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darmitage / PhyloClean
Created June 1, 2012 03:37
Cleaning up OTU tables and Phylogenies
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)
@darmitage
darmitage / NaiiveD
Created July 25, 2012 23:49
Naiive Diversity Profiles + Rarefaction
require(picante)
require(gtools)
require(reshape)
###########################################################
### For calculation of Naiive (Z = I) diversity profiles ###
###########################################################
@darmitage
darmitage / batcall_classify
Created September 18, 2012 17:49
Classification of zero-crossings bat calls using machine learning
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/")
@darmitage
darmitage / PseudomonasSharedCode
Last active March 23, 2016 23:08
Data and code for EcoLetts submission
require(AICcmodavg)
require(mgcv)
require(boot)
require(car)
require(MASS)
require(repmis)
require(pscl)
#Read in data from my public dropbox folder
dropURL <- "https://dl.dropboxusercontent.com/u/26280366/Papers/EcoLetts/AreaNrgPseudoFinal.csv"