Files in bailey-lab/coiaf
Complexity of Infection Estimation with Allele Frequencies
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug-report.md
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature-request.md
.github/ISSUE_TEMPLATE/maintenance.md
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.gitignore
.pre-commit-config.yaml
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/assertions.R
R/bootstrap.R
R/check-inputs.R
R/check_freq_method.R
R/coiaf-package.R
R/compute_coi.R
R/optimize.R
R/plot_results.R
R/probability.R
R/process.R
R/regression.R
R/sensitivity.R
R/simulate.R
R/themes.R
R/theoretical_coi.R
R/utils-pipe.R
R/utils-tidy-eval.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
coiaf.Rproj
data-raw/example_real_data.R
data/example_real_data.rda
inst/WORDLIST
inst/testdata/test_real_data.rds
man/bootstrap_ci.Rd
man/coiaf-package.Rd
man/compute_coi.Rd
man/compute_coi_regression.Rd
man/cont_sensitivity.Rd
man/disc_sensitivity.Rd
man/distance_curves.Rd
man/error_plot.Rd
man/example_real_data.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/figures/logo_background.jpg
man/figures/logo_v1.png
man/figures/logo_v1_no_white.png
man/figures/logo_v2_dark_green.png
man/figures/logo_v2_light_green.png
man/likelihood.Rd
man/optimize_coi.Rd
man/optimize_coi_regression.Rd
man/pipe.Rd
man/plot-simulation.Rd
man/process.Rd
man/process_real.Rd
man/process_sim.Rd
man/rbetabinom.Rd
man/rdirichlet.Rd
man/sensitivity_plot.Rd
man/sensitivity_plot_element.Rd
man/sim_biallelic.Rd
man/single_sensitivity.Rd
man/theme_coiaf.Rd
man/theoretical_coi.Rd
man/tidyeval.Rd
man/world_map.Rd
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/spelling.R
tests/testthat.R
tests/testthat/_snaps/deprecated-arguments.md
tests/testthat/_snaps/process.md
tests/testthat/_snaps/simulate/autoplot-method-works.svg
tests/testthat/_snaps/simulate/can-pass-additional-params.svg
tests/testthat/_snaps/simulate/plot-method-works.svg
tests/testthat/_snaps/themes/default-theme.svg
tests/testthat/_snaps/themes/theme-coiaf.svg
tests/testthat/_snaps/theoretical_coi.md
tests/testthat/issue_18.rds
tests/testthat/test-assertions.R
tests/testthat/test-check-inputs.R
tests/testthat/test-check_freq_method.R
tests/testthat/test-compute_coi.R
tests/testthat/test-deprecated-arguments.R
tests/testthat/test-probability.R
tests/testthat/test-process.R
tests/testthat/test-simulate.R
tests/testthat/test-themes.R
tests/testthat/test-theoretical_coi.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/example_real_data.Rmd
vignettes/figures/continuous/talpha_1.png
vignettes/figures/continuous/talpha_2.png
vignettes/figures/continuous/tbin.png
vignettes/figures/continuous/tbin_size.png
vignettes/figures/continuous/tcoi.png
vignettes/figures/continuous/tcoverage_1.png
vignettes/figures/continuous/tcoverage_2.png
vignettes/figures/continuous/tepsilon.png
vignettes/figures/continuous/tloci_1.png
vignettes/figures/continuous/tloci_2.png
vignettes/figures/continuous/tover.png
vignettes/figures/continuous/toverall.png
vignettes/figures/continuous/trelated.png
vignettes/figures/continuous/tseq.png
vignettes/figures/discrete/talpha_1.png
vignettes/figures/discrete/talpha_2.png
vignettes/figures/discrete/tbin.png
vignettes/figures/discrete/tbin_size.png
vignettes/figures/discrete/tcoi.png
vignettes/figures/discrete/tcoverage_1.png
vignettes/figures/discrete/tcoverage_2.png
vignettes/figures/discrete/tepsilon.png
vignettes/figures/discrete/tloci_1.png
vignettes/figures/discrete/tloci_2.png
vignettes/figures/discrete/tover.png
vignettes/figures/discrete/toverall.png
vignettes/figures/discrete/trelated.png
vignettes/figures/discrete/tseq.png
vignettes/saved_analysis_continuous.rds
vignettes/saved_analysis_discrete.rds
vignettes/sensitivity_analysis_continuous.Rmd
vignettes/sensitivity_analysis_discrete.Rmd
vignettes/simulator_details.Rmd
