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 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. |
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.
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)