A quick R example
Today, I needed to convert a series of state matrices into presence-absence matrices. In order to automate this conversion, I wrote the following R code. (The initiated will recognize the output as a species-range matrix.)
1.a. Generate example input
m = matrix(data=c("A","B","C"), nrow=3, ncol=1)
rownames(m) = c("t1", "t2", "t3")
m
[,1]
t1 “A”
t2 “B”
t3 “C”
1.b. Alternatively, one could load a table from file
t = as.matrix(read.csv("~/test.csv", header=FALSE))
m = as.matrix(t[,2])
rownames(m) = t[,1]
2. Generate the presence-absence matrix
l = length(unique(m[,1]))
m = cbind(m, matrix(rep(0,l), nrow=nrow(m), ncol=l))
colnames(m)=c(NA,c(unique(m[,1])))
for (i in c(unique(m[,1]))) {m[which(m[,1] %in% i), i]=1}
m = m[,-1]
m
A B C
t1 “1” “0” “0”
t2 “0” “1” “0”
t3 “0” “0” “1”
EDIT: If any of the entries in the state matrix were to contain a combination of states (e.g., “A and B”), the following code should be used at step #2:
tmp = unique(m[,1])
new = tmp[-which(tmp==tmp[grepl(" and ", tmp)])]
addon = unlist(strsplit(tmp[grepl(" and ", tmp)], ' and '))
ul = unique(c(new,addon))
l = length(ul)
m = cbind(m, matrix(rep(0,l), nrow=nrow(m), ncol=l))
colnames(m)=c(NA,ul)
for (i in ul) {m[which(grepl(i, m[,1])), i]=1}
m = m[,-1]
Die