Package: epiparameter 0.2.0.9000

Joshua W. Lambert

epiparameter: Library of Epidemiological Parameters with Helper Functions and Classes

Library of epidemiological parameters for infectious diseases and a set of classes and helper functions.

Authors:Joshua W. Lambert [aut, cre, cph], Adam Kucharski [aut, cph], Carmen Tamayo [aut], Hugo Gruson [ctb, rev], Sebastian Funk [ctb], Pratik Gupte [rev]

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epiparameter.pdf |epiparameter.html✨
epiparameter/json (API)
NEWS

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

Peer review:

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

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:

data-accessdata-packageepidemiologyepiverseprobability-distribution

8.77 score 32 stars 1 packages 80 scripts 30 exports 14 dependencies

Last updated 8 days agofrom:54b7bf17cb. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winOKOct 10 2024
R-4.5-linuxOKOct 10 2024
R-4.4-winOKOct 10 2024
R-4.4-macOKOct 10 2024
R-4.3-winOKOct 10 2024
R-4.3-macOKOct 10 2024

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:backportscheckmateclidistcretedistributionalfansigenericsgluelifecyclenumDerivpillarrlangutf8vctrs

{epiparameter} Extraction Bias Analysis

Rendered fromextract-bias.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2024-07-10
Started: 2023-04-28

Current database

Rendered fromdatabase.Rmdusingknitr::rmarkdownon Oct 10 2024.

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

Data Collation and Synthesis Protocol

Rendered fromdata_protocol.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2024-10-09
Started: 2023-03-02

Design Principles for {epiparameter}

Rendered fromdesign_principles.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2024-10-07
Started: 2023-11-15

Getting Started with {epiparameter}

Rendered fromepiparameter.Rmdusingknitr::rmarkdownon Oct 10 2024.

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

Parameter extraction and conversion in {epiparameter}

Rendered fromextract_convert.Rmdusingknitr::rmarkdownon Oct 10 2024.

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
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
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_parameterized
Check if distribution in <epiparameter> is truncatedis_truncated
Mean method for <epiparameter> classmean.epiparameter
Table of epidemiological distributionsparameter_tbl
Plot method for <epiparameter> classplot.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