Files in lineagefreq

Lineage Frequency Dynamics from Genomic Surveillance Counts

NEWS.md README.md R/score.R R/utils-validation.R R/power-analysis.R R/lineagefreq-package.R R/pipe-api.R R/growth-advantage.R R/engine-fga.R R/methods-coef.R R/data.R R/methods-print.R R/detect-emergence.R R/coerce.R R/simulate.R R/methods-plot.R R/lfq-data.R R/read-counts.R R/engine-registry.R R/backtest.R R/engine-mlr.R R/fit-model.R R/forecast.R R/convert.R R/engine-hier-mlr.R R/utils-plot.R R/utils-stan.R R/preprocess.R R/methods-tidy.R R/engine-garw.R R/engine-piantham.R inst/doc/model-comparison.R inst/doc/model-comparison.Rmd inst/doc/surveillance-workflow.Rmd inst/doc/surveillance-workflow.R inst/doc/real-data-analysis.R inst/doc/introduction.R inst/doc/introduction.Rmd inst/doc/real-data-analysis.Rmd tests/testthat.R tests/testthat/helper-skip-stan.R tests/testthat/test-v020.R tests/testthat/test-validation-ba2.R tests/testthat/test-infrastructure.R tests/testthat/test-engine-mlr.R tests/testthat/test-engine-fga.R tests/testthat/test-lfq-data.R tests/testthat/test-backtest.R tests/testthat/test-growth-advantage.R tests/testthat/test-methods.R tests/testthat/test-fit-model.R tests/testthat/test-engine-piantham.R tests/testthat/test-preprocess.R tests/testthat/test-engine-garw.R tests/testthat/test-score.R tests/testthat/test-simulate.R tests/testthat/test-forecast.R tests/testthat/test-engine-hier-mlr.R tests/testthat/test-cdc-data.R tests/testthat/test-detect-emergence.R tests/testthat/test-power-analysis.R vignettes/model-comparison.Rmd vignettes/surveillance-workflow.Rmd vignettes/introduction.Rmd vignettes/real-data-analysis.Rmd man/score_forecasts.Rd man/summary.lfq_fit.Rd man/augment.lfq_fit.Rd man/filter_sparse.Rd man/as_lfq_data.Rd man/collapse_lineages.Rd man/simulate_dynamics.Rd man/reexports.Rd man/cdc_sarscov2_jn1.Rd man/sequencing_power.Rd man/print.lfq_fit.Rd man/growth_advantage.Rd man/lfq_engines.Rd man/compare_models.Rd man/summarize_emerging.Rd man/lfq_score.Rd man/tidy.lfq_fit.Rd man/as.data.frame.lfq_data.Rd man/backtest.Rd man/influenza_h3n2.Rd man/lfq_fit.Rd man/is_lfq_data.Rd man/read_lineage_counts.Rd man/autoplot.lfq_fit.Rd man/lfq_data.Rd man/lfq_version.Rd man/coef.lfq_fit.Rd man/register_engine.Rd man/cdc_ba2_transition.Rd man/lfq_advantage.Rd man/autoplot.lfq_forecast.Rd man/glance.lfq_fit.Rd man/lfq_stan_available.Rd man/forecast.Rd man/forecast.lfq_fit.Rd man/lineagefreq-package.Rd man/lfq_summary.Rd man/fit_model.Rd man/unregister_engine.Rd man/lfq_forecast.Rd man/plot_backtest.Rd man/sarscov2_us_2022.Rd