Below are functions that were utilized in the making of this primer with links to their respective packages. Note that this list was automatically generated and might be missing some functions.

Part I:

Introduction

No functions used in this chapter.

Getting ready to use R

Function Package
clonecorrect poppr
mlg poppr
seppop adegenet

Part II:

Data Preparation

Function Package
read.genalex poppr
splitStrata adegenet

First Analysis

Function Package
genind2df adegenet
genotype_curve poppr
info_table poppr
locus_table poppr
mlg.table poppr
poppr poppr

Populations strata: subsetting and clone correction

Function Package
clonecorrect poppr
locus_table poppr
nameStrata adegenet
popNames adegenet
setPop adegenet
splitStrata adegenet
strata adegenet
treemap treemap

Locus stats, heterozygosity, HWE

Function Package
hw.test pegas
info_table poppr
informloci poppr
locus_table poppr
missingno poppr
nLoc adegenet
poppr poppr
popsub poppr
seppop adegenet
tab adegenet

Genotypic richness, diversity, and evenness

Function Package
mlg.table poppr
poppr poppr
rarecurve vegan
setPop adegenet
splitStrata adegenet

Linkage disequilibrium

Function Package
clonecorrect poppr
ia poppr
popsub poppr
strata adegenet

Population structure: \(G_{ST}\), genetic distance, and clustering

Function Package
Gst_Hedrick mmod
aboot poppr
add.scale.bar ape
axisPhylo ape
bruvo.boot poppr
find.clusters adegenet
genind2genpop adegenet
ladderize ape
nInd adegenet
nameStrata adegenet
nj ape
nodelabels ape
other adegenet
plot.phylo ape
pop adegenet
popsub poppr
provesti.dist poppr
strata adegenet

Minimum Spanning Networks

Function Package
bruvo.msn poppr
diss.dist poppr
imsn poppr
other adegenet
plot_poppr_msn poppr
poppr.msn poppr
popsub poppr
setPop adegenet
splitStrata adegenet
summary adegenet

AMOVA

Function Package
as.genclone poppr
nInd adegenet
other adegenet
poppr.amova poppr
strata adegenet

Discriminant analysis of principal components (DAPC)

Function Package
dapc adegenet
loadingplot adegenet
nPop adegenet
other adegenet
pop adegenet
seploc adegenet
tab adegenet
xvalDapc adegenet

Part III

Population genomics and HTS

No functions used in this chapter.