Package: epiparameter 0.4.1.9000

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 Cuartero [aut], Hugo Gruson [ctb, rev], Sebastian Funk [ctb], Pratik Gupte [rev], James M. Azam [rev], Chris Hartgerink [rev], Tim Taylor [rev], London School of Hygiene and Tropical Medicine, LSHTM [cph]

epiparameter_0.4.1.9000.tar.gz
epiparameter_0.4.1.9000.zip(r-4.7)epiparameter_0.4.1.9000.zip(r-4.6)epiparameter_0.4.1.9000.zip(r-4.5)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epiparameter/json (API)

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

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

Pkgdown/docs 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.

On CRAN:

Conda:

data-accessdata-packageepidemiologyepiverseprobability-distribution

9.67 score 37 stars 1 packages 168 scripts 290 downloads 29 exports 25 dependencies

Last updated from:291bfd2490. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK206
source / vignettesOK216
linux-release-x86_64OK209
macos-release-arm64OK206
macos-oldrel-arm64OK156
windows-develOK223
windows-releaseOK229
windows-oldrelOK230
wasm-releaseOK117

Exports:as_epiparameterassert_epiparametercalc_disc_dist_quantilecdfconvert_params_to_summary_statsconvert_summary_stats_to_paramscreate_citationcreate_metadatacreate_method_assesscreate_prob_distributioncreate_regioncreate_summary_statscreate_uncertaintydiscretisediscretizeepiparameterepiparameter_dbextract_paramgenerateget_citationget_parametersis_continuousis_epiparameteris_epiparameter_paramsis_parameterisedis_parameterizedis_truncatedparameter_tbltest_epiparameter

Dependencies:askpassbackportscachemcheckmateclicurldistcretedistributionalepiparameterDBfastmapgenericsgluehttr2lifecyclemagrittrnumDerivopensslpillarR6rappdirsrlangsysutf8vctrswithr

Data Collation and Synthesis Protocol
About the package | Objective of | Contributing to the package | Scope of package | Guide to identifying distributions in the literature | Guide to data refinement once sources identified | Guide to extracting parameters | Data quality assessment in | Guide to the {epiparameter} review process | Updating parameters in the database | Database of excluded papers | References
Rendered fromdata_protocol.Rmdusingknitr::rmarkdown

Last update: 2025-01-08
Started: 2023-03-02

Design Principles for {epiparameter}
Scope | Output | Package architecture | Design decisions | Dependencies | Contribute
Rendered fromdesign_principles.Rmdusingknitr::rmarkdown

Last update: 2024-11-22
Started: 2023-11-15

Current database
Rendered fromdatabase.Rmdusingknitr::rmarkdown

Last update: 2024-10-09
Started: 2024-05-23

Getting Started with {epiparameter}
Use case | Library of epidemiological parameters | Single set of epidemiological parameters | Benefit of <epiparameter> | Subsetting database | Distribution functions | Plotting epidemiological distributions | Accessors | Parameter conversion and extraction | Conversion | Extraction | Adding library entries and contributing to
Rendered fromepiparameter.Rmdusingknitr::rmarkdown

Last update: 2024-10-09
Started: 2022-10-18

Parameter extraction and conversion in {epiparameter}
Conversion versus extraction | Conversions | Conversion functions | Gamma distribution | Using a character string to name distribution | Using an <epiparameter> | Lognormal distribution | Weibull distribution | Negative binomial distribution | Geometric distribution | Extraction | Use cases | Assuming distributions | References
Rendered fromextract_convert.Rmdusingknitr::rmarkdown

Last update: 2024-10-09
Started: 2023-04-27

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
Package optionsepiparameter_default_options
PDF, CDF, PMF, quantiles and random number generation for <epiparameter> objectscdf.epiparameter density.epiparameter epiparameter_distribution_functions generate.epiparameter quantile.epiparameter
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