GitHub - StephanieTodd/diversity_struct_Btropica: Analyses and data for Cons Gen manuscript 'Diversity and structure of Bettongia tropica: using population genetics to guide reintroduction and help prevent the extinction of an endangered Australian marsupial.'

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Analyses and data for Cons Gen manuscript 'Diversity and structure of Bettongia tropica: using population genetics to guide reintroduction and help prevent the extinction of an endangered Australian marsupial.'

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
Ne_Estimator		Ne_Estimator
SambaR		SambaR
data		data
functions		functions
scripts		scripts
.gitignore		.gitignore
Readme.Rmd		Readme.Rmd
Readme.nb.html		Readme.nb.html
dartR_notebook2.Rmd		dartR_notebook2.Rmd
diversity_structure_Btropica.Rproj		diversity_structure_Btropica.Rproj

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---
title: "Instructions for DArT-R bettong population genetics analysis"
output: html_notebook
---

# Instructions

1) Quality control = scripts/01_QC2.R'
2) Main script = 'dartR_notebook2.Rmd' Most of the analysis is done here

'controller.R' allows main script to be called externally (without opening up .Rmd file) 

running 'dartR_notebook2.Rmd' requires:
- genlight dataset  'Rdata[datversion]/mappinggl[datversion].Rdata'  produced from '01_QC2.R' 
- "02_global_variables_dartR.R"
- "Functions_dartR_notebook.R" (this is main function file)
- various other functions in "functions" folder
- output from 'Ne_Estimator' software...
  
  
Ne_Estimator must be run separetely!!
 * to estimate r2 (Linkage Disequilibrium) and do most of Ne calculations 
 * everything is in  'Ne_Estimator' directory
 * genlight data must be first converted into genid 'gi' format
 * then use (dont just source!) 'gi2genpop.R' to convert and export data to genepop format required by Ne Estimator (saved to .gen files)
 * now run NeLR with the following paremeters:
    * 'output files in tabular format for top 3 crit values' box checked to create 'LDxLD.txt' output.
    * uncheck methods other than NeLD
    * use critical values = 0.01,0.02,0.05
    * uncheck 'also run without frequency restriction'
    * >>> run
  * then: open up LDxLD text files and copy down to fill columns one & two e.g. "1:3_18/11/16    75"


SambaR also run separately, with separate .Rproj
'SambaR/scripts/SambaR2.R' is main analysis file


### DATA
'indvidual_metadata_6213_v3.csv' is the latest