Hi Gavin, Many thanks for your help and interest. Regards, Laura > Subject: RE: [R] Error in plot.envfit(ef, p.max = 0.1) : (subscript) > logical subscript too long > From: gavin.simp...@ucl.ac.uk > To: lauram...@hotmail.com > CC: r-help@r-project.org > Date: Mon, 31 Dec 2012 23:05:31 +0100 > > Hi Laura, > > Following a bit of further digging, I noticed that the bug was in not > handling the levels of the factor constraints appropriately. In your > data set 12 rows (observations) were deleted because of missing data. > These observations meant that one or more of the factor variables had > more levels() than actually used in the subset of data analysed. > > I have checked in some fixes for this which removes the extraneous > levels: > > https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=vegan&revision=2342 > > We are currently planning a release for some time in the new year, but > in the meantime, you can get a copy of the development version of Vegan > from R-forge once the new binary has been built (needs to be Rev 2342 or > later to include this fix but only Rev 2341 has been built thus far): > > https://r-forge.r-project.org/R/?group_id=68 > > I've CC'd this back to R-Help for the record. > > Thanks for taking the time to post about this and for sending me your > data so I could track this down quickly. > > All the best and Happy New Year. > > G > > On Mon, 2012-12-31 at 14:17 +0000, Laura Martínez Suz wrote: > > Hi Gavin, > > > > > > Thank you! It works now, that's great, many thanks. I have spent hours > > trying to see what I was doing wrong, I'm not very good in R.. > > > > > > That was my first email to the R community, should I "officialy" reply > > to you? > > > > > > All the best for you as well and happy New Year! > > > > > > Laura > > > > > > > > > Subject: RE: [R] Error in plot.envfit(ef, p.max = 0.1) : (subscript) > > logical subscript too long > > > From: gavin.simp...@ucl.ac.uk > > > To: lauram...@hotmail.com > > > CC: lauram...@um.es > > > Date: Mon, 31 Dec 2012 12:02:09 +0100 > > > > > > Hi Laura, > > > > > > Thanks for this. There is a bug which has lead me to discover > > another > > > bug in that same section of code. The issue you uncovered is that > > you > > > have factor variables but none are significant at the level you > > > requested and we don't handle the "no significant factors" case > > > explicitly. That led me to find another bug in that I don't think > > this > > > code to select significant factors ever worked correctly. > > > > > > I'll need to speak to Jari about this as he wrote the code, but he > > is > > > away at the moment. I'll see about coming up with a fix for this. > > > > > > In the meantime, I presume this will work for you as the factors are > > not > > > significant, just drop them before doing the envfit() call: > > > > > > facs <- sapply(enviromentaldata_file, is.factor) > > > env <- enviromentaldata_file[, !facs] > > > > > > ef <- envfit(species, env, permutations = 999, na.rm = TRUE) > > > > > > plot(species, display = "sites") > > > plot(ef, p.max = 0.1) > > > > > > HTH and thanks for providing the data. I'll delete it now. > > > > > > All the best, > > > > > > Gavin > > > > > > On Sun, 2012-12-30 at 15:25 +0000, Laura Martínez Suz wrote: > > > > Hi Gavin, > > > > > > > > > > > > Many thanks! Here they go, named as in the scripts. > > > > > > > > > > > > species_matrix is the file with the relative abundance of each > > species > > > > (394) related to the total number of species in each plot (22). > > > > > > > > > > > > environmentaldata_file corresponds to data from the 22 plots in > > the > > > > same order than in the species file. > > > > > > > > > > > > I wanted to see which factors are affecting the dissimilarities in > > > > community composition among plots and plot the significant ones as > > > > vectors at p<0.1. > > > > > > > > > > > > Sorry if it becomes a silly thing and thanks again for your > > offer.. > > > > and yes, please, delete them! :) > > > > > > > > > > > > Regards, > > > > > > > > > > > > Laura > > > > > > > > > > > > > Subject: Re: [R] Error in plot.envfit(ef, p.max = 0.1) : > > (subscript) > > > > logical subscript too long > > > > > From: gavin.simp...@ucl.ac.uk > > > > > To: lauram...@hotmail.com > > > > > CC: r-help@r-project.org > > > > > Date: Sun, 30 Dec 2012 13:16:56 +0100 > > > > > > > > > > On Sat, 2012-12-29 at 20:40 +0000, Laura Martínez Suz wrote: > > > > > > Hello there, > > > > > > I'm trying to plot vectors with p<0.1 in a NMDS ordination > > plot > > > > using p.max. Below the scripts I'm using. I guess I'm missing > > > > something! could you please give me a hand? > > > > > > > > > > > > species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, > > dis="sites")plot(ef,p.max=0.1) > > > > > > Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical > > > > subscript too long > > > > > > Many thanks! > > > > > > Laura > > > > > > > > > > Hi Laura, > > > > > > > > > > Can you send the data to me **off list** so I can run through > > the > > > > code > > > > > under the debugger and see what is causing the error? I can see > > > > where > > > > > the subscripting occurs related to p.max but can't immediately > > see > > > > under > > > > > what circumstances the subscript could ever get longer than the > > > > object > > > > > being subscripted. > > > > > > > > > > I promise to delete the data once I have tracked the problem > > down. > > > > > > > > > > Cheers, > > > > > > > > > > G > > > > > > > > > > -- > > > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ > > %~%~ > > > > % > > > > > 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 > > > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ > > %~%~ > > > > % > > > > > > > > > > > > > > > -- > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ > > % > > > 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 > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ > > % > > > > > > > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > 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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > [[alternative HTML version deleted]]
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