Files in sequoia
Pedigree Inference from SNPs
MD5
NEWS.md
NAMESPACE
DESCRIPTION
cleanup.win
cleanup
R/getAssignable.R
R/RelPlot.R
R/PlotAgePrior.R
R/PlotPairLL.R
R/Utils.R
R/getRelM.R
R/Data_documentation.R
R/SNPstats.R
R/CalcMaxMismatch.R
R/MkAgePrior.R
R/PedPolish.R
R/PlotPedComp.R
R/GetMaybeRel.R
R/Prepare.R
R/GenoConvert.R
R/CalcPairLL.R
R/Sequoia_Main.R
R/ErrToM.R
R/PedToNum.R
R/CalcRped.R
R/CheckGeno.R
R/ConfProb.R
R/CountGenerations.R
R/CalcBYprobs.R
R/SimGeno.R
R/zzz.R
R/CalcOHLLR.R
R/EstEr.R
R/CheckLifeHist.R
R/WriteToFiles.R
R/ComparePairs.R
R/FindFamilies.R
R/ComparePeds.R
R/DuplicateCheck.R
R/SeqListSummary.R
R/Sequoia_F90wrappers.R
src/SimGenoErrors.f90
src/init.c
src/MkRelA.f90
src/ester.f90
src/sequoia-win.def
src/Sequoia.f90
inst/CITATION
inst/doc/flowchart.pdf
inst/doc/PedComp.R
inst/doc/vignette_mtDNA.pdf.asis
inst/doc/vignette-main.Rmd
inst/doc/quick_start_example1.rmd
inst/doc/vignette-main.html
inst/doc/PedComp.Rmd
inst/doc/vignette-main.R
inst/doc/vignette_mtDNA.pdf
inst/doc/PedComp.html
inst/doc/flowchart.pdf.asis
inst/doc/vignette-age.Rmd
inst/doc/vignette-age.R
inst/doc/quick_start_example1.R
inst/doc/quick_start_example1.html
inst/doc/vignette-age.pdf
inst/extdata/Inherit_patterns.csv
inst/extdata/Inherit_patterns.xlsx
build/vignette.rds
vignettes/SummarySeq_deer_sibships.png
vignettes/vignette_mtDNA.pdf.asis
vignettes/ARER-cats.pdf
vignettes/vignette-main.Rmd
vignettes/Errs-time-deer.png
vignettes/SummarySeq_deer.png
vignettes/clustering_mat_helps_pat.pdf
vignettes/Errs-time-deer.pdf
vignettes/Errs-time-HSg5.png
vignettes/clustering_mat_helps_pat.png
vignettes/Errs-time-HSg5.pdf
vignettes/quick_start_example1.rmd
vignettes/hexbin.pdf
vignettes/ARER-cats.png
vignettes/PedComp.Rmd
vignettes/Deer-AgePriorExtra.png
vignettes/RelPlot-griffin.pdf
vignettes/agedif-AU.png
vignettes/agepriors-pipeline.pdf
vignettes/selfed_parent.png
vignettes/flowchart.pdf.asis
vignettes/vignette-age.Rmd
vignettes/hexbin.png
vignettes/RelPlot-griffin.png
vignettes/Rped_scatter.png
vignettes/Errs-effect.pdf
vignettes/agepriors-pipeline.png
vignettes/Errs-effect.png
vignettes/sequoia_refs.bib
vignettes/libs/anchor-sections-1.1.0/anchor-sections-symbol.css
vignettes/libs/anchor-sections-1.1.0/anchor-sections-hash.css
vignettes/libs/anchor-sections-1.1.0/anchor-sections-icon.css
vignettes/libs/anchor-sections-1.1.0/anchor-sections.css
vignettes/libs/anchor-sections-1.1.0/anchor-sections.js
vignettes/libs/gitbook-2.6.7/js/plugin-fontsettings.js
vignettes/libs/gitbook-2.6.7/js/plugin-clipboard.js
vignettes/libs/gitbook-2.6.7/js/app.min.js
vignettes/libs/gitbook-2.6.7/js/plugin-search.js
vignettes/libs/gitbook-2.6.7/js/plugin-sharing.js
vignettes/libs/gitbook-2.6.7/js/clipboard.min.js
vignettes/libs/gitbook-2.6.7/js/jquery.highlight.js
vignettes/libs/gitbook-2.6.7/js/lunr.js
vignettes/libs/gitbook-2.6.7/js/plugin-bookdown.js
vignettes/libs/gitbook-2.6.7/css/plugin-bookdown.css
vignettes/libs/gitbook-2.6.7/css/plugin-search.css
vignettes/libs/gitbook-2.6.7/css/style.css
vignettes/libs/gitbook-2.6.7/css/plugin-fontsettings.css
vignettes/libs/gitbook-2.6.7/css/plugin-highlight.css
vignettes/libs/gitbook-2.6.7/css/plugin-table.css
vignettes/libs/gitbook-2.6.7/css/plugin-clipboard.css
vignettes/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
vignettes/libs/jquery-3.6.0/jquery-3.6.0.min.map
vignettes/libs/jquery-3.6.0/jquery-3.6.0.min.js
vignettes/libs/jquery-3.6.0/jquery-3.6.0.js
data/LH_griffin.txt
data/Ped_HSg5.txt
data/Ped_griffin.txt
data/Geno_griffin.rda
data/LH_HSg5.txt
data/FieldMums_griffin.txt
data/SimGeno_example.RData
data/Conf_griffin.rda
data/Inherit_patterns.RData
data/SeqOUT_HSg5.rda
data/MaybeRel_griffin.rda
data/SeqOUT_griffin.rda
data/Geno_HSg5.rda
man/rc.Rd
man/VennSquares.Rd
man/Inherit_patterns.Rd
man/PlotSeqSum.Rd
man/LH_HSg5.Rd
man/PlotSnpStats.Rd
man/LH_griffin.Rd
man/FieldMums_griffin.Rd
man/tryCatch.W.E.Rd
man/SimGeno_example.Rd
man/getAssignCat.Rd
man/FortifyPairs.Rd
man/SummarySeq.Rd
man/DuplicateCheck.Rd
man/Geno_HSg5.Rd
man/SibMatch.Rd
man/ErrPerSNP.Rd
man/MkGenoErrors.Rd
man/EstConf.Rd
man/EstEr.Rd
man/CalcPairLL.Rd
man/FindFamilies.Rd
man/PedStripFID.Rd
man/Vcomp.Rd
man/CalcMaxMismatch.Rd
man/MergeFill.Rd
man/CalcBYprobs.Rd
man/OHperSNP.Rd
man/writeSeq.Rd
man/PlotPairLL.Rd
man/ParamToSpecs.Rd
man/LLRplot.Rd
man/GetLLRAge.Rd
man/MakeAgePrior.Rd
man/DoErrors.Rd
man/PedPolish.Rd
man/NumToID.Rd
man/GetRelA.Rd
man/PedCompare.Rd
man/CalcCorners.Rd
man/FoldSibGPs.Rd
man/GenoConvert.Rd
man/Ped_griffin.Rd
man/SpecsToParam.Rd
man/writeColumns.Rd
man/CalcOHLLR.Rd
man/PlotAgePrior.Rd
man/orderLH.Rd
man/CountAgeDif.Rd
man/ComparePairs.Rd
man/CheckParams.Rd
man/SnpStats.Rd
man/ErrToM.Rd
man/CalcLL.Rd
man/DyadCompare.Rd
man/SmoothAP.Rd
man/SeqParSib.Rd
man/Conf_griffin.Rd
man/GetMaybeRel.Rd
man/MkAPdefault.Rd
man/PedToNum.Rd
man/CheckAP.Rd
man/SeqOUT_griffin.Rd
man/mtSame2Dif.Rd
man/CheckLH.Rd
man/MkFortParams.Rd
man/sequoia.Rd
man/MaybeRel_griffin.Rd
man/getGenerations.Rd
man/GetDescendants.Rd
man/GetAncestors.Rd
man/CheckGeno.Rd
man/PlotRelPairs.Rd
man/PlotPedComp.Rd
man/SimGeno.Rd
man/GetDummifiable.Rd
man/GetRelM.Rd
man/LHConvert.Rd
man/Ped_HSg5.Rd
man/CalcRped.Rd
man/Geno_griffin.Rd
man/SeqOUT_HSg5.Rd
