Dear R-Helpers,
I am working on a dataset containing ca. 500 specimens of 17 different
species. The data is three text columns, followed by ca 70 columns of
binary data.
I'm trying to write a function that will allow me to interactively
exclude species using the inofrmation in the third text column. My
function, matrix.slicer, appears to work as I intend. However, when I
pass the resulting matrix to my homemade principal coordinates
function, pcoa, the results include all of the data, with nothing
excluded.
I've read the help for factors, levels, subset, [, and some threads
here relating to subsetting and drop=true issues, but I'm afraid I just
don't understand what I need to do. I've pasted the functions below -
any help would be appreciated. Thanks!
Tyler Smith
matrix.slicer <- function(mat, label.vector){
selector <- 999
print("Select species to remove from the matrix, 0 to finish")
while (selector != 0){
selector <- menu( levels( factor(mat[,label.vector])))
if (selector==0)break
print (c("Removed: ",
levels(factor(mat[,label.vector]))[selector]))
mat <- subset (mat, mat[,label.vector]!=levels (factor (mat
[,label.vector]))[selector])
}
return (mat)
}
gel.data <- matrix.slicer (gel.data,3)
disttemp <- as.matrix(vegdist(gel.data[,-(1:3)], method="jaccard"))
dist <- sqrt(disttemp)
PCOA <- pcoa (dist)
--
Tyler Smith
