

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.simpson@ucl.ac.uk
> To: lauramsuz@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.simpson@ucl.ac.uk
> > > To: lauramsuz@hotmail.com
> > > CC: lauramsuz@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.simpson@ucl.ac.uk
> > > > > To: lauramsuz@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
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> 
 		 	   		  
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