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'))

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:

25 exports 5 stars 4.36 score 131 dependencies 1 dependents 35 mentions 65 scripts 1.3k downloads

Last updated 11 months agofrom:628ed9418a. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 09 2024
R-4.5-win	NOTE	Sep 09 2024
R-4.5-linux	NOTE	Sep 09 2024
R-4.4-win	OK	Sep 09 2024
R-4.4-mac	OK	Sep 09 2024
R-4.3-win	OK	Sep 09 2024
R-4.3-mac	OK	Sep 09 2024

Exports:addline addpoly allel.rich allele.dist costdistances emigration gd.kosman gd.smouse genleastcost init.popgensim landgenreport lgrMMRR mutation null.all opt.landgen p2p pairwise.fstb pairwise.propShared popgenreport pops2genind read.genetable reproduction run.popgensim spautocor wassermann

Dependencies:ade4 adegenet ape askpass backports base64enc bit bit64 boot broom broom.helpers bslib cachem calibrate cards cli clipr cluster colorspace combinat commonmark cpp11 crayon crosstalk curl data.table digest dismo dplyr evaluate fansi farver fastmap fontawesome forcats fs gap gap.datasets gdata gdistance generics genetics GGally ggplot2 ggstats glue gtable gtools haven highr hms htmltools htmlwidgets httpuv httr igraph isoband jquerylib jsonlite knitr labeling labelled later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime mmod munsell mvtnorm nlme openssl patchwork pegas permute pillar pixmap pkgconfig plotly plyr png prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs raster rbibutils RColorBrewer Rcpp RcppArmadillo Rdpack readr reshape2 RgoogleMaps rlang rmarkdown sass scales segmented seqinr shiny sourcetools sp stringi stringr sys terra tibble tidyr tidyselect tinytex tzdb utf8 vctrs vegan viridisLite vroom withr xfun xtable yaml

PopGenReport Introduction

Rendered fromPopGenReportIntroduction.Rnwusingknitr::knitron Sep 09 2024.

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

Tutorial landgenreport

Rendered fromTutorial_landgenreport.rnwusingknitr::knitron Sep 09 2024.

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

Tutorial Optimizer

Rendered fromTutorial_optimizer.Rnwusingknitr::knitron Sep 09 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function to add lines to landscape	addline
Function to add a polygon to a landscape	addpoly
Calculates the allelic richness for a genind object	allel.rich
Counts and visualises allele frequencies across loci and subpopulations	allele.dist
Bilby data set	bilby
Calculates cost distances for a given landscape (resistance matrix)	costdistances
Function to execute emigration on a pops object	emigration
Individual genetic distance calculation based on Kosman & Leonhard 2005	gd.kosman
Individual genetic distance calculation based on Smouse and Peakall 1999	gd.smouse
Least-cost path analysis based on a friction matrix	genleastcost
Initialise a spatial meta-population for a popgen simulation	init.popgensim
A simulated genind data set with spatial coordinates	landgen
Create a landscape genetic report	landgenreport
Multiple Matrix Regression with Randomization analysis	lgrMMRR
Function to execute mutation on a pop data.frame	mutation
Checks for the presence of and determine the frequency of null alleles	null.all
Function for optimising a landscape genetic analysis based on resistance layers	opt.landgen
Function to calculate dispersal distances based on cost distances	p2p
Calculates pairwise fsts using a genind object (very fast)	pairwise.fstb
Calculates proportion of shared alleles per pairs of populations	pairwise.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 object	pops2genind
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.frame	reproduction
Run a time-forward popgen simulation	run.popgensim
Spatial autocorrelation following Smouse and Pekall 1999	spautocor
Partial Mantel tests on costdistance matrices	wassermann