Package: sequoia 2.11.4.0

sequoia: Pedigree Inference from SNPs

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<doi:10.1111/1755-0998.12665>) for more information.

Authors:Jisca Huisman [aut, cre]

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NEWS

# Install 'sequoia' in R:

install.packages('sequoia', repos = c('https://jiscah.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jiscah/sequoia/issues

Uses libs:

fortran– Runtime library for GNU Fortran applications

Datasets:

Conf_griffin - Example output from estimating confidence probabilities: griffins
FieldMums_griffin - Example field-observed mothers: griffins
Geno_HSg5 - Example genotype file: 'HSg5'
Geno_griffin - Example genotype file: Griffins
Inherit_patterns - Inheritance patterns
LH_HSg5 - Example life history file: 'HSg5'
LH_griffin - Example life history data: griffins
MaybeRel_griffin - Example output from check for relatives: griffins
Ped_HSg5 - Example pedigree: 'HSg5'
Ped_griffin - Example pedigree: griffins
SeqOUT_HSg5 - Example output from pedigree inference: 'HSg5'
SeqOUT_griffin - Example output from pedigree inference: griffins
SimGeno_example - Example genotype file: 'HSg5'

On CRAN:

pedigree pedigree-reconstruction pedigrees sequoia snp snp-data

37 exports 25 stars 2.54 score 3 dependencies 72 scripts 1.1k downloads

Last updated 3 months agofrom:470859fc9d. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 14 2024
R-4.5-win-x86_64	NOTE	Sep 14 2024
R-4.5-linux-x86_64	NOTE	Sep 14 2024
R-4.4-win-x86_64	NOTE	Sep 14 2024
R-4.4-mac-x86_64	NOTE	Sep 14 2024
R-4.4-mac-aarch64	NOTE	Sep 14 2024
R-4.3-win-x86_64	NOTE	Sep 14 2024
R-4.3-mac-x86_64	NOTE	Sep 14 2024
R-4.3-mac-aarch64	NOTE	Sep 14 2024

Exports:CalcBYprobs CalcMaxMismatch CalcOHLLR CalcPairLL CalcRped CheckGeno ComparePairs DyadCompare ErrToM EstConf EstEr FindFamilies GenoConvert GetAncestors getAssignCat GetDescendants getGenerations GetLLRAge GetMaybeRel GetRelM LHConvert MakeAgePrior MkGenoErrors PedCompare PedPolish PedStripFID PlotAgePrior PlotPairLL PlotPedComp PlotRelPairs PlotSeqSum sequoia SimGeno SnpStats SummarySeq writeColumns writeSeq

Dependencies:cli plyr Rcpp

Mitochondrial haplotypes

Rendered fromvignette_mtDNA.pdf.asisusingR.rsp::asison Sep 14 2024.

Last update: 2023-12-14
Started: 2023-12-14

PedCompare Example (Griffin Pedigree)

Jisca Huisman ( jisca.huisman @ gmail.com )

Rendered fromPedComp.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-01-10
Started: 2021-03-26

Quick start example 1: Simulated data

J Huisman

Rendered fromquick_start_example1.rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2023-01-20
Started: 2021-03-26

Sequoia - Age 'Prior'

Jisca Huisman

Rendered fromvignette-age.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-06-16
Started: 2021-03-26

Sequoia flowchart

Rendered fromflowchart.pdf.asisusingR.rsp::asison Sep 14 2024.

Last update: 2021-04-29
Started: 2021-04-29

Sequoia User Guide