Error with custom distance in aboot with PA data

[zkamvar]

library(poppr)
#> Loading required package: adegenet
#> Loading required package: ade4
#> Registered S3 method overwritten by 'spdep':
#>   method   from
#>   plot.mst ape
#> 
#>    /// adegenet 2.1.1 is loaded ////////////
#> 
#>    > overview: '?adegenet'
#>    > tutorials/doc/questions: 'adegenetWeb()' 
#>    > bug reports/feature requests: adegenetIssues()
#> Registered S3 method overwritten by 'pegas':
#>   method      from
#>   print.amova ade4
#> This is poppr version 2.8.3. To get started, type package?poppr
#> OMP parallel support: available
data(Aeut)
bindist <- function(x){ stopifnot(is.genind(x)); dist(tab(x), method = "binary") }
aboot(Aeut, dist = function(x) bootgen2genind(x) %>% bindist)
#> Error in .setupMethodsTables(fdef, initialize = TRUE): no slot of name "group" for this object of class "derivedDefaultMethod"

^{Created on 2019-12-02 by the reprex package (v0.3.0)}

This originated from a discussion on the poppr forum.

[zkamvar]

Here's the traceback:

13: .setupMethodsTables(fdef, initialize = TRUE)
12: (function (fdef, env = environment(fdef), check = TRUE, inherited = FALSE) 
    {
        name <- if (inherited) 
            ".AllMTable"
        else ".MTable"
        if (check && !exists(name, envir = env, inherits = FALSE)) {
            .setupMethodsTables(fdef, initialize = TRUE)
            if (!exists(name, envir = env, inherits = FALSE)) 
                stop("invalid methods table request")
        }
        get(name, envir = env)
    })(new("derivedDefaultMethod", .Data = function (bg) 
    {
        standardGeneric("bootgen2genind")
    }, target = new("signature", .Data = "matrix", names = "bg", 
        package = "methods"), defined = new("signature", .Data = "ANY", 
        names = "bg", package = "methods"), generic = "bootgen2genind"))
11: bootgen2genind(x)
10: bootgen2genind(x)
9: eval(lhs, parent, parent)
8: eval(lhs, parent, parent)
7: bootgen2genind(x) %>% bindist at #1
6: (function (x) 
   bootgen2genind(x) %>% bindist)(x = c(1L, 1L, 1L, 1L, 1L, 1L, 
 
<SNIP>

5: do.call(DISTFUNK, distargs)
4: as.dist(D)
3: TREEFUNK(do.call(DISTFUNK, distargs))
2: treefunk(xboot)
1: aboot(Aeut[1:10, 1:10], dist = function(x) bootgen2genind(x) %>% 
       bindist)

[zkamvar]

Internally, aboot converts the PA genind object to a matrix, so we can create a bootgen2genind method for matrix, but it might just be better to recommend to people to extract the matrix itself before using bootgen2genind() on PA data.