Man pages for survinger
Design-Adjusted Inference for Pathogen Lineage Surveillance
| dot-assert_columns_exist | Assert required columns exist in a data frame |
| dot-assert_surv_class | Assert object inherits from a specific surv_* class |
| dot-assert_surv_design | Assert object inherits from surv_design |
| dot-date_to_epiweek | Convert Date vector to ISO epiweek strings (YYYY-Wnn) |
| dot-generate_unequal_shares | Generate unequal shares summing to 1 |
| dot-kish_eff_n | Kish effective sample size |
| dot-make_strata_key | Create strata key string from data frame rows |
| dot-map_weights_to_obs | Map stratum-level weights to individual observations |
| dot-resolve_time_column | Resolve user-specified time column |
| dot-surv_colors | survinger color palette |
| dot-validate_seq_rates | Validate and clamp sequencing rates to (0, 1] |
| dot-wilson_ci | Wilson score interval for a proportion |
| glance.surv | One-row summary of survinger model |
| new_surv_allocation | Internal constructor for surv_allocation |
| new_surv_delay_fit | Internal constructor for surv_delay_fit |
| new_surv_prevalence | Internal constructor for surv_prevalence |
| plot.surv | Plot methods for survinger objects |
| reexports | Objects exported from other packages |
| sarscov2_surveillance | Example SARS-CoV-2 genomic surveillance data |
| 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 |
| survinger-package | survinger: Design-Adjusted Inference for Pathogen Lineage... |
| 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 |
