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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