Package index • epiparameter

epiparameter classes

epiparameter object

Class constructor, validator, and methods

epiparameter(): Create an <epiparameter> object

discretise() discretize(): Discretises a continuous distribution in an <epiparameter> object

as.data.frame(<epiparameter>): as.data.frame() method for <epiparameter> class

as.function(<epiparameter>): as.function() method for <epiparameter> class

c(<epiparameter>) c(<multi_epiparameter>): c() method for <epiparameter> class

family(<epiparameter>): Family method for the <epiparameter> class

format(<epiparameter>): Format method for <epiparameter> class

get_citation(<epiparameter>): Get citation from an <epiparameter> object

get_parameters(<epiparameter>) get_parameters(<multi_epiparameter>): Get parameters from an <epiparameter> object

is_parameterised() is_parameterized(): Check if <epiparameter> or list of <epiparameter> objects contains a distribution and distribution parameters

mean(<epiparameter>): Mean method for <epiparameter> class

plot(<epiparameter>): Plot method for <epiparameter> class

print(<epiparameter>): Print method for <epiparameter> class

assert_epiparameter(): Assert an object is a valid <epiparameter> object

test_epiparameter(): Test whether an object is a valid <epiparameter> object

aggregate(<multi_epiparameter>): Aggregate multiple <epiparameter> objects into a single <epiparameter> object.

as.data.frame(<multi_epiparameter>): as.data.frame() method for <multi_epiparameter> class

get_citation(<multi_epiparameter>): Get citation from a list of <epiparameter> objects

print(<multi_epiparameter>): Print method for <multi_epiparameter> class

Accessors

Get data from epi classes

get_citation(): Get citation from an object

get_parameters(): Get parameters from an object

epiparameter helper functions

Functions to help construct <epiparameter> objects

create_citation(): Create a citation for an <epiparameter> object

create_metadata(): Specify metadata associated with data set

create_method_assess(): Specify methodological aspects of distribution fitting

create_prob_distribution(): Create a distribution object

create_region(): Specify the geography of the data entry

create_summary_stats(): Specify reported summary statistics

create_uncertainty(): Specify distribution parameter uncertainty

epiparameter from {epiparameter} library

Retrieve <epiparameter> object directly from database

epiparameter_db(): Create <epiparameter> object(s) directly from the epiparameter library (database)

Coercion

Convert data from and to <epiparameter>

as_epiparameter(): Convert to an <epiparameter> object

as_epiparameter(<data.frame>): Convert <data.frame> to an <epiparameter> object

Explore epiparameters

Table of epi parameters

parameter_tbl(): Table of epidemiological distributions

Distribution functions

Functions for operating on <epiparameter> distributions

density(<epiparameter>) cdf(<epiparameter>) quantile(<epiparameter>) generate(<epiparameter>): PDF, CDF, PMF, quantiles and random number generation for <epiparameter> objects

Parameter extraction

Extract distribution parameters from summary statistics

extract_param(): Calculate the parameters of a parametric probability distribution from reported values of percentiles, or median and range

Parameter conversion

Convert distribution parameter to summary statistics and vice versa

convert_params_to_summary_stats(): Convert the parameter(s) of a distribution to summary statistics

convert_summary_stats_to_params(): Convert the summary statistics of a distribution to parameters

Epi object checking

Check an object is of a certain type or feature

is_continuous(): Check if distribution in <epiparameter> is continuous

is_epiparameter(): Check object is an <epiparameter>

is_epiparameter_params(): Check whether the vector of parameters for the probability distribution are in the set of possible parameters used in the epiparameter package

is_parameterised() is_parameterized(): Check if <epiparameter> or list of <epiparameter> objects contains a distribution and distribution parameters

is_truncated(): Check if distribution in <epiparameter> is truncated

Utility function

calc_disc_dist_quantile(): Calculate the quantiles of a probability distribution based on the vector of probabilities and time data (e.g. time since infection)

Package data

Data stored in the package

epireview_core_cols: A vector of character strings with the core column names of the epidemiological parameter data exported by the epireview R package.

Options

epiparameter_options: Package options