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_pkgdown.yml
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/
_pkgdown.yml
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url: https://adrian-lison.github.io/EpiSewer/
template:
bootstrap: 5
bslib:
bootswatch: flatly
pkgdown-nav-height: 80px
primary: '#1f407a'
secondary: '#53a8ed'
success: '#53a8ed'
home:
sidebar:
structure:
- links
- license
- citation
- authors
articles:
- title: Introduction
navbar: Introduction
contents:
- model-specification
- detailed-example
- title: Modeling details
navbar: Modeling details
contents:
- model-definition
- load_per_case
reference:
- title: EpiSewer
contents:
- sewer_data
- sewer_assumptions
- EpiSewer
- title: Measurements module
desc: Modeling functions for the measurement process
contents:
- model_measurements
- starts_with("concentrations_")
- starts_with("noise_")
- starts_with("LOD_")
- title: Sampling module
desc: Modeling functions for the sampling process
contents:
- model_sampling
- starts_with("outliers_")
- starts_with("sample_effects_")
- title: Sewage module
desc: Modeling functions for the sewage process
contents:
- model_sewage
- starts_with("flows_")
- starts_with("residence_dist_")
- title: Shedding module
desc: Modeling functions for the shedding process
contents:
- model_shedding
- starts_with("shedding_dist_")
- starts_with("incubation_dist_")
- starts_with("load_per_case_")
- starts_with("load_variation_")
- title: Infections module
desc: Modeling functions for the infection process
contents:
- model_infections
- R_estimate_splines
- R_estimate_rw
- R_estimate_ets
- R_estimate_approx
- starts_with("generation_dist_")
- starts_with("seeding_")
- starts_with("infection_noise")
- title: Forecast module
desc: Modeling functions for specifying forecasts
contents:
- model_forecast
- starts_with("horizon_")
- title: Model fitting
desc: Functions to specify and run the sampling of EpiSewer models
contents:
- set_fit_opts
- sampler_stan_mcmc
- model_stan_opts
- set_results_opts
- sewer_compile
- run
- title: Plotting
desc: Functions for plotting
contents:
- plot_R
- plot_growth_report
- plot_growth_rate
- plot_doubling_time
- plot_infections
- plot_load
- plot_concentration
- plot_prior_posterior
- plot_LOD
- plot_sample_effects
- title: Specification
desc: Helper functions for specifying distributions and other assumptions
contents:
- starts_with("get_discrete_")
- suggest_load_per_case
- title: Preprocessing
desc: Functions for preprocessing data
contents: mark_outlier_spikes_median
- title: Utilities
desc: Utility functions
contents:
- component_functions
- modeldata_init
- get_checksums
- summarize_fit