[R-sig-eco] NA error in envfit
Jari Oksanen
jari.oksanen at oulu.fi
Thu Dec 5 14:07:19 CET 2013
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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