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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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."
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