 0.5,
    stacklabels=FALSE, sampsize=FALSE, horiz=TRUE, vlab="Haplotype frequency", ...)
## S3 method for class 'mixstock.data'
print(x,...)

Arguments

object	a matrix with (R+1) columns and (H) rows, where the columns specify R sources plus a mixed population, and the rows specify distinct marker classes (e.g. mitochondrial haplotypes)
x	a mixstock.data object
prop	reduce data to frequencies?
legend	add a legend to the plot?
colors	colors denoting different markers
horiz	logical: plot bars horizontally?
leg.space	space to leave for legend (fraction at top of graph)
leg.ncol	number of columns for legend (default is 3 for horizontal barplots, 1 for vertical)
leg.cex	character size for legend
mix.off	spacing offset for bar(s) representing mixed stock(s)
stacklabels	(logical) put source names on multiple lines?
sampsize	(logical) add text showing sample sizes?
nmix	number of mixed stocks (default 1)
sourcesize	either a numeric vector of relative source sizes, or "first" or "last" to specify that the first or last row of the matrix contains the source sizes
vlab	label for value axis
...	additional arguments to barplot

Value

mixstock.data objects have the following components:

R	number of sources
H	number of marker classes (haplotypes)
sourcesamp	samples from sources, in an HxR matrix
mixsamp	a vector of sample from the mixed population

print.mixstock.data and plot.mixstock.data give textual and graphical summaries of the results

Note

While vertical barplots are more familiar, horizontal barplots are useful for displaying long source/mixed stock names

Author(s)

Ben Bolker

Examples

x <- matrix(c(23,34,10,10,11,4,4,5,2),byrow=TRUE,nrow=3)
dx <- as.mixstock.data(x)
dx
plot(dx)

mixstock documentation built on May 2, 2019, 6:48 p.m.