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phy = read.tree("mytree.tre") | |
samp = read.table("OTUtable.txt", head = T, sep = "") | |
#lists taxa in OTU table that are not in the phylogeny, and removes them | |
samp = (samp[rowSums(samp) != 0, , drop=FALSE]) | |
samp = t(samp) | |
phy = prune.sample(samp, phy) | |
labs <- phy$tip.label | |
length(labs) | |
ncol(samp) |
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require(picante) | |
require(gtools) | |
require(reshape) | |
########################################################### | |
### For calculation of Naiive (Z = I) diversity profiles ### | |
########################################################### |
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require(kernlab) | |
require(caret) | |
require(e1071) | |
require(nnet) | |
require(randomForest) | |
set.seed(34873458) | |
#Open call library (needs name (eg. MYLU), and parameters) | |
setwd = ("Dropbox/Anabat files/Dave's Florida Bat Calls/") |
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