trouble importing genalex

nick.a...@gmail.com

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Aug 7, 2015, 1:06:17 AM8/7/15

to poppr

Hello,

I am struggling simply importing a genalex into poppr. Any help would be greatly appreciated.

portion of my data... two populations, 1 locus with two alleles

> x<-getfile()
> x
$files
[1] "/Users/nickwong/Library/R/3.1/library/poppr/files/test.csv"

$path
[1] "/Users/nickwong/Library/R/3.1/library/poppr/files"

> myData<-read.genalex(x$files, ploidy = 2, geo = FALSE, region = FALSE)
Error in if (any(gena.mat == "0") & ploidy < 3) { : 
  missing value where TRUE/FALSE needed
> traceback()
1: read.genalex(x$files, ploidy = 2, geo = FALSE, region = FALSE)

> 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_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] poppr_2.0.2    adegenet_2.0.0 ade4_1.7-2    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0      spdep_0.5-88     plyr_1.8.3       pegas_0.8-1     
 [5] LearnBayes_2.15  tools_3.2.1      boot_1.3-16      digest_0.6.8    
 [9] nlme_3.1-120     gtable_0.1.2     lattice_0.20-31  mgcv_1.8-6      
[13] Matrix_1.2-1     igraph_1.0.1     shiny_0.12.2     DBI_0.3.1       
[17] parallel_3.2.1   proto_0.3-10     coda_0.17-1      cluster_2.0.1   
[21] dplyr_0.4.2      stringr_1.0.0    grid_3.2.1       R6_2.1.0        
[25] phangorn_1.99.14 sp_1.1-1         ggplot2_1.0.1    reshape2_1.4.1  
[29] seqinr_3.1-3     deldir_0.1-9     magrittr_1.5     nnls_1.4        
[33] scales_0.2.5     htmltools_0.2.6  MASS_7.3-40      splines_3.2.1   
[37] assertthat_0.1   permute_0.8-4    mime_0.3         ape_3.3         
[41] colorspace_1.2-6 xtable_1.7-4     httpuv_1.3.3     quadprog_1.5-5  
[45] stringi_0.5-5    munsell_0.4.2    vegan_2.3-0

First time posting - hope this is enough.

Thanks very much

Nick

Zhian Kamvar

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Aug 7, 2015, 11:11:22 AM8/7/15

to poppr

Hi Nick,

Thank you for your email and thank you for supplying the necessary diagnostic information. I believe you've discovered an edge case. I have tried it on some random data using the same entries and have run into an error as well (although not the same error). I will investigate this when I get in next week. Since you have one locus, I would suggest removing the first two rows of your spreadsheet and collapsing the last two columns into a single column (separating the alleles with "/") and importing that using read.table and then using df2genind like so:

my_df <- read.table("myData.csv", sep = ",", header = TRUE)
my_data <- df2genind(my_df[-c(1, 2), , drop = FALSE], ind.names = my_df$ind, pop.names = my_df$pop, ploidy = TRUE, sep = "/")

Additionally:

[1] "/Users/nickwong/Library/R/3.1/library/poppr/files/test.csv"

This is from your output. You should not be saving files in your R library. This is a space only for packages. The example using getfile was simply an example using files that I could ship with poppr.

> myData<-read.genalex(x$files, ploidy = 2, geo = FALSE, region = FALSE) Error in if (any(gena.mat == "0") & ploidy < 3) { : missing value where TRUE/FALSE needed > traceback() 1: read.genalex(x$files, ploidy = 2, geo = FALSE, region = FALSE)

This error is telling me that there was a missing value in your data. You might have had extra rows or columns that didn't appear to have data in them; however given the error I got, the problem might go deeper.

Again, I will be investigating this further and will have it fixed in the next release.

Cheers,

Zhian

Zhian Kamvar

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Aug 9, 2015, 5:49:30 PM8/9/15

to poppr

Hello,

The issue should be fixed.

To fix it without re-installing poppr from source: https://gist.github.com/zkamvar/b64078a0d04d2452c905 (Note: if you choose this route, you must do this every time you restart R)
If you want to fix it by installing from source, please install from github (Instructions here: https://github.com/grunwaldlab/poppr#stable-and-development-versions)
Link to the issue: https://github.com/grunwaldlab/poppr/issues/58

Cheers,

Zhian

Camillo Rodriguiez

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Feb 26, 2016, 6:17:59 PM2/26/16

to poppr

Dear Zhean,

I am struggling exactly with the same problem of Nick. I have followed all the steps to reinstall POPPR from github, but I still can not import my GenAlex file into POPPR.

>p_cubensis2012<-read.genalex("/Users/milobello29/Desktop/lina.csv")

Error in if (any(gena.mat == "0") & ploidy < 3) { :

missing value where TRUE/FALSE needed

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.10.4 (Yosemite)

locale:

[1] C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] phangorn_2.0.2 ape_3.4 poppr_2.1.0 adegenet_2.0.1 ade4_1.7-3

loaded via a namespace (and not attached):

[1] Rcpp_0.12.3 spdep_0.5-92 git2r_0.13.1 plyr_1.8.3 pegas_0.8-2

[6] LearnBayes_2.15 tools_3.2.2 boot_1.3-17 digest_0.6.9 memoise_1.0.0

[11] nlme_3.1-121 gtable_0.1.2 lattice_0.20-33 mgcv_1.8-7 Matrix_1.2-2

[16] igraph_1.0.1 shiny_0.13.1 DBI_0.3.1 curl_0.9.6 parallel_3.2.2

[21] coda_0.18-1 knitr_1.12.3 withr_1.0.1 httr_1.1.0 dplyr_0.4.3

[26] stringr_1.0.0 cluster_2.0.3 devtools_1.10.0 grid_3.2.2 R6_2.1.2

[31] sp_1.2-2 ggplot2_2.0.0 reshape2_1.4.1 seqinr_3.1-3 deldir_0.1-9

[36] magrittr_1.5 nnls_1.4 scales_0.3.0 htmltools_0.3 MASS_7.3-43

[41] splines_3.2.2 assertthat_0.1 mime_0.4 permute_0.9-0 colorspace_1.2-6

[46] xtable_1.8-2 httpuv_1.3.3 quadprog_1.5-5 stringi_1.0-1 munsell_0.4.3

[51] vegan_2.3-3

portion of my data... 13 populations, 7 locus with two alleles

Any help would be greatly appreciated.

Please, help me!

Julian

Zhian Kamvar

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Feb 26, 2016, 7:28:15 PM2/26/16

to Camillo Rodriguiez, poppr

Hi Camillo,

It's difficult to tell what might be causing the problem from this image. I think it might have something to do with how missing data are handled. I've made a change to the github version. Can you try that and see if it makes a difference?

devtools::install_github("grunwaldlab/poppr@24c8838977")

Best,

Zhian

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