mefa (version 1.1-4)

xcount: 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, \dots)

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

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

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.

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.

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.

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

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))