[R-sig-eco] singletons and doubletons in vegan
Hi all, I am running species accumulation curves for several data-sets, and am also playing with some estimators with this function in vegan: SF.estimators-poolaccum(SF.data,permutations=1000) SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap plot(SF.estimators) # illustrates graphs for all estimators summary(SF.estimators,display=jack2) # gives jack2 stats Does any of you know how can I get the info about singletons and doubletons? best wishes João João Canning Clode, Ph.D Research Associate Smithsonian Environmental Research Center 647 Contees Wharf Road Edgewater, MD 21037 Email: canning-clo...@si.edumailto:canning-clo...@si.edu Web: www.canning-clode.comhttp://www.canning-clode.com ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] singletons and doubletons in vegan
On Wed, 2012-02-01 at 07:32 -0500, Canning-Clode, Joao wrote: Hi all, I am running species accumulation curves for several data-sets, and am also playing with some estimators with this function in vegan: SF.estimators-poolaccum(SF.data,permutations=1000) SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap plot(SF.estimators) # illustrates graphs for all estimators summary(SF.estimators,display=jack2) # gives jack2 stats Does any of you know how can I get the info about singletons and doubletons? What info do you want? Working out which spp are singletons and doubletons from the input data is quite simple for the entire pool of samples (he says, hoping I i] understood and ii] got this right ;-): cs - colSums(SF.data 0) singlet - cs == 1L doublet - cs == 2L singlet[which(singlet)] doublet[which(doublet)] E.g. ## Load example data set from vegan data(BCI) ## compute the column sums cs - colSums(BCI 0) ## logicals for singleton and doubleton singlet - cs == 1L doublet - cs == 2L ## which species are... singlet[which(singlet)] doublet[which(doublet)] ## number of singletons and doubletons... sum(singlet) sum(doublet) HTH G best wishes João João Canning Clode, Ph.D Research Associate Smithsonian Environmental Research Center 647 Contees Wharf Road Edgewater, MD 21037 Email: canning-clo...@si.edumailto:canning-clo...@si.edu Web: www.canning-clode.comhttp://www.canning-clode.com ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] singletons and doubletons in vegan
On 01/02/2012, at 14:34 PM, Canning-Clode, Joao wrote: Hi all, I am running species accumulation curves for several data-sets, and am also playing with some estimators with this function in vegan: SF.estimators-poolaccum(SF.data,permutations=1000) SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap plot(SF.estimators) # illustrates graphs for all estimators summary(SF.estimators,display=jack2) # gives jack2 stats Does any of you know how can I get the info about singletons and doubletons? What information do you need? If you want to know the names of singleton and doubleton *occurrences* on plots, you can use (with the BCI data in vegan): freq - colSums(BCI0) which(freq==1) which(freq==2) If you want to something similar for counts (individuals), you just change the command to find the 'freq'. If you want to know how many singleton and doubleton species you have in each of your sampling units, you can use rowSums(BCI[, freq==1] 0) rowSums(BCI[, freq==2] 0) If you want to know how may species have exactly one individual (stem) in a sampling unit, just use rowSums(BCI==1) Was the information you asked among these things, or do you want to have something more? Cheers, Jari Oksanen -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
