[adegenet-forum] Problems with genind object

[Tagliamonte,Massimiliano S]

Hi Logan,


Out of curiosity, do your population or sample names include non alphanumeric characters? Such as dots, as an example? If they do, try and remove those characters, see if it helps. Make sure the new names are still unique.


Good luck with your analyses,

Max


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Immunology
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Logan Clark <clarklc at appstate.edu>
Sent: Thursday, November 2, 2017 3:10 PM
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Problems with genind object

Hi, I am working on a project involving microsatellite data in a relatively standard diploid species. I have 141 samples across 17 loci and my alleles formatted as 168/184 for a heterozygote and 168/168 for a homozygote. I have been able to transfer my data from a .csv file to a dataframe then to a genind object using df2genind. I have been able to run other statistics on the genind object I have created such as HWE, but I am trying to use the chao_bootstrap function in mmod with this object and I keep getting the error message

 "Error in tapply(y, pop(x), mean, na.rm = TRUE) :
  arguments must have same length"

I'm not really sure what this means or how to fix it. I am trying to run the individuals as one population, but I am not sure if that is have any effect. Should I create another vector of 1's to code for the population and concatenate the two? Does anyone have any advice on how to solve this problem? Thank you in advance for any help with this issue.

--
Logan Clark
Graduate Student
Biology Department
Appalachian State University
P: 252-370-0034
E: clarklc at appstate.edu<mailto:clarklc at appstate.edu>

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