Error with aboot function when trying to use a custom distance on presence/absence data

eoisriouéaép apoeidoisfdsd

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Dec 2, 2019, 4:46:20 AM12/2/19

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I am trying to use a custom distance on presence/absence data with the function aboot but I keep getting the same error:

Error in .setupMethodsTables(fdef, initialize = TRUE) : 
  no slot of name "group" for this object of class "derivedDefaultMethod"
Called from: .setupMethodsTables(fdef, initialize = TRUE

I get the same message when using the Aeut dataset and the custom function "bindist" provided as example:

data(Aeut)
bindist <- function(x){ stopifnot(is.genind(x)) dist(tab(x), method = "binary") }
aboot(Aeut, dist = function(x) bootgen2genind(x) %>% bindist)

Zhian Kamvar

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Dec 2, 2019, 4:51:34 AM12/2/19

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Hello,

That definitely looks like a bug. I'll open an issue and try to get it fixed soon.

Best,

Zhian

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eoisriouéaép apoeidoisfdsd

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Dec 2, 2019, 5:24:16 AM12/2/19

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Great, thank you Zhian!

Can you let me know when this is fixed? I'll keep an eye on this thread!

Thanks again

Le lundi 2 décembre 2019 10:51:34 UTC+1, Zhian Kamvar a écrit :

Hello,

That definitely looks like a bug. I'll open an issue and try to get it fixed soon.

Best,
Zhian

On Mon, Dec 2, 2019 at 9:46 AM eoisriouéaép apoeidoisfdsd <apoei...@gmail.com> wrote:

I am trying to use a custom distance on presence/absence data with the function aboot but I keep getting the same error:

Error in .setupMethodsTables(fdef, initialize = TRUE) : 
  no slot of name "group" for this object of class "derivedDefaultMethod"
Called from: .setupMethodsTables(fdef, initialize = TRUE

I get the same message when using the Aeut dataset and the custom function "bindist" provided as example:

data(Aeut)
bindist <- function(x){ stopifnot(is.genind(x)) dist(tab(x), method = "binary") }
aboot(Aeut, dist = function(x) bootgen2genind(x) %>% bindist)

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Zhian Kamvar

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Dec 2, 2019, 5:27:20 AM12/2/19

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I'll make sure to post back here once I have some time to track down and fix the bug. In the meantime, I've opened an issue here: https://github.com/grunwaldlab/poppr/issues/210

Best,

Zhian

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Zhian Kamvar

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Dec 6, 2019, 10:51:30 AM12/6/19

to eoisriouéaép apoeidoisfdsd, poppr

Hello,

The issue is the fact that aboot simply takes the matrix from presence/absence data instead of converting it to a bootgen object. You should be able to run the command like so and get the same answer:

aboot(tab(Aeut), dist = dist, method = "binary")

I will still work on generating a better warning and update here when I have done so.

Best,

Zhian

eoisriouéaép apoeidoisfdsd

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Dec 10, 2019, 10:04:01 AM12/10/19

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Dear Zhian,

This solved my problem indeed, thank you for looking into it

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