inst/doc/HierDpart.R

In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ---- install-----------------------------------------------------------------
#Install from CRAN
#install.packages("HierDpart")
## or you can get the latest version of HierDpart from github
#library(devtools)

#install_github("xinghuq/HierDpart")

library("HierDpart")


## ---- library-----------------------------------------------------------------
# example genepop file
f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")

## -----------------------------------------------------------------------------
qD(infile,q=0,ncode=3)

## ----fig1, fig.height = 5, fig.width = 8.5, fig.align = "center"--------------
qDplot(infile,q="all",ncode=3)

## -----------------------------------------------------------------------------
HAr=HierAr(infile, nreg=4, r=c(7,4,2,3), ncode=3)
print(HAr)

## -----------------------------------------------------------------------------
HiD=HierD(infile, nreg=4, r=c(7,4,2,3), ncode=3)
print(HiD)

## -----------------------------------------------------------------------------
He=HierHe(infile, nreg=4, r=c(7,4,2,3), ncode=3)
print(He)

## -----------------------------------------------------------------------------
Hier_Fst=HierFst(infile, nreg=4, r=c(7,4,2,3), ncode=3)
print(Hier_Fst)

## -----------------------------------------------------------------------------
Hier_D=HierD(infile, nreg=4, r=c(7,4,2,3), ncode=3)
print(Hier_D)