# Lineage Frequency Dynamics from Genomic Surveillance Counts

## Documentation for package ‘lineagefreq’ version 0.2.0

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

## Help Pages

as.data.frame.lfq_data | Convert lfq_data to long-format tibble
as_lfq_data | Coerce to lfq_data
as_lfq_data.data.frame | Coerce to lfq_data
as_lfq_data.lfq_data | Coerce to lfq_data
augment.lfq_fit | Augment data with fitted values from an lfq_fit object
autoplot.lfq_fit | Plot lineage frequency model results
autoplot.lfq_forecast | Plot a lineage frequency forecast
backtest | Rolling-origin backtesting of lineage frequency models
cdc_ba2_transition | CDC SARS-CoV-2 variant proportions: BA.1 to BA.2 transition (US, 2022)
cdc_sarscov2_jn1 | CDC SARS-CoV-2 variant proportions: JN.1 emergence (US, 2023-2024)
coef.lfq_fit | Extract coefficients from a lineage frequency model
collapse_lineages | Collapse rare lineages into an aggregate group
compare_models | Compare model engines from backtest scores
filter_sparse | Filter sparse time points and lineages
fit_model | Fit a lineage frequency model
forecast | Forecast lineage frequencies (generic)
forecast.lfq_fit | Forecast lineage frequencies
glance.lfq_fit | Glance at an lfq_fit object
growth_advantage | Extract growth advantage estimates
influenza_h3n2 | Simulated influenza A/H3N2 clade frequency data
is_lfq_data | Test if an object is an lfq_data object
lfq_advantage | Pipe-friendly growth advantage extraction
lfq_data | Create a lineage frequency data object
lfq_engines | List available modeling engines
lfq_fit | Pipe-friendly model fitting
lfq_forecast | Pipe-friendly forecasting
lfq_score | Pipe-friendly backtesting + scoring
lfq_stan_available | Check if 'CmdStan' backend is available
lfq_summary | Convert lfq_fit results to a summary tibble
lfq_version | Package version and system information
plot_backtest | Plot backtest scores
print.lfq_fit | Print a lineage frequency model
read_lineage_counts | Read lineage count data from a CSV file
register_engine | Register a custom modeling engine
sarscov2_us_2022 | Simulated SARS-CoV-2 variant frequency data (US, 2022)
score_forecasts | Score backtest forecast accuracy
sequencing_power | Sequencing power analysis
simulate_dynamics | Simulate lineage frequency dynamics
summarize_emerging | Summarize emerging lineages
summary.lfq_fit | Summarise a lineage frequency model
tidy.lfq_fit | Tidy an lfq_fit object
unregister_engine | Remove a registered engine