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-boun...@r-project.org
> [r-sig-ecology-boun...@r-project.org] on behalf of Stephen Sefick
> [sas0...@auburn.edu]
> Sent: 04 December 2013 22:01
> To: Mitchell, Kendra
> Cc: r-sig-ecology@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]]
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
> --
> Stephen Sefick
> **************************************************
> Auburn University
> Biological Sciences
> 331 Funchess Hall
> Auburn, Alabama
> 36849
> **************************************************
> sas0...@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
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
--
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
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
