Lineage Frequency Dynamics from Genomic Surveillance Counts
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Documentation for package ‘lineagefreq’ version 0.2.0
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 |