Hi,
I'm trying to run NMDS (non-metric multidimensional scaling) with R vegan
(metaMDS) but I have a few NAs in my data set. I've tried to run it 2 ways.

The first way with my entire data set which includes variables such as ID,
sex, exposure, treatment, sodium, potassium, chloride....

mydata.mds<-metaMDS(dat)

I get the following error:

 in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) { :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In Ops.factor(left, right) : < not meaningful for factors
2: In Ops.factor(left, right) : < not meaningful for factors
3: In Ops.factor(left, right) : < not meaningful for factors
4: In Ops.factor(left, right) : < not meaningful for factors
5: In Ops.factor(left, right) : < not meaningful for factors

The second way with only those last biochemical variables (29 in total).

mydata.mds<-metaMDS(measurements)

I get this error:

Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0)) {
:
  missing value where TRUE/FALSE needed

My go to "na.rm=TRUE" does nothing. Any ideas on how to account for NAs and
if so which of the above options I should be using?
Thanks!
Elizabeth

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