.DS_Store
.Rbuildignore
.Rhistory
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/.DS_Store
R/optimize_bigM.R
R/optimize_m.R
R/optimize_n.R
R/vis_depth.R
R/vis_loci.R
R/vis_snps.R
RADstackshelpR.Rproj
README.Rmd
README.md
_pkgdown.yml
cran-comments.md
docs/.DS_Store
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/.DS_Store
docs/articles/brown.trout.validation.html
docs/articles/brown.trout.validation_files/.DS_Store
docs/articles/brown.trout.validation_files/figure-html/.DS_Store
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-11-1.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-11-2.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-12-1.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-5-1.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-5-2.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-5-3.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-8-1.png
docs/articles/brown.trout.validation_files/figure-html/unnamed-chunk-8-2.png
docs/articles/brown.trout.validation_files/header-attrs-2.10/header-attrs.js
docs/articles/index.html
docs/articles/optimize_denovo.html
docs/articles/optimize_denovo_files/.DS_Store
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-10-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-3-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-3-2.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-3-3.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-4-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-4-2.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-5-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-5-2.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-5-3.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-6-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-7-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-7-2.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-9-1.png
docs/articles/optimize_denovo_files/figure-html/unnamed-chunk-9-2.png
docs/articles/optimize_denovo_files/header-attrs-2.10/header-attrs.js
docs/articles/quality.control.vignette.html
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-1.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-10.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-11.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-12.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-13.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-14.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-15.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-16.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-17.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-18.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-19.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-2.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-20.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-21.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-22.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-23.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-24.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-25.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-26.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-27.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-28.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-29.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-3.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-30.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-31.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-32.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-33.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-34.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-35.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-36.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-37.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-38.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-39.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-4.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-40.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-41.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-42.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-43.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-44.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-45.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-5.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-6.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-7.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-8.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-3-9.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-5-1.png
docs/articles/quality.control.vignette_files/figure-html/unnamed-chunk-5-2.png
docs/articles/quality.control.vignette_files/header-attrs-2.10/header-attrs.js
docs/articles/reproducible.vignette.html
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-3-1.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-3-2.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-3-3.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-5-1.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-5-2.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-7-1.png
docs/articles/reproducible.vignette_files/figure-html/unnamed-chunk-7-2.png
docs/articles/reproducible.vignette_files/header-attrs-2.10/header-attrs.js
docs/articles/trt.bigM.png
docs/articles/trt.m.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/figures/logo.png
docs/reference/figures/make.logo.R
docs/reference/figures/unnamed-chunk-10-1.png
docs/reference/figures/unnamed-chunk-5-1.png
docs/reference/figures/unnamed-chunk-5-2.png
docs/reference/figures/unnamed-chunk-5-3.png
docs/reference/figures/unnamed-chunk-7-1.png
docs/reference/figures/unnamed-chunk-7-2.png
docs/reference/figures/unnamed-chunk-9-1.png
docs/reference/figures/unnamed-chunk-9-2.png
docs/reference/index.html
docs/reference/optimize_bigM.html
docs/reference/optimize_m.html
docs/reference/optimize_n.html
docs/reference/vis_depth-1.png
docs/reference/vis_depth.html
docs/reference/vis_loci-1.png
docs/reference/vis_loci.html
docs/reference/vis_snps-1.png
docs/reference/vis_snps.html
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/RMarkdown.qc.submit.script.sh
inst/extdata/bigM1.vcf.gz
inst/extdata/bigM2.vcf.gz
inst/extdata/bigM3.vcf.gz
inst/extdata/bigM4.vcf.gz
inst/extdata/bigM5.vcf.gz
inst/extdata/bigM6.vcf.gz
inst/extdata/bigM7.vcf.gz
inst/extdata/bigM8.vcf.gz
inst/extdata/denovo.stacks.pipeline.sh
inst/extdata/fastqcr.Rmd
inst/extdata/m3.vcf.gz
inst/extdata/m4.vcf.gz
inst/extdata/m5.vcf.gz
inst/extdata/m6.vcf.gz
inst/extdata/m7.vcf.gz
inst/extdata/make.toy.vcf.datsets.R
inst/extdata/nequalsm.vcf.gz
inst/extdata/nequalsmminus1.vcf.gz
inst/extdata/nequalsmplus1.vcf.gz
inst/extdata/optimize.m.output.RDS
inst/extdata/rhub.cran.checks.R
man/.DS_Store
man/.Rhistory
man/figures/.DS_Store
man/figures/logo.png
man/figures/make.logo.R
man/figures/unnamed-chunk-10-1.png
man/figures/unnamed-chunk-5-1.png
man/figures/unnamed-chunk-5-2.png
man/figures/unnamed-chunk-5-3.png
man/figures/unnamed-chunk-7-1.png
man/figures/unnamed-chunk-7-2.png
man/figures/unnamed-chunk-9-1.png
man/figures/unnamed-chunk-9-2.png
man/optimize_M.Rd
man/optimize_bigM.Rd
man/optimize_n.Rd
man/vis_depth.Rd
man/vis_loci.Rd
man/vis_snps.Rd
paper/fig1.png
paper/paper.bib
paper/paper.md
pkgdown/.DS_Store
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/.DS_Store
tests/testthat/test-optimize_bigM.R
tests/testthat/test-optimize_m.R
tests/testthat/test-optimize_n.R
tests/testthat/test-vis_depth.R
tests/testthat/test-vis_loci.R
tests/testthat/test-vis_snps.R
tests/testthat/testthat.R
vignettes/.DS_Store
vignettes/.Rhistory
vignettes/brown.trout.validation.Rmd
vignettes/optimize_denovo.Rmd
vignettes/quality.control.vignette.Rmd
vignettes/reproducible.vignette.Rmd
vignettes/trt.bigm.png
vignettes/trt.m.png