[R-sig-eco] NA error in envfit

Wed Dec 4 21:01:42 CET 2013

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
>
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>
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-- 
Stephen Sefick
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Auburn University
Biological Sciences
331 Funchess Hall
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sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
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