Package: PopGenReport 3.1

PopGenReport: A Simple Framework to Analyse Population and Landscape Genetic Data

Provides beginner friendly framework to analyse population genetic data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit <http://www.popgenreport.org/>.

Authors:Bernd Gruber [aut, cre], Aaron Adamack [aut]

PopGenReport_3.1.tar.gz
PopGenReport_3.1.zip(r-4.5)PopGenReport_3.1.zip(r-4.4)PopGenReport_3.1.zip(r-4.3)
PopGenReport_3.1.tgz(r-4.4-any)PopGenReport_3.1.tgz(r-4.3-any)
PopGenReport_3.1.tar.gz(r-4.5-noble)PopGenReport_3.1.tar.gz(r-4.4-noble)
PopGenReport_3.1.tgz(r-4.4-emscripten)PopGenReport_3.1.tgz(r-4.3-emscripten)
PopGenReport.pdf |PopGenReport.html✨
PopGenReport/json (API)

# Install 'PopGenReport' in R:
install.packages('PopGenReport', repos = c('https://green-striped-gecko.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/green-striped-gecko/popgenreport/issues

Datasets:
  • bilby - Bilby data set
  • landgen - A simulated genind data set with spatial coordinates
  • possums - A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]

On CRAN:

7.33 score 5 stars 1 packages 77 scripts 1.2k downloads 35 mentions 25 exports 119 dependencies

Last updated 1 years agofrom:628ed9418a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winNOTENov 08 2024
R-4.5-linuxNOTENov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winOKNov 08 2024
R-4.3-macOKNov 08 2024

Exports:addlineaddpolyallel.richallele.distcostdistancesemigrationgd.kosmangd.smousegenleastcostinit.popgensimlandgenreportlgrMMRRmutationnull.allopt.landgenp2ppairwise.fstbpairwise.propSharedpopgenreportpops2genindread.genetablereproductionrun.popgensimspautocorwassermann

Dependencies:ade4adegenetapeaskpassbase64encbootbslibcachemcalibratecliclustercolorspacecombinatcommonmarkcpp11crayoncrosstalkcurldata.tabledigestdismodplyrevaluatefansifarverfastmapfontawesomeforcatsfsgapgap.datasetsgdatagdistancegenericsgeneticsGGallyggplot2ggstatsgluegtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemmodmunsellmvtnormnlmeopensslpatchworkpegaspermutepillarpixmappkgconfigplotlyplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRdpackreshape2RgoogleMapsrlangrmarkdownsassscalessegmentedseqinrshinysourcetoolsspstringistringrsysterratibbletidyrtidyselecttinytexutf8vctrsveganviridisLitewithrxfunxtableyaml

PopGenReport Introduction

Rendered fromPopGenReportIntroduction.Rnwusingknitr::knitron Nov 08 2024.

Last update: 2015-06-25
Started: 2015-04-15

Tutorial landgenreport

Rendered fromTutorial_landgenreport.rnwusingknitr::knitron Nov 08 2024.

Last update: 2015-04-15
Started: 2015-04-15

Tutorial Optimizer

Rendered fromTutorial_optimizer.Rnwusingknitr::knitron Nov 08 2024.

Last update: 2016-11-24
Started: 2016-11-24

Readme and manuals

Help Manual

Help pageTopics
Function to add lines to landscapeaddline
Function to add a polygon to a landscapeaddpoly
Calculates the allelic richness for a genind objectallel.rich
Counts and visualises allele frequencies across loci and subpopulationsallele.dist
Bilby data setbilby
Calculates cost distances for a given landscape (resistance matrix)costdistances
Function to execute emigration on a pops objectemigration
Individual genetic distance calculation based on Kosman & Leonhard 2005gd.kosman
Individual genetic distance calculation based on Smouse and Peakall 1999gd.smouse
Least-cost path analysis based on a friction matrixgenleastcost
Initialise a spatial meta-population for a popgen simulationinit.popgensim
A simulated genind data set with spatial coordinateslandgen
Create a landscape genetic reportlandgenreport
Multiple Matrix Regression with Randomization analysislgrMMRR
Function to execute mutation on a pop data.framemutation
Checks for the presence of and determine the frequency of null allelesnull.all
Function for optimising a landscape genetic analysis based on resistance layersopt.landgen
Function to calculate dispersal distances based on cost distancesp2p
Calculates pairwise fsts using a genind object (very fast)pairwise.fstb
Calculates proportion of shared alleles per pairs of populationspairwise.propShared
This is the main function of the package. It analyses an object of class 'genind' and then creates a report containing the results of the analysis. There are several routines that can be optionally included in the analysis and there are multiple output options including a PDF with the report, R-code and an object ('fname.results') containing all of the results, which can be used for further analyses.popgenreport
Function converts pops to a genind objectpops2genind
A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]possums
Function to convert textfiles into a genind object (the format required for popgenreport)read.genetable
Function to execute reproduction on a pop data.framereproduction
Run a time-forward popgen simulationrun.popgensim
Spatial autocorrelation following Smouse and Pekall 1999spautocor
Partial Mantel tests on costdistance matriceswassermann