Package 'pgacmdr' reference manual

Package 'pgacmdr'

Title:	Interactive Shiny Application for Population Genetics
Description:	PGA-cmdr is an interactive 'shiny' application for population genetics analyses of multilocus individual genotype data from codominant markers (microsatellites, allozymes, SNPs). It covers data import and formatting, allele frequencies and missing data, observed and expected heterozygosity, F-statistics (FIS, FST, FIT) following Weir and Cockerham (1984) <doi:10.1111/j.1558-5646.1984.tb05657.x>, and gene diversities (HS, HT) following Nei and Chesser (1983) <doi:10.1111/j.1469-1809.1983.tb00993.x>. Analyses include local and global panmixia tests, population subdivision with a G-based test of genotypic differentiation, pairwise linkage disequilibrium tests, null allele frequency estimation with the ENA correction of Chapuis and Estoup (2007) <doi:10.1093/molbev/msl191>, and isolation by distance using the regression of Rousset (1997) <doi:10.1093/genetics/145.4.1219> and a Mantel test. Confidence intervals are obtained by bootstrap over individuals, sub-samples or loci, and p-values by Monte Carlo permutation, computed in parallel in C++ via 'Rcpp' and 'OpenMP'. All computations run locally and no data leave the user's computer.
Authors:	Naffiou Kadiri [aut, cre], Vincent Manzanilla [aut], Thierry de Meeûs [aut], INTERTRYP, IRD, CIRAD [cph]
Maintainer:	Naffiou Kadiri <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.0
Built:	2026-10-20 05:12:26 UTC
Source:	https://github.com/KadNaf/PGA-cmdr

Title:

Interactive Shiny Application for Population Genetics

Description:

PGA-cmdr is an interactive 'shiny' application for population genetics analyses of multilocus individual genotype data from codominant markers (microsatellites, allozymes, SNPs). It covers data import and formatting, allele frequencies and missing data, observed and expected heterozygosity, F-statistics (FIS, FST, FIT) following Weir and Cockerham (1984) <doi:10.1111/j.1558-5646.1984.tb05657.x>, and gene diversities (HS, HT) following Nei and Chesser (1983) <doi:10.1111/j.1469-1809.1983.tb00993.x>. Analyses include local and global panmixia tests, population subdivision with a G-based test of genotypic differentiation, pairwise linkage disequilibrium tests, null allele frequency estimation with the ENA correction of Chapuis and Estoup (2007) <doi:10.1093/molbev/msl191>, and isolation by distance using the regression of Rousset (1997) <doi:10.1093/genetics/145.4.1219> and a Mantel test. Confidence intervals are obtained by bootstrap over individuals, sub-samples or loci, and p-values by Monte Carlo permutation, computed in parallel in C++ via 'Rcpp' and 'OpenMP'. All computations run locally and no data leave the user's computer.

Authors:

Naffiou Kadiri [aut, cre], Vincent Manzanilla [aut], Thierry de Meeûs [aut], INTERTRYP, IRD, CIRAD [cph]

Maintainer:

Naffiou Kadiri <[email protected]>

License:

MIT + file LICENSE

Version:

0.1.0

Built:

2026-10-20 05:12:26 UTC

Source:

https://github.com/KadNaf/PGA-cmdr

Help Index

Application Server

Description

Application Server

Usage

app_server(input, output, session)
app_server(input, output, session)

Arguments

input, output, session

Shiny server arguments.

Application UI

Description

Application UI

Usage

app_ui()
app_ui()

Value

A shinydashboard::dashboardPage object.

Run the PGA-cmdr application

Description

Run the PGA-cmdr application

Usage

run_app(...)
run_app(...)

Arguments

...

Arguments passed to shinyApp.

Value

A shiny.appobj (invisibly).

Examples

## Not run: 
  pgacmdr::run_app()

## End(Not run)
## Not run: 
  pgacmdr::run_app()

## End(Not run)