CODEWITHSUNDEEP
r
Ruth P
Ruth P

Reputation: 41

How to fix an error message "Error in round(pwfst, 3) : non-numeric argument to mathematical function"

I am using

pwfst <-stamppFst(gl, nboots=1, percent=95, nclusters=1)
round(pwfst,3)

This works perfectly if nboots = 1, but when I try nboots = 3, I get the following error:

Error in round(pwfst, 3) : non-numeric argument to mathematical function

I want to eventually use nboots = 100

I have read several posts with

non-numeric argument to mathematical function

But none relate to this problem. One post advised advised ensuring I only had the necessary packages loaded. I have done that and no change.

Has anyone any ideas please? thanks.

EDIT: pwfstis not a list. It has this form - there are 5 more columns

              Bees Nest Ridge_12 Bees Nest Ridge_15 Broken Back Trail Cousins Creek
Bees Nest Ridge_12                 NA                 NA                NA            NA
Bees Nest Ridge_15              0.092                 NA                NA            NA
Broken Back Trail               0.124              0.067                NA            NA
Cousins Creek                   0.396              0.352             0.376            NA
Sawpit Rd                       0.104              0.046             0.077         0.349
Wallaby Rocks                   0.450              0.384             0.421         0.540
Bees Nest Ridge_13              0.161              0.098             0.132         0.403
Wingen Maid                     0.433              0.376             0.409         0.537
Bees Nest Ridge_14              0.086              0.025             0.056         0.354

Second edit:

str(pwfst)

returns

num [1:9, 1:9] NA 0.0922 0.1243 0.3964 0.1038 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:9] "Bees Nest Ridge_12" "Bees Nest Ridge_15" "Broken Back Trail" "Cousins Creek" ...
  ..$ : chr [1:9] "Bees Nest Ridge_12" "Bees Nest Ridge_15" "Broken Back Trail" "Cousins Creek" ...

Hopefully that is enough info for someone to be able to help me. Thanks, Ruth P

Upvotes: 0

Views: 88

Answers (1)

Lennyy
Lennyy

Reputation: 6132

The documentation for the stamppFst() function reads: "If nboots<2, no bootstrapping is performed and therefore only a matrix of Fst values is returned." Therefore, when pwfst is a result of an analysis using 1 boot you supply a matrix to the round function, which the round function can handle. In other cases (when nboots >= 2), you supply a list to the round function, which it is not able to handle this way.

If pwfst is a list, you could run lapply(pwfst, round) so that it runs round on every matrix in the list.

Upvotes: 1

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