R: Design-Adjusted Inference for Pathogen Lineage Surveillance

# Design-Adjusted Inference for Pathogen Lineage Surveillance

## Documentation for package ‘survinger’ version 0.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

as.data.frame.surv_adjusted | Combined design-weighted and delay-adjusted prevalence
as.data.frame.surv_allocation | Optimize sequencing allocation across strata
as.data.frame.surv_nowcast | Nowcast lineage counts correcting for reporting delays
as.data.frame.surv_prevalence | Estimate lineage prevalence with design weights
glance.surv | One-row summary of survinger model
glance.surv_adjusted | One-row summary of survinger model
glance.surv_delay_fit | One-row summary of survinger model
glance.surv_prevalence | One-row summary of survinger model
plot.surv | Plot methods for survinger objects
plot.surv_adjusted | Plot methods for survinger objects
plot.surv_allocation | Plot methods for survinger objects
plot.surv_delay_fit | Plot methods for survinger objects
plot.surv_design | Plot methods for survinger objects
plot.surv_nowcast | Plot methods for survinger objects
plot.surv_power_curve | Compute power curve for detection across prevalence range
plot.surv_prevalence | Plot methods for survinger objects
print.summary.surv_design | Create a genomic surveillance design object
print.surv_adjusted | Combined design-weighted and delay-adjusted prevalence
print.surv_allocation | Optimize sequencing allocation across strata
print.surv_delay_fit | Estimate reporting delay distribution
print.surv_design | Create a genomic surveillance design object
print.surv_nowcast | Nowcast lineage counts correcting for reporting delays
print.surv_prevalence | Estimate lineage prevalence with design weights
sarscov2_surveillance | Example SARS-CoV-2 genomic surveillance data
summary.surv_design | Create a genomic surveillance design object
surv_adjusted_prevalence | Combined design-weighted and delay-adjusted prevalence
surv_bind | Combine multiple prevalence estimates
surv_compare_allocations | Compare multiple allocation strategies
surv_compare_estimates | Compare weighted vs naive prevalence estimates
surv_design | Create a genomic surveillance design object
surv_design_effect | Compute design effect over time
surv_detection_probability | Variant detection probability under current design
surv_estimate | Pipe-friendly surveillance analysis
surv_estimate_delay | Estimate reporting delay distribution
surv_filter | Subset a surveillance design by filter criteria
surv_lineage_prevalence | Estimate lineage prevalence with design weights
surv_naive_prevalence | Compute naive (unweighted) lineage prevalence
surv_nowcast_lineage | Nowcast lineage counts correcting for reporting delays
surv_optimize_allocation | Optimize sequencing allocation across strata
surv_plot_allocation | Plot allocation plan
surv_plot_sequencing_rates | Plot sequencing rate inequality across strata
surv_power_curve | Compute power curve for detection across prevalence range
surv_prevalence_by | Estimate prevalence by subgroup
surv_quality | Compute surveillance quality metrics
surv_report | Generate a comprehensive surveillance system report
surv_reporting_probability | Compute cumulative reporting probability
surv_required_sequences | Required sequences for target detection probability
surv_sensitivity | Sensitivity analysis across methods
surv_set_weights | Override design weights with custom values
surv_simulate | Simulate genomic surveillance data
surv_table | Format prevalence results for knitr tables
surv_update_rates | Update sequencing rates in a surveillance design
theme_survinger | Publication-quality ggplot2 theme
tidy.surv | Extract tidy estimates from survinger objects
tidy.surv_adjusted | Extract tidy estimates from survinger objects
tidy.surv_allocation | Extract tidy estimates from survinger objects
tidy.surv_delay_fit | Extract tidy estimates from survinger objects
tidy.surv_nowcast | Extract tidy estimates from survinger objects
tidy.surv_prevalence | Extract tidy estimates from survinger objects