as.mixstock.data {mixstock}R Documentation

class for marker data from sources and mixed stocks

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, ...)
## 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
... 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)

[Package mixstock version 0.9 Index]