xcount {mefa}R Documentation

Makes an Object of Class 'xcount'

Description

The function makes an object of class 'xcount' from an object of class 'sscount'.

Usage

xcount(ssc, segment = 0, segment.name = NULL)

## S3 method for class 'xcount':
print(x, cutoff = 25, ...)

## S3 method for class 'xcount':
plot(x, type = "hist", rug = FALSE, logscale = FALSE, ...)

Arguments

ssc an object of class 'sscount'.
segment identifier of the segment within the 'sscount' object to make the crosstabulation, the default 0 refers to "all" segments. It can have more than one element (but less than or equal to the number of elements in the segment list). When it is a vector, corresponding levels are combined and named as specified by segment.name.
segment.name character, it has effect only when segment has more than one element. If not specified, segment value in the result is set to "mixed" (if all segments are listed, it is set to "all").
x an object of class 'xcount'.
type character, can be "hist" for histogram, "rank" for rank abundance/occurence curves and "biplot" for plot abundance vs. occurence data.
rug logical, if TRUE, add rug to the plot (default is FALSE). It has effect only if type="hist".
logscale logical, if TRUE, plotted values are $log10(y+1)$ transformed. Default FALSE leaves the values intact.
cutoff number of samples/species with zero toal count to be listed.
... other arguments.

Details

If data in the 'sscount' object are of measurement type, digits value is inherited from the 'sscount' object and used in crosstabulation. For large (>2) digit values, computing time may take several seconds. Current implementation of handling measurement type data is based on the inflate function, which is not fully vectorized.

The print method produces 4 graphs in one window, displaying histograms (type = "hist") or rank abundance/incidence curves (type = "rank") of the vectors ninds, srichn, specabund and specoccur. If the data are of presence/absence and not abundance type, only srichn and specoccur are displayed. These values are based on the function marmat. The option (type = "biplot") deisplays 2 graphs, one for samples and one for species, combining presence/absence and abundance data in same plots.

Value

A result is an object of class 'xcount'.

data matrix containing count data of sample/species crosstabulation. Crosstabulation results the same dimensions for data matrices of each segments.
call returns the call.
segment segment of the 'sscount' object of which the crosstabulation was made, or "all".
digits inherited from the 'sscount' object.
nsamples number of rows (samples) in data.
nspecies number of columns (species) in data.
totalcount sum of count or measurement in data.
presences sum of presences in data.
ninds a vector, containing number of individuals (or sum of measurement values) within samples.
srichn a vector, containing number of species (based on occurences) within samples.
specabund a vector, containing number of individuals (or sum of measurement values) within species.
specoccur a vector, containing number of occurences within species.

Author(s)

Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/

See Also

as.xcount, check.attrib, marmat, mefa, sscount, xorder

Examples

### Example 1: simple atrificial data

ss <- data.frame(
cbind(
c("sample1","sample1","sample2","sample2","sample3","sample4"),
c("species1","species1","species1","species2","species3","zero.count"),
c("male","female","male","female","male","male")
),
c(1, 2, 10, 3, 4, 1)
)
colnames(ss) <- c("sample.id", "species.id", "gender", "catch")

xc1 <- xcount(sscount(ss, zc="zero"))
xc1

xc2 <- xcount(sscount(ss, zc="zero.count"))
xc2

xc3 <- xcount(sscount(ss, zc="zero.count"), 0)
xc3

xc4 <- xcount(sscount(ss, zc="zero.count"), 1)
xc4

### Example 2: field data of the dolina

## Not run: 
data(dol.count, dol.sample, landsnail)

dssc <- sscount(dol.count, zc="zero.count", fill=TRUE)
dssc

(xc <- xcount(dssc))
plot(xc, type="hist")
plot(xc, type="rank", logscale = TRUE)
plot(xc, type="biplot")

xcount(dssc, "broken")
xcount(dssc, c("adult", "juvenile"))
xcount(dssc, c(1,4), "mixed")
xcount(dssc, c(1:3))
## End(Not run)

[Package mefa version 1.1-2 Index]