Package: junctions 2.1.0

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 (2020, <doi:10.1101/2020.09.10.292441>).

Authors:Thijs Janzen [aut, cre]

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junctions.pdf |junctions.html✨
junctions/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

cpp

4.71 score 2 stars 17 scripts 253 downloads 1 mentions 17 exports 14 dependencies

Last updated 12 months agofrom:2e5e740c13. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 08 2025
R-4.5-win-x86_64OKJan 08 2025
R-4.5-linux-x86_64OKJan 08 2025
R-4.4-win-x86_64OKJan 08 2025
R-4.4-mac-x86_64OKJan 08 2025
R-4.4-mac-aarch64OKJan 08 2025
R-4.3-win-x86_64OKJan 08 2025
R-4.3-mac-x86_64OKJan 08 2025
R-4.3-mac-aarch64OKJan 08 2025

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:clifansigluelifecyclemagrittrnloptrpillarpkgconfigRcppRcppParallelrlangtibbleutf8vctrs

junctions Vignette

Thijs Janzen

Rendered fromjunctions_vignette.Rmdusingknitr::rmarkdownon Jan 08 2025.

Last update: 2022-02-24
Started: 2017-11-08

Overview_of_the_junctions_package

Thijs Janzen

Rendered fromOverview_of_the_junctions_package.Rmdusingknitr::rmarkdownon Jan 08 2025.

Last update: 2021-05-26
Started: 2021-05-06

Phased and unphased data

Thijs Janzen

Rendered fromphased_and_unphased_data.Rmdusingknitr::rmarkdownon Jan 08 2025.

Last update: 2022-02-24
Started: 2020-09-14

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