check.attrib {mefa} | R Documentation |
Check Consistency of 'xcount' Object and Attribute Table
Description
This function checks consistency of an object of class 'xcount' and an attribute table (data frame) by comparing row/column names (as sample/species identifiers) and values in an index column of the data frame.
Usage
check.attrib(xc, which = c("samples", "species"), attrib, index = 0)
Arguments
xc |
an object of class 'xcount'. |
which |
switch for rows ("samples" ) or columns ("species" ) of the 'xcount' object to be compared
according to index . |
attrib |
data frame to be checked. NA values are counted. |
index |
column identifier within attrib to be compared according to row/column names (as sample/species
identifiers) of the 'xcount' object according to value of which .
By default, index = 0 , and rownames are taken as identifiers. |
Value
call |
returns the call. |
set.relation |
"equal" means the two sets (row/column names of the 'xcount' object and elements in the index column) are equal, "inclusion" means the two sets are inclusive and no missing elements found, "intersect" means the two sets intersect (required elements are listed in missing ), "separate" means the two sets have no common elements (required elements are listed in missing ). |
duplicate |
a list of duplicate elements or NULL . |
missing |
a list of missing elements or NULL . |
na |
indicates the number of NA values found in attrib . |
Author(s)
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
See Also
mefa
, xcount
, 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")
spectab <- as.data.frame(rbind(
c("species3", "family1", "1"),
c("species2", "family2", "5"),
c("species1", "family1", "2"),
c("species5", "family2", "1"),
c("species4", "family1", "10")
))
colnames(spectab) <- c("species", "taxonomy", "size")
sampletab <- as.data.frame(rbind(
c("sample3", "bad"),
c("sample1", "good"),
c("sample2", "good"),
c("sample4", "bad")))
colnames(sampletab) <- c("sample", "quality")
xct <- xcount(sscount(ss))
check.attrib(xct, "samples", sampletab, 1)
check.attrib(xct, "species", spectab, 1)
check.attrib(xct, "species", spectab, 2)
check.attrib(xct, "species", spectab[2:5,], 1)
check.attrib(xct, "species", spectab[4:5,], 1)
### Example 2: field data of Villany Hills
## Not run:
data(vtable, vsample, landsnail)
vt <- as.xcount(vtable, FALSE)
check.attrib(vt, which="species", landsnail, 2)
check.attrib(vt, which="samples", vsample, 1)
## End(Not run)
[Package
mefa version 1.1-2
Index]