Re: [R-sig-eco] Error with raup distance, in metaMDS
Thank you very much Brian. Best, Manuel On 28/03/2011 06:07 a.m., Brian Inouye wrote: There are other dissimilarity metrics that could also be used, each with different assumptions of course. Raup-Crick is a reasonable choice of distance metric, but I'm not sure if the current version of vegdist() has been updated to reflect discussion in Chase et al 2011 in Ecosphere (http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1). -Brian On 3/28/2011 12:00 PM,Manuel Spínolamspinol...@gmail.com wrote: Is the Raup--Crick dissimilarity metric the only option for a presence/absence data in vegdist or using binary = T could I use any other dissimilarity metric? Best, Manuel snip On 27/03/2011 09:07 a.m., Jari Oksanen wrote: Manuel, As I read it, the error message comes from isoMDS() that does not accept zero distances, and you have decided to ignore this (by setting zerodist = ignore). Either you or isoMDS must give up, and I think it is easier for you: try setting 'zerodist = add', and confess that isoMDS() wins your dispute. Another message you got is from vegdist() which only tells you that empty species (= that do not occur in your data) will influence your data. That is only informational, and not an error. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal website: Lobito de río https://sites.google.com/site/lobitoderio/ Institutional website: ICOMVIS http://www.icomvis.una.ac.cr/ [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Error with raup distance in metaMDS
On 26/03/11 17:35 PM, Manuel Spínola mspinol...@gmail.com wrote: Dear list members, I got an error message working with RaupCrick distance in metaMDS. flora.mds = metaMDS(indicadora, distance = raup, trace = FALSE, zerodist = ignore) Error in isoMDS(dist, k = k, trace = isotrace) : zero or negative distance between objects 1 and 2 In addition: Warning message: In distfun(comm, method = distance, ...) : data have empty species which influence the results im method raup Manuel, As I read it, the error message comes from isoMDS() that does not accept zero distances, and you have decided to ignore this (by setting zerodist = ignore). Either you or isoMDS must give up, and I think it is easier for you: try setting 'zerodist = add', and confess that isoMDS() wins your dispute. Another message you got is from vegdist() which only tells you that empty species (= that do not occur in your data) will influence your data. That is only informational, and not an error. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Error with raup distance in metaMDS
Dear list members, I got an error message working with RaupCrick distance in metaMDS. flora.mds = metaMDS(indicadora, distance = raup, trace = FALSE, zerodist = ignore) Error in isoMDS(dist, k = k, trace = isotrace) : zero or negative distance between objects 1 and 2 In addition: Warning message: In distfun(comm, method = distance, ...) : data have empty species which influence the results im method raup Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal website: Lobito de río https://sites.google.com/site/lobitoderio/ Institutional website: ICOMVIS http://www.icomvis.una.ac.cr/ [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
