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MicrosoftInternetExplorer4
Dear R-helpers,
I was wondering whether there are any good books and/or website
links that introduce mark-recapture analysis in R. In particular, I am
interested in exploratory data analysis of resighting data and how to
create capture histories from dataframes in R.
Thank you very much for your reply in advance!
Cheers,
Anne
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Anne Link wrote:> > Normal 0 21 false false > false > MicrosoftInternetExplorer4 > > > Dear R-helpers, > > ? I was wondering whether there are any good books and/or website > links that introduce mark-recapture analysis in R. In particular, I am > interested in exploratory data analysis of resighting data and how to > create capture histories from dataframes in R. > > Thank you very much for your reply in advance! > > ? Cheers, > > Anne > -- >Don't know about books, web sites, but the excellent new "sos" package lists three packages with mark-recapture capabilities: Rcapture, fishmethods, and mra (install.packages("sos"); findFn("mark-recapture") -- View this message in context: http://www.nabble.com/Introduction-to-mark-recapture-analysis-in-R--tp25871729p25872838.html Sent from the R help mailing list archive at Nabble.com.
oops, library("sos") after install.packages("sos") and
before
findFn("mark-recapture") ...
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View this message in context:
http://www.nabble.com/Introduction-to-mark-recapture-analysis-in-R--tp25871729p25872847.html
Sent from the R help mailing list archive at Nabble.com.
On Oct 13, 2009, at 8:00 AM, Anne-Katrin Link wrote:> > I was wondering whether there are any good books and/or > website > links that introduce mark-recapture analysis in R. In particular, I am > interested in exploratory data analysis of resighting data and how to > create capture histories from dataframes in R. > > Thank you very much for your reply in advance!Have you looked at the citations you get in the package that come back from the obvious search strategy? http://search.r-project.org/cgi-bin/namazu.cgi?query=%22capture-recapture%22&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08&idxname=views And I thought I remembered a posting from the author of: Ecological Models and Data in R (Hardcover) by Benjamin M. Bolker .... saying that such methods were discussed and exemplified. But I cannot find the link to confirm my memory on this point. (And now that I check to see if more knowledgeable persons might have already answered this, I see that Bolker himself says "he doesn't know about books", so my memory may have been "manufactured". http://finzi.psych.upenn.edu/R/library/Rcapture/doc/RcaptureJSS.pdf And I am not a biologist so have no experience on what would be the "best book". David Winsemius, MD Heritage Laboratories West Hartford, CT
Another package that is not on CRAN or other R depository is RMark. It works with the software MARK which does the computation. You can find RMark at http://www.phidot.org/software/mark/rmark/ and MARK from http://www.phidot.org/software/mark/index.html From the same site you'll find a very comprehensive electronic book (that describes how to use MARK (http://www.phidot.org/software/mark/docs/book/) and it has an appendix (http://www.phidot.org/software/mark/docs/book/pdf/app_3.pdf)that describes use of RMark. You may also want to look at the RMark workshop notes (http://www.phidot.org/software/mark/rmark/RMarkWorkshopNotes.pdf). <http://www.phidot.org/software/mark/rmark/RMarkWorkshopNotes.pdf> RMark does contain some routines that do CJS and JS models solely in R (see ?cjs and ?js) but they are experimental at this point. RMark was not put on CRAN because with the above exceptions it does require MARK which is a separate piece of FORTRAN software that runs only in WINDOWS, although it possible to obtain a LINUX version with some work. MARK is freely available software as an executable but is not open-source per se. Source for RMark is available from the above sites. With regard to creating capture histories in R, that is easily accomplished with the table function. For example, if x is a dataframe of capture/recapture events with fields ID (unique identifier) and Occasion is a factor variable for the capture occasion then chmat=with (x, table(ID,Occasion)) will create a count of captures by ID and Occasion. If an animal can be caught more than once per occasion then add: chmat[chmat>0]=1 Then you can change to capture history strings with: apply(chmat,1,paste,sep="") Here is a simple example (with nonsense data) x=data.frame(ID=floor(10*runif(100))+1,Occasion=floor(5*runif(100))+1) chmat=with (x, table(ID,Occasion)) chmat[chmat>0]=1 ch=apply(chmat,1,paste,collapse="") table(ch) If you wanted to include individual covariates you would not use the last table(ch) statement but would tie back to any individual data. regards --jeff Anne-Katrin Link wrote:> Normal 0 21 false false > false > MicrosoftInternetExplorer4 > > > Dear R-helpers, > > I was wondering whether there are any good books and/or website > links that introduce mark-recapture analysis in R. In particular, I am > interested in exploratory data analysis of resighting data and how to > create capture histories from dataframes in R. > > Thank you very much for your reply in advance! > > Cheers, > > Anne > > ------------------------------------------------------------------------ > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
see https://stat.ethz.ch/pipermail/r-sig-ecology/2008-May/000160.html hth, Kingsford On Tue, Oct 13, 2009 at 6:00 AM, Anne-Katrin Link <anne.link at gmx.de> wrote:> Normal ? ? ? ?0 ? ? ? ?21 ? ? ? ? ? ? ? ? ? ? ? ?false ? ? ? ?false > false > MicrosoftInternetExplorer4 > > > Dear R-helpers, > > ? ? ? ? ?I was wondering whether there are any good books and/or website > links that introduce mark-recapture analysis in R. In particular, I am > interested in exploratory data analysis of resighting data and how to > create capture histories from dataframes in R. > > Thank you very much for your reply in advance! > > ? ? ? ? ?Cheers, > > Anne > -- > Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 - > sicherer, schneller und einfacher! http://portal.gmx.net/de/go/atbrowser > > ? ? ? ?[[alternative HTML version deleted]] > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >