Package: junctions 2.1.4

junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018, <doi:10.1101/058107>) and Janzen (2022, <doi:10.1111/1755-0998.13519>).

Authors:Thijs Janzen [aut, cre]

junctions_2.1.4.tar.gz
junctions_2.1.4.zip(r-4.7)junctions_2.1.4.zip(r-4.6)junctions_2.1.4.zip(r-4.5)
junctions_2.1.4.tgz(r-4.6-x86_64)junctions_2.1.4.tgz(r-4.6-arm64)junctions_2.1.4.tgz(r-4.5-x86_64)junctions_2.1.4.tgz(r-4.5-arm64)
junctions_2.1.4.tar.gz(r-4.7-arm64)junctions_2.1.4.tar.gz(r-4.7-x86_64)junctions_2.1.4.tar.gz(r-4.6-arm64)junctions_2.1.4.tar.gz(r-4.6-x86_64)
junctions_2.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
junctions/json (API)

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

Bug tracker:https://github.com/thijsjanzen/junctions/issues

Pkgdown/docs site:https://thijsjanzen.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.08 score 2 stars 20 scripts 668 downloads 1 mentions 17 exports 13 dependencies

Last updated from:c71e9bd210. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK162
linux-devel-x86_64OK201
source / vignettesOK237
linux-release-arm64OK159
linux-release-x86_64OK156
macos-release-arm64OK89
macos-release-x86_64OK243
macos-oldrel-arm64OK146
macos-oldrel-x86_64OK182
windows-develOK112
windows-releaseOK122
windows-oldrelOK135
wasm-releaseOK163

Exports:calc_kcalculate_matestimate_timeestimate_time_diploidestimate_time_haploidestimate_time_one_chromlog_likelihood_diploidlog_likelihood_haploidnumber_of_junctionsnumber_of_junctions_backcrossnumber_of_junctions_dinumber_of_junctions_markerssim_backcrossingsim_fin_chromsim_inf_chromsim_phased_unphasedtime_error

Dependencies:cligluelifecyclemagrittrnloptrpillarpkgconfigRcppRcppParallelrlangtibbleutf8vctrs

Overview_of_the_junctions_package
title: "Overview_of_the_junctions_package"author: "Thijs Janzen"date: "5/6/2021"output: rmarkdown::html_vignettevignette: >%\VignetteIndexEntry | Overview of the junctions package | Simulation functions | Phased and unphased simulations | Mathematical simulations | Backcrossing | Inferring the time since admixture | Junction based methods | Local ancestry based methods | Likelihood functions | Expected number of junctions | Mathematical expressions
Rendered fromOverview_of_the_junctions_package.Rmdusingknitr::rmarkdown

Last update: 2026-03-06
Started: 2021-05-06

Phased and unphased data
Simulating data | Inferring the time since admixture | Population size | Simulating data with error
Rendered fromphased_and_unphased_data.Rmdusingknitr::rmarkdown

Last update: 2026-03-06
Started: 2020-09-14

Junctions
Junctions vignette | An infinite chromosome in a finite population | Including Random Markers | A Finite chromosome in a finite population | Other equations available
Rendered fromjunctions_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-03-06
Started: 2017-11-08

Readme and manuals

Help Manual

Help pageTopics
Extending The Theory of Junctionsjunctions-package junctions
Calculate the limit of the number of junctionscalc_k
Function to calculate the maximum accurate timecalculate_mat
Estimate the time since the onset of hybridization, using the number of junctionsestimate_time
estimates the time since admixture, given diploid ancestry data.estimate_time_diploid
estimate time using likelihood for a single chromosomeestimate_time_haploid
Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers on a single chromosomeestimate_time_one_chrom
calculate the log likelihood of observing diploid ancestry data.log_likelihood_diploid
log likelihood of the time since admixture for a haploid genomelog_likelihood_haploid
Calculate the average number of junctionsnumber_of_junctions
Calculate the average number of junctions during backcrossingnumber_of_junctions_backcross
Calculate the expected number of junctions between two markers separated by a given amount of recombinationnumber_of_junctions_di
Calculate the expected total number of junctions in a chromosome, given the distribution of markersnumber_of_junctions_markers
Function to simulate data using a back crossing schemesim_backcrossing
Individual Based Simulation of the accumulation of junctionssim_fin_chrom
Individual Based Simulation of the accumulation of junctionssim_inf_chrom
Individual Based Simulation of the accumulation of junctionssim_phased_unphased
Estimate the error in the time estimatetime_error