[R-sig-genetics] pegas::amova()
Eric Crandall
eric.d.crandall at gmail.com
Thu Jul 23 02:40:41 CEST 2015
Hi Zhian,
Thanks for your quick reply, and sorry for being a bit slow on this end.
Perhaps it is something specific to my system. I cannot run your example. See below.
Thanks again,
Eric
library('pegas')
data(microbov)
set.seed(20150409)
mic20 <- microbov[sample(nInd(microbov), 20)]
microdf <- data.frame(other(mic20))
d <- dist(tab(mic20))
amova(d ~ spe/breed, data = microdf, nperm = 0)
Error in FUN(X[[i]], ...) : 'bin' must be numeric or a factor
SPE <<- as.factor(microdf$spe)
BREED <<- as.factor(microdf$breed)
amova(d ~ SPE/BREED, nperm = 0)
Error in FUN(X[[i]], ...) : 'bin' must be numeric or a factor
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdata_2.17.0 hierfstat_0.04-14 gtools_3.5.0 iNEXT_2.0.3 strataG_0.9.4 plyr_1.8.3 mmod_1.3.0 pegas_0.8-1 adegenet_2.0.0 ape_3.3
[11] seqinr_3.1-3 ade4_1.7-2
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 spdep_0.5-88 mapdata_2.2-4 LearnBayes_2.15 tools_3.2.1 boot_1.3-17 digest_0.6.8 gtable_0.1.2 nlme_3.1-121 lattice_0.20-33 Matrix_1.2-2
[12] igraph_1.0.1 shiny_0.12.1 DBI_0.3.1 parallel_3.2.1 proto_0.3-10 coda_0.17-1 dplyr_0.4.2 stringr_1.0.0 maps_2.3-10 swfscMisc_1.0.3 grid_3.2.1
[23] R6_2.1.0 sp_1.1-1 ggplot2_1.0.1 reshape2_1.4.1 deldir_0.1-9 magrittr_1.5 scales_0.2.5 htmltools_0.2.6 MASS_7.3-43 splines_3.2.1 assertthat_0.1
[34] mime_0.3 colorspace_1.2-6 xtable_1.7-4 httpuv_1.3.2 stringi_0.5-5 munsell_0.4.2
> On Jul 20, 2015, at 1:31 PM, Zhian Kamvar <kamvarz at science.oregonstate.edu> wrote:
>
> Hi Eric,
>
> Can you provide a minimum working example and post your session information?
>
> The following example works for me (adapted from https://github.com/emmanuelparadis/pegas/pull/2#issue-67437033):
>
> library('pegas')
> data(microbov)
> set.seed(20150409)
> mic20 <- microbov[sample(nInd(microbov), 20)]
> microdf <- data.frame(other(mic20))
> d <- dist(tab(mic20))
> amova(d ~ spe/breed, data = microdf, nperm = 0)
>
> SPE <<- as.factor(microdf$spe)
> BREED <<- as.factor(microdf$breed)
> amova(d ~ SPE/BREED, nperm = 0)
>
>> sessionInfo()
> R version 3.2.1 (2015-06-18)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.4 (Yosemite)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] pegas_0.8-1 adegenet_2.0.0 ade4_1.7-2 ape_3.3
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.11.6 spdep_0.5-88 plyr_1.8.3 LearnBayes_2.15 tools_3.2.1
> [6] boot_1.3-16 digest_0.6.8 nlme_3.1-120 gtable_0.1.2 lattice_0.20-31
> [11] Matrix_1.2-1 igraph_1.0.1 shiny_0.12.1 DBI_0.3.1 parallel_3.2.1
> [16] proto_0.3-10 coda_0.17-1 dplyr_0.4.2 stringr_1.0.0 grid_3.2.1
> [21] R6_2.1.0 sp_1.1-1 ggplot2_1.0.1 reshape2_1.4.1 seqinr_3.1-3
> [26] deldir_0.1-9 magrittr_1.5 scales_0.2.5 htmltools_0.2.6 MASS_7.3-41
> [31] splines_3.2.1 assertthat_0.1 mime_0.3 colorspace_1.2-6 xtable_1.7-4
> [36] httpuv_1.3.2 stringi_0.5-5 munsell_0.4.2
>
> The data frame implementation works now, so you can use your strata directly instead of pulling the levels from it:
>
> my_strata <- strata(my_data)
> amova_out <- pegas::amova(dists~l2/l1, data = my_strata, nperm=nperm, is.squared=T)
>
> Additionally, poppr has a wrapper to ADE4's implementation of AMOVA that explicitly handles strata called poppr.amova.
>
> Cheers,
> Zhian
>
>
>> On Jul 20, 2015, at 12:16 , Eric Crandall <eric.d.crandall at gmail.com> wrote:
>>
>> Hi Emmanuel or others,
>>
>> I was directed here to ask a question about the amova function in pegas. Hopefully this is the right place.
>>
>> I have been using pegas::amova() in a function that loops over a database of species to calculate amova at up to three hierarchical levels. My function recently broke, apparently due to a recent update <https://cran.r-project.org/web/packages/pegas/NEWS> to Pegas - specifically this change:
>>
>> o amova() failed when the factors in the rhs of the formula were
>> in a data frame. Thanks to Zhian Kamvar for the fix.
>>
>> As a workaround to for pegas:amova not being able to use a dataframe of factors, I was assigning the factors to the global environment:
>>
>> level1factor<<-as.factor(sp[[l1]])
>> level2factor<<-as.factor(sp[[l2]])
>> amova_out<-pegas::amova(dists~level2factor/level1factor, nperm=nperm, is.squared=T)
>>
>>
>> Now, after the update, my function is throwing an error. The traceback goes
>>
>> 4 stop("'bin' must be numeric or a factor")
>> 3 FUN(X[[i]], ...)
>> 2 lapply(gr, tabulate)
>> 1 pegas::amova(dists ~ level2factor/level1factor, nperm = nperm,
>> is.squared = T)
>>
>> As far as I can tell, the objects that I am submitting to tabulate() in gr via lapply() ARE factors.
>>
>> When I try to reproduce the problem by running step by step through the pegas::amova function, everything works fine.
>>
>> So I am stumped for now. Does anyone have any ideas?
>>
>>
>> Many thanks,
>>
>> Eric Crandall
>>
>>
>>
>> PS - I’m very happy to see strata being added to genind objects in adegenet. Will these eventually be usable by pegas::amova or a similar amova function?
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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