Package: epiparameter 0.4.0

Joshua W. Lambert

epiparameter: Classes and Helper Functions for Working with Epidemiological Parameters

Classes and helper functions for loading, extracting, converting, manipulating, plotting and aggregating epidemiological parameters for infectious diseases. Epidemiological parameters extracted from the literature are loaded from the 'epiparameterDB' R package.

Authors:Joshua W. Lambert [aut, cre, cph], Adam Kucharski [aut, cph], Carmen Tamayo [aut], Hugo Gruson [ctb, rev], Sebastian Funk [ctb], Pratik Gupte [rev], James M. Azam [rev], Chris Hartgerink [rev], Tim Taylor [rev]

epiparameter_0.4.0.tar.gz
epiparameter_0.4.0.tar.gz(r-4.5-noble)epiparameter_0.4.0.tar.gz(r-4.4-noble)
epiparameter_0.4.0.tgz(r-4.4-emscripten)epiparameter_0.4.0.tgz(r-4.3-emscripten)
epiparameter.pdf |epiparameter.html✨
epiparameter/json (API)
NEWS

# Install 'epiparameter' in R:
install.packages('epiparameter', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/epiverse-trace/epiparameter/issues

Pkgdown site:https://epiverse-trace.github.io

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

4.98 score 1 packages 105 scripts 30 exports 16 dependencies

Last updated 2 hours agofrom:861e27f34b. Checks:2 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 08 2025
R-4.5-linuxOKJan 08 2025

Exports:as_epiparameterassert_epiparametercalc_disc_dist_quantilecdfconvert_params_to_summary_statsconvert_summary_stats_to_paramscreate_citationcreate_metadatacreate_method_assesscreate_prob_distributioncreate_regioncreate_summary_statscreate_uncertaintydiscretisediscretizeepidist_dbepiparameterepiparameter_dbextract_paramgenerateget_citationget_parametersis_continuousis_epiparameteris_epiparameter_paramsis_parameterisedis_parameterizedis_truncatedparameter_tbltest_epiparameter

Dependencies:backportscachemcheckmateclidistcretedistributionalepiparameterDBfastmapgenericsgluelifecyclenumDerivpillarrlangutf8vctrs

{epiparameter} Extraction Bias Analysis

Rendered fromextract-bias.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Current database

Rendered fromdatabase.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Data Collation and Synthesis Protocol

Rendered fromdata_protocol.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Design Principles for {epiparameter}

Rendered fromdesign_principles.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Getting Started with {epiparameter}

Rendered fromepiparameter.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Parameter extraction and conversion in {epiparameter}

Rendered fromextract_convert.Rmdusingknitr::rmarkdownon Jan 08 2025.

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Readme and manuals

Help Manual

Help pageTopics
Aggregate multiple <epiparameter> objects into a single <epiparameter> object.aggregate.multi_epiparameter
Convert to an <epiparameter> objectas_epiparameter
Convert <data.frame> to an <epiparameter> objectas_epiparameter.data.frame
'as.data.frame()' method for <epiparameter> classas.data.frame.epiparameter
'as.data.frame()' method for <multi_epiparameter> classas.data.frame.multi_epiparameter
'as.function()' method for <epiparameter> classas.function.epiparameter
Assert an object is a valid <epiparameter> objectassert_epiparameter
'c()' method for <epiparameter> classc.epiparameter c.multi_epiparameter
Calculate the quantiles of a probability distribution based on the vector of probabilities and time data (e.g. time since infection)calc_disc_dist_quantile
Convert the parameter(s) of a distribution to summary statisticsconvert_params_to_summary_stats convert_params_to_summary_stats.character convert_params_to_summary_stats.epiparameter
Convert the summary statistics of a distribution to parametersconvert_summary_stats_to_params convert_summary_stats_to_params.character convert_summary_stats_to_params.epiparameter
Create a citation for an <epiparameter> objectcreate_citation
Specify metadata associated with data setcreate_metadata
Specify methodological aspects of distribution fittingcreate_method_assess
Create a distribution objectcreate_prob_distribution
Specify the geography of the data entrycreate_region
Specify reported summary statisticscreate_summary_stats
Specify distribution parameter uncertaintycreate_uncertainty
Discretises a continuous distribution in an <epiparameter> objectdiscretise discretise.default discretise.epiparameter discretize
Create an <epiparameter> objectepiparameter
Create <epiparameter> object(s) directly from the epiparameter library (database)epiparameter_db
PDF, CDF, PMF, quantiles and random number generation for <epiparameter> objectscdf.epiparameter density.epiparameter epiparameter_distribution_functions generate.epiparameter quantile.epiparameter
Package optionsepiparameter_options
A vector of 'character' strings with the core column names of the epidemiological parameter data exported by the 'epireview' R package.epireview_core_cols
Calculate the parameters of a parametric probability distribution from reported values of percentiles, or median and rangeextract_param
Family method for the <epiparameter> classfamily.epiparameter
Format method for <epiparameter> classformat.epiparameter
Get citation from an objectget_citation
Get citation from an <epiparameter> objectget_citation.epiparameter
Get citation from a list of <epiparameter> objectsget_citation.multi_epiparameter
Get parameters from an objectget_parameters
Get parameters from an <epiparameter> objectget_parameters.epiparameter get_parameters.multi_epiparameter
Check if distribution in <epiparameter> is continuousis_continuous
Check object is an <epiparameter>is_epiparameter
Check whether the vector of parameters for the probability distribution are in the set of possible parameters used in the epiparameter packageis_epiparameter_params
Check if <epiparameter> or list of <epiparameter> objects contains a distribution and distribution parametersis_parameterised is_parameterised.epiparameter is_parameterised.multi_epiparameter is_parameterized
Check if distribution in <epiparameter> is truncatedis_truncated
'lines()' method for <epiparameter> classlines.epiparameter
Mean method for <epiparameter> classmean.epiparameter
Table of epidemiological distributionsparameter_tbl
Plot method for <epiparameter> classplot.epiparameter
'plot()' method for <multi_epiparameter> classplot.multi_epiparameter
Print method for <epiparameter> classprint.epiparameter
Print method for <multi_epiparameter> classprint.multi_epiparameter
Test whether an object is a valid <epiparameter> objecttest_epiparameter