Man pages for ern
Effective Reproduction Number Estimation
| agg_to_daily | Infer daily counts from aggregates |
| attach_startdate_agg | Attach start date from first observation for aggregated data... |
| attach_t | Attach internal time index column |
| attach_t_agg | Attach time index (number of days) column. Exclude first day... |
| check_cl.input_format | Check the format of input clinical data |
| check_df.input_daily | Check if input data is already daily |
| check_dist | Check distributions |
| check_for_deconv | Check that deconvolution inputs are compatible |
| check_prm.daily | Check parameters for daily data inference |
| check_prm.daily.check | Check parameters for daily data inference check |
| check_prm.R | Check parameters for Rt calculation |
| check_prm.smooth | Check parameters for smoothing |
| cl.data | Sample of aggregated clinical reports |
| correct_underreporting | Correct underreporting by scaling up |
| deconv | Wrapper for deconvolution with a given distribution |
| deconvolution_RL | Richardson-Lucy Deconvolution. |
| deconv_ww_inc | Deconvoluting Wastewater Data to Incidence |
| def_dist | Define a family of distributions. |
| draw_from_gamma | Draw from gamma for a parameter specified in a distribution... |
| estimate_R_cl | Estimate the effective reproduction from clinical report data |
| estimate_R_cl_rep | Ensemble estimate of Rt |
| estimate_R_cl_single | A single realization of the Rt estimate |
| estimate_R_ww | Estimate the effective reproduction from wastewater... |
| extract_mcmc_values | Extract MCMC chains from a JAGS object |
| fit_jags_aggreg | Fit JAGS model to aggregated data |
| get_discrete_dist | Get a discretized, truncated version of a distribution |
| get_realizations | Retrieve realizations for aggregated to daily inference |
| get_use_dates | Get dates for which to use (trust) inferred daily reports |
| inc2R_one_iter | Helper function. Converts wastewater to Rt after sampling one... |
| incidence_to_R | Estimate Rt using EpiEstim |
| linear_int_daily | Daily incidence from linear interpolation |
| na_to_0 | Replace NAs with 0s in vector |
| plot_diagnostic_cl | Diagnostic plot for R estimation from clinical report data |
| plot_diagnostic_ww | Diagnostic plot for R estimation from wastewater data |
| plot_dist | Plot a distribution |
| plot_gelman_rubin | Plot the Gelman Rubin statistic for all parameters. |
| plot_traces | Plot MCMC traces |
| reports_to_incidence | Infer incidence from reports via a series of deconvolutions |
| reshape_fit_jags | Reshape JAGS fit object |
| sample_a_dist | Sample parameters for a single distribution from a family of... |
| sample_from_dist | Sample from a distribution (currently only implemented for a... |
| sample_post_ee | Helper function - sample from EpiEstim's R posterior... |
| smooth_cl | Smooth realizations from estimating daily reports |
| smooth_ww | Smooth wastewater data (using pre-processed wastewater) |
| summarise_by_date_iters | Summarise observations by date for raw iterations from an... |
| summarise_report_counts | Summarise daily inferred reports based on original reporting... |
| summary_postsamples | Helper function that summarises posterior samples of Rt from... |
| ww.data | Sample of wastewater concentration |
