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strataG

Description

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

Installation

To install the stable version (v. 1.0.4) from CRAN:

install.packages('strataG')

To install the latest version from GitHub:

# make sure you have Rtools installed
if (!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)

Contact

You can see the most recent changes to the package in the NEWS.md file: https://github.com/EricArcher/strataG/blob/master/NEWS.md

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Version

Install

install.packages('strataG')

Monthly Downloads

77

Version

1.0.5

License

GNU General Public License

Maintainer

Eric Archer

Last Published

December 5th, 2016

Functions in strataG (1.0.5)

as.data.frame.gtypes

Convert gtypes To data.frame
mafft

MAFFT Alignment
mega

Read and Write MEGA
neiDa

Nei's Da
nucleotideDivergence

Nucleotide Divergence
stratify

Stratify gtypes
strataSplit

Split Strata
as.matrix,gtypes-method

Convert gtypes To matrix
freq2GenData

Convert Haplotype Frequency Matrices
hweTest

Hardy-Weinberg Equilibrium
idRows

gtypes ID Rows
fstToNm

Nm from Fst
as.multidna

Convert to multidna
baseFreqs

Base Frequencies
dolph.msats

Dolphin Microsatellite Genotypes
dolph.haps

Dolphin mtDNA Haplotype Sequences
expectedNumAlleles

Expected Number of Alleles
fasta

Read and Write FASTA
gtypes2loci

Convert Between gtypes And loci objects.
gtypes2phyDat

Convert Between gtypes And phyDat objects.
labelHaplotypes

Find and label haplotypes
iupacCode

IUPAC Code
mRatio

M ratio
msats.g

Dolphin Microsatellite gtypes Object
privateAlleles

Private Alleles
propUniqueAlleles

Proportion Unique Alleles
strataG-internal

Internal Functions
dolph.seqs

Dolphin mtDNA D-loop Sequences
fixedDifferences

Fixed Differences
dolph.strata

Dolphin Genetic Stratification and Haplotypes
fixedSites

Fixed Sites
genepop

Run GENEPOP
strataG-package

Summaries and population structure analyses of DNA sequence genotypic data
bowhead.snp.position

Bowhead Whale SNP Genotype Groups
bowhead.snps

Bowhead Whale SNP Genotypes
df2gtypes

Convert a data.frame to gtypes
dloop.g

Dolphin dLoop gtypes Object
fusFs

Fu's Fs
initialize,gtypes-method

gtypes Constructor
gelato

GELATo - Group ExcLusion and Assignment Test
is.gtypes

Test if object is gtypes
gtypes-class

gtypes Class
mostDistantSequences

Most Distant Sequences
permuteStrata

Permute strata
phase

PHASE
mostRepresentativeSequences

Representative Sequences
readGenData

Read Genetic Data
removeSequences

Remove Sequences
summarizeSeqs

Sequence Summaries
summarizeLoci

Locus Summaries
validIupacCodes

Valid IUPAC Codes
variableSites

Variable Sites
alleleFreqs

Allele Frequencies
alleleFreqFormat

Compiles and Formats Allele Frequencies
evanno

Run Evanno Method on STRUCTURE Results
dupGenotypes

Duplicate Genotypes
nucleotideDiversity

Nucleotide Diversity
Hstats

Population structure statistics
numAlleles

Number of Alleles
popStructTest

Population Differentiation Tests
trimNs

Trim N's From Sequences
theta

Theta
fastsimcoal.input

Input functions for fastsimcoal parameters
fastsimcoal

Run fastsimcoal
gtypes.accessors

gtypes Accessors
gtypes2genind

Convert Between gtypes And genind objects.
simGammaHaps

Simulate Haplotypes
show,gtypes-method

Show a gtypes object
summary,gtypes-method

Summarize gtypes Object
tajimasD

Tajima's D
write.gtypes

Write gtypes
write.nexus.snapp

Write NEXUS File for SNAPP
alleleSplit

Split Alleles For Diploid Data
allelicRichness

Allelic Richness
clumpp

Run CLUMPP
createConsensus

Consensus Sequence
haplotypeLikelihoods

Haplotype Likelihoods
heterozygosity

Observed and Expected Heterozygosity
LDgenepop

Linkage Disequlibrium
lowFreqSubs

Low Frequency Substitutions
numGensEq

Number of Generations to Equilibrium
sequence2gtypes

Convert Sequences To gtypes
numMissing

Number Missing Data
sharedLoci

Shared Loci
structure

STRUCTURE
structurePlot

Plot STRUCTURE Results
wrightFst

Wright's Fst
write.arlequin

Write Arlequin Input Files
jackHWE

Hardy-Weinberg Equlibrium Jackknife
TiTvRatio

Transition / Transversion Ratio
qaqc

Quality Assurance/Quality Control