[R-sig-eco] NA error in envfit

Thu Dec 5 15:12:28 CET 2013

Hai,

building and installing from github is quite easy with the devtools
package (thanks to Hadley!):

# install devtools
install.packages('devtools')
require(devtools)

# install vegan from github
install_github('vegan', 'jarioksa')


Cheers,

Eduard Szöcs


On 12/05/2013 02:07 PM, Jari Oksanen wrote:
> Hello,
> 
> I think I saw something like this in autumn (northern hemisphere) when a variable had constant values with no variation, and envfit did not know how to scale the arrow. 
> 
> We fixed this in the development version of vegan in R-Forge on September 29. Unfortunately R-Forge is again dysfunctional and cannot build the package, but if you are able to do that yourself you can try to see if the problem is fixed there. The same files are also in github, but you need to build the package yourself there too. I'm working with a minor release of vegan (2.0-10) which may be published on Monday 9 Dec, but there are no guarantees that it will have this envfit fix or be released like planned (you know, the best laid plans of mice and men...) 
> 
> It may be easiest to see if a constant "variable" is the culprit, and remove that if needed. If this is not the case, we need more info and a *reproducible* example. We haven't got any now, and I cannot reproduce your problem.
> 
> Cheers, Jari Oksanen
> ________________________________________
> From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of Stephen Sefick [sas0025 at auburn.edu]
> Sent: 04 December 2013 22:01
> To: Mitchell, Kendra
> Cc: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] NA error in envfit
> 
> Kendra,
> 
> Something is wrong in X or P; find out what the foreign function call is
>   and then you may be able to track down the offending data problem.
> Maybe a logarithm somewhere? This is probably not much help; I don't
> have much experience with envfit.
> 
> Stephen
> 
> On 12/03/2013 07:06 PM, Mitchell, Kendra wrote:
>> I'm running a bunch of NMS with vectors fitted (slicing and dicing a large dataset in different ways).  I'm suddenly getting an error  from envfit
>>
>> f.bSBS.org.fit<-envfit(f.bSBS.org.nms, f.bSBS.org.env, permutations=999, na.rm=TRUE)
>>
>> Error in vectorfit(X, P, permutations, strata, choices, w = w, ...) :
>>    NA/NaN/Inf in foreign function call (arg 1)
>> In addition: Warning message:
>> In vectorfit(X, P, permutations, strata, choices, w = w, ...) :
>>    NAs introduced by coercion
>>
>> I can plot the NMS and even run ordifit on individual env variables, so can't figure out what the problem is.   There aren't any NA/NaN/Inf in either of those data that I can find.  I've tried running it without na.rm=TRUE and still get the error.  Guidance on how to fix this would be appreciated.
>>
>> Here's the whole slicing process and str for the data
>>
>>
>> f.bSBS.org<-f.env$zone.hor=="bSBS.1"
>> f.bSBS.org.tyc<-f.tyc[f.bSBS.org,f.bSBS.org]
>> f.bSBS.org.env<-subset(f.env, f.env$zone.hor=="bSBS.1")
>> f.bSBS.org.nms<-metaMDS(as.dist(f.bSBS.org.tyc), k=3, trymin=50, trymax=250, wascores=FALSE)
>> f.bSBS.org.fit<-envfit(f.bSBS.org.nms, f.bSBS.org.env, permutations=999, na.rm=TRUE)
>>
>>
>> str(f.bSBS.org.env)
>> 'data.frame':    63 obs. of  14 variables:
>>   $ zone         : Factor w/ 6 levels "bIDF","bSBS",..: 2 2 2 2 2 2 2 2 2 2 ...
>>   $ site         : Factor w/ 18 levels "A7","A8","A9",..: 12 12 12 12 12 12 12 12 12 12 ...
>>   $ om           : Factor w/ 4 levels "0","1","2","3": 2 2 2 3 3 3 2 2 2 3 ...
>>   $ compaction   : num  1 1 1 1 1 1 1 1 1 1 ...
>>   $ herbicide    : num  0 0 0 0 0 0 0 0 0 0 ...
>>   $ horizon      : Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
>>   $ Water_content: num  50.3 50.3 50.3 50.1 50.1 ...
>>   $ DNA_ug_g     : num  71.2 71.2 71.2 68.6 68.6 ...
>>   $ C            : num  30.5 30.5 30.5 28.4 28.4 ...
>>   $ N            : num  0.863 0.863 0.863 0.81 0.81 ...
>>   $ pH_H2O       : num  4.63 4.63 4.63 4.49 4.49 ...
>>   $ CN           : num  35.3 35.3 35.3 35.1 35.1 ...
>>   $ f.env$zone   : Factor w/ 6 levels "bIDF","bSBS",..: 2 2 2 2 2 2 2 2 2 2 ...
>>   $ zone.hor     : chr  "bSBS.1" "bSBS.1" "bSBS.1" "bSBS.1" ...
>>
>> str(f.bSBS.org.nms)
>> List of 35
>>   $ nobj      : int 63
>>   $ nfix      : int 0
>>   $ ndim      : num 3
>>   $ ndis      : int 1953
>>   $ ngrp      : int 1
>>   $ diss      : num [1:1953] 0.00424 0.00437 0.05169 0.07522 0.11039 ...
>>   $ iidx      : int [1:1953] 12 8 55 56 52 7 56 12 59 52 ...
>>   $ jidx      : int [1:1953] 7 6 18 55 8 3 18 3 12 49 ...
>>   $ xinit     : num [1:189] 0.654 0.837 0.438 0.105 -0.313 ...
>>   $ istart    : int 1
>>   $ isform    : int 1
>>   $ ities     : int 1
>>   $ iregn     : int 1
>>   $ iscal     : int 1
>>   $ maxits    : int 200
>>   $ sratmx    : num 1
>>   $ strmin    : num 1e-04
>>   $ sfgrmn    : num 1e-07
>>   $ dist      : num [1:1953] 0.0679 0.0231 0.3598 0.1248 0.1422 ...
>>   $ dhat      : num [1:1953] 0.0455 0.0455 0.2076 0.2076 0.2076 ...
>>   $ points    : num [1:63, 1:3] -0.1256 0.1224 0.267 0.2374 -0.0427 ...
>>    ..- attr(*, "dimnames")=List of 2
>>    .. ..$ : chr [1:63] "LL001" "LL002" "LL003" "LL007" ...
>>    .. ..$ : chr [1:3] "MDS1" "MDS2" "MDS3"
>>    ..- attr(*, "centre")= logi TRUE
>>    ..- attr(*, "pc")= logi TRUE
>>    ..- attr(*, "halfchange")= logi FALSE
>>   $ stress    : num 0.157
>>   $ grstress  : num 0.157
>>   $ iters     : int 180
>>   $ icause    : int 3
>>   $ call      : language metaMDS(comm = as.dist(f.bSBS.org.tyc), k = 3, trymax = 250, wascores = FALSE, trymin = 50)
>>   $ model     : chr "global"
>>   $ distmethod: chr "user supplied"
>>   $ distcall  : chr "as.dist.default(m = f.bSBS.org.tyc)"
>>   $ distance  : chr "user supplied"
>>   $ converged : logi TRUE
>>   $ tries     : num 23
>>   $ engine    : chr "monoMDS"
>>   $ species   : logi NA
>>   $ data      : chr "as.dist(f.bSBS.org.tyc)"
>>   - attr(*, "class")= chr [1:2] "metaMDS" "monoMDS"
>>
>>
>> --
>> Kendra Maas Mitchell, Ph.D.
>> Post Doctoral Research Fellow
>> University of British Columbia
>> 604-822-5646
>>
>>       [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
> 
> --
> Stephen Sefick
> **************************************************
> Auburn University
> Biological Sciences
> 331 Funchess Hall
> Auburn, Alabama
> 36849
> **************************************************
> sas0025 at auburn.edu
> http://www.auburn.edu/~sas0025
> **************************************************
> 
> Let's not spend our time and resources thinking about things that are so
> little or so large that all they really do for us is puff us up and make
> us feel like gods.  We are mammals, and have not exhausted the annoying
> little problems of being mammals.
> 
>                                  -K. Mullis
> 
> "A big computer, a complex algorithm and a long time does not equal
> science."
> 
>                                -Robert Gentleman
> 
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> 
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> 


-- 
Eduard Szöcs
Quantitative Landscape Ecology
Institute for Environmental Sciences
University Koblenz-Landau
Fortstrasse 7
76829 Landau
Germany
http://www.uni-koblenz-landau.de/landau/fb7/umweltwissenschaften/landscape-ecology/Staff/eduardszoecs