| xcount {mefa} | R Documentation |
The function makes an object of class 'xcount' from an object of class 'sscount'.
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, ...)
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 lessthan 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 is vector. 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. |
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 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 the same plot.
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. |
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
as.xcount, check.attrib, marmat, mefa,
sscount, xorder
### 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)