Hi,
Your output dataset is bit confusing as it contains Sites that were not in the
input.
Using your input dataset, I am getting this:
dat1<- read.table(text="
Species Site Date
a 1 1
b 1 1
b 1 2
c 1 3
",sep="",header=TRUE,stringsAsFactors=FALSE)
dat1$Present<- 1
dat2<-expand.grid(unique(dat1$Species),unique(dat1$Site),unique(dat1$Date))
colnames(dat2)<- colnames(dat1)
res<-merge(dat1,dat2,by=c("Species","Site","Date"),all=TRUE)
res[is.na(res)]<- 0
res<-res[order(res$Date),]
res
# Species Site Date Present
#1 a 1 1 1
#4 b 1 1 1
#7 c 1 1 0
#2 a 1 2 0
#5 b 1 2 1
#8 c 1 2 0
#3 a 1 3 0
#6 b 1 3 0
#9 c 1 3 1
A.K.
----- Original Message -----
From: Matthew Venesky <mvene...@gmail.com>
To: r-help@r-project.org
Cc:
Sent: Monday, April 29, 2013 11:12 AM
Subject: [R] expanding a presence only dataset into presence/absence
Hello,
I'm working with a very large dataset (250,000+ lines in its' current form)
that includes presence only data on various species (which is nested within
different sites and sampling dates). I need to convert this into a dataset
with presence/absence for each species. For example, I would like to expand
"My current data" to "Desired data":
My current data
Species Site Date
a 1 1
b 1 1
b 1 2
c 1 3
Desired data
Species Present Site Date
a 1 1 1
b 1 1 1
c 0 1 1
a 0 2 2
b 1 2 2
C 0 2 2
a 0 3 3
b 0 3 3
c 1 3 3
I've scoured the web, including Rseek and haven't found a resolution (and
note that a similar question was asked sometime in 2011 without an answer).
Does anyone have any thoughts? Thank you in advance.
--
Matthew D. Venesky, Ph.D.
Postdoctoral Research Associate,
Department of Integrative Biology,
The University of South Florida,
Tampa, FL 33620
Website: http://mvenesky.myweb.usf.edu/
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