Function reference • epict

Core functions

Core Functions used for fitting models with preprocessed observations.

epict(): Model Cycle Thresholds

Preprocess

Functions for preprocessing observations.

epict_check_obs(): Check proccessed observations meet the package specification

epict_check_raw_obs(): Check unproccessed observations meet the package specification

epict_clean_factors(): Clean up factor levels

epict_drop_na_ct(): Drop Ct values with no data

epict_filter_ids(): Filter infection IDs based on characteristics

epict_flag_spurious_obs(): Flag potentially spurious observations

epict_make_time_rel(): Make time relative to first date of the test.

epict_make_time_rel_to_first_uncensored(): Make time relative to first uncensored test per ID

Model tools

Functions that assist with designing and setting up models.

adjustment_formula(): Specify the cycle threshold adjustment model formula

epict_formula_as_list(): Format formula data for use with stan

epict_individual_priors_as_list(): Format individual-level priors for use in stan

epict_inference_opts(): Format inference options for use with stan

epict_model_opts(): Format formula data for use with stan

epict_obs_as_list(): Format observed data for use with stan

epict_onset_obs_as_list(): Format observed symptom onset data for use with stan

epict_population_priors_as_list(): Format population-level priors for use in stan

epict_posterior_as_prior(): Extract summarised posteriors to use as priors

piecewise_formula(): Specify the cycle threshold adjustment model formula

select_piecewise_parameters(): Select the parameters to adjust in the piecewise model

Model

Functions for fitting models.

epict_convert_to_list(): Format observations and model settings for use with stan

epict_inits(): Set up initial conditions for model

epict_model(): Load and compile the Cycle thresholds model

epict_priors(): Default model priors

Postprocess

Functions for postprocessing model output.

update_variable_labels(): FUNCTION_TITLE

Plot

Functions for plotting observations and model output

Generate data

Functions for generating simulated data.

Datasets

Package datasets used in examples and by users to explore the package functionality.

Utilities

Utility tools and functionality