Files in survinger

Design-Adjusted Inference for Pathogen Lineage Surveillance

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

LICENSE

R/utils-validation.R R/02-allocation.R R/04-delay.R R/12-advanced.R R/08-diagnostics.R R/99-pub-theme.R R/00-classes.R R/data.R R/11-report.R R/06-detection.R R/survinger-package.R R/09-plot-methods.R R/utils-weights.R R/utils-time.R R/03-prevalence.R R/05-adjusted.R R/13-infrastructure.R R/07-simulate.R R/10-tidy-methods.R R/01-design.R

inst/CITATION

inst/doc/allocation-optimization.html

inst/doc/allocation-optimization.Rmd inst/doc/allocation-optimization.R

inst/doc/real-world-ecdc.html

inst/doc/real-world-ecdc.R inst/doc/delay-correction.R inst/doc/survinger.Rmd inst/doc/survinger.R inst/doc/delay-correction.Rmd inst/doc/real-world-ecdc.Rmd

inst/doc/delay-correction.html

inst/doc/survinger.html

build/vignette.rds

tests/testthat.R tests/testthat/test-07-simulate.R tests/testthat/test-02-allocation.R tests/testthat/test-05-adjusted.R tests/testthat/test-06-detection.R tests/testthat/test-00-classes.R tests/testthat/helper-setup.R tests/testthat/test-12-validation.R tests/testthat/test-10-advanced.R tests/testthat/test-09-enhancements.R tests/testthat/test-01-design.R tests/testthat/test-04-delay.R tests/testthat/test-08-diagnostics.R tests/testthat/test-11-infrastructure.R tests/testthat/test-03-prevalence.R vignettes/allocation-optimization.Rmd vignettes/survinger.Rmd vignettes/delay-correction.Rmd vignettes/real-world-ecdc.Rmd

vignettes/figures/fig8_dashboard.png

vignettes/figures/fig6_triple.png

vignettes/figures/fig3_allocation.png

vignettes/figures/ecdc_delay.png

vignettes/figures/figB_bias_source.png

vignettes/figures/fig7_bias_heatmap.png

vignettes/figures/figA_necessity.png

vignettes/figures/ecdc_adjusted.png

vignettes/figures/ecdc_compare.png

vignettes/figures/fig1_inequality.png

vignettes/figures/fig4_nowcast.png

vignettes/figures/figC_ci_comparison.png

vignettes/figures/fig5_allocation.png

vignettes/figures/ecdc_allocation.png

vignettes/figures/fig2_compare.png

vignettes/figures/fig6_benchmark.png

vignettes/figures/fig4_delay.png

vignettes/figures/ecdc_nowcast.png

vignettes/figures/fig7_detection.png

vignettes/figures/fig5_nowcast.png

vignettes/figures/fig3_bias_heatmap.png

vignettes/figures/ecdc_rates.png

data/sarscov2_surveillance.rda

man/surv_naive_prevalence.Rd man/dot-map_weights_to_obs.Rd man/surv_compare_estimates.Rd man/reexports.Rd man/surv_design.Rd man/plot.surv.Rd man/new_surv_allocation.Rd man/theme_survinger.Rd man/surv_estimate_delay.Rd man/surv_design_effect.Rd man/surv_sensitivity.Rd man/tidy.surv.Rd man/surv_optimize_allocation.Rd man/surv_estimate.Rd man/dot-generate_unequal_shares.Rd man/dot-assert_columns_exist.Rd man/dot-validate_seq_rates.Rd man/surv_set_weights.Rd man/dot-assert_surv_design.Rd man/surv_lineage_prevalence.Rd man/surv_filter.Rd man/glance.surv.Rd man/dot-resolve_time_column.Rd man/dot-wilson_ci.Rd man/surv_simulate.Rd man/new_surv_delay_fit.Rd man/surv_plot_allocation.Rd man/surv_nowcast_lineage.Rd man/dot-assert_surv_class.Rd man/surv_adjusted_prevalence.Rd man/dot-kish_eff_n.Rd man/surv_prevalence_by.Rd man/surv_report.Rd man/surv_bind.Rd man/dot-date_to_epiweek.Rd man/surv_compare_allocations.Rd man/dot-surv_colors.Rd man/new_surv_prevalence.Rd man/surv_detection_probability.Rd man/surv_quality.Rd man/surv_reporting_probability.Rd man/surv_table.Rd man/survinger-package.Rd man/surv_plot_sequencing_rates.Rd man/dot-make_strata_key.Rd man/sarscov2_surveillance.Rd man/surv_update_rates.Rd man/surv_required_sequences.Rd man/surv_power_curve.Rd

man/figures/figA_necessity.png

man/figures/fig6_benchmark.png

man/figures/fig3_bias_heatmap.png

survinger documentation built on April 27, 2026, 9:10 a.m.