vignettes/HierDpart.R

In xinghuq/HierDpart: Partitioning 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

f1 <- function(f) system.file("extdata", f,package="HierDpart")


## -----------------------------------------------------------------------------
qD(f1("Island.gen"),q=0,ncode=3)

## ----fig1, fig.height = 5, fig.width = 8.5, fig.align = "center"--------------
qDplot(f1("Island.gen"),q="all",ncode=3)

## -----------------------------------------------------------------------------
HAr=HierAr(f1("Island.gen"), nreg=4, r=c(7,4,2,3), ncode=3)
print(HAr)

## -----------------------------------------------------------------------------
HiD=HierD(f1("Island.gen"), nreg=4, r=c(7,4,2,3), ncode=3)
print(HiD)

## -----------------------------------------------------------------------------
He=HierHe(f1("Island.gen"), nreg=4, r=c(7,4,2,3), ncode=3)
print(He)

## -----------------------------------------------------------------------------
Hier_Fst=HierFst(f1("Island.gen"), nreg=4, r=c(7,4,2,3), ncode=3)
print(Hier_Fst)

## -----------------------------------------------------------------------------
Hier_D=HierD(f1("Island.gen"), nreg=4, r=c(7,4,2,3), ncode=3)
print(Hier_D)