Package: epireview 1.4.8

Sangeeta Bhatia

epireview: Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)

Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.

Authors:Rebecca Nash [aut], Christian Morgenstern [aut], Cosmo Santoni [aut], Sangeeta Bhatia [aut, cre], Richard Sheppard [aut], Joseph Hicks [aut], Gina Cuomo-Dannenburg [aut], Ruth McCabe [aut], Kelly McCain [aut], Joshua Lambert [aut], Anne Cori [aut], Thomas Rawson [aut], Patrick Doohan [aut], Tristan Naidoo [aut], Shazia Ruybal-Pesántez [aut], Anna Vicco [aut]

epireview_1.4.8.tar.gz
epireview_1.4.8.zip(r-4.7)epireview_1.4.8.zip(r-4.6)epireview_1.4.8.zip(r-4.5)
epireview_1.4.8.tgz(r-4.6-any)epireview_1.4.8.tgz(r-4.5-any)
epireview_1.4.8.tar.gz(r-4.7-any)epireview_1.4.8.tar.gz(r-4.6-any)
epireview_1.4.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epireview/json (API)

# Install 'epireview' in R:

install.packages('epireview', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/epireview/issues

Pkgdown/docs site:https://mrc-ide.github.io

On CRAN:

6.44 score 36 stars 12 scripts 42 exports 49 dependencies

Last updated from:612e8d82ee (on main). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	179
source / vignettes	OK	205
linux-release-x86_64	OK	167
macos-release-arm64	OK	101
macos-oldrel-arm64	OK	131
windows-devel	OK	130
windows-release	OK	139
windows-oldrel	OK	140
wasm-release	OK	140

Exports:article_column_type assign_qa_score check_column_types check_df_for_meta check_ulim color_palette country_palette custom_palette delays_to_days filter_cols filter_df_for_metamean filter_df_for_metaprop forest_plot forest_plot_delay_int forest_plot_doubling_time forest_plot_incubation_period forest_plot_infectious_period forest_plot_r0 forest_plot_rt forest_plot_serial_interval get_incubation_period get_key_columns get_parameter invert_inverse_params load_epidata load_epidata_raw mark_multiple_estimates model_column_type outbreak_column_type param_pm_uncertainty parameter_column_type parameter_palette pretty_article_label priority_pathogens qa_questions reorder_studies reparam_gamma shape_palette short_parameter_type theme_epireview update_article_info value_type_palette

Dependencies:base64enc bit bit64 cli clipr cpp11 crayon distcrete dplyr epitrix farver generics ggforce ggplot2 glue gtable hms isoband jsonlite labeling lifecycle magrittr MASS pillar pkgconfig polyclip prettyunits progress purrr R6 RColorBrewer readr rlang S7 scales sodium stringi stringr systemfonts tibble tidyr tidyselect tweenr tzdb utf8 vctrs viridisLite vroom withr

Epidemiological Parameters: Ebola Bundibugyo Virus (BVD)

Rendered fromebola_vignette_BVD.Rmdusingknitr::rmarkdown

Last update: 2026-05-29
Started: 2026-05-29

Help page	Topics
Define the column types for the article data frame	article_column_type
Assign quality assessment score to each article	assign_qa_score
Checks that the column types of the input csv matches the column types expected by epireview.	check_column_types
Sanity checks before meta-analysis	check_df_for_meta
Check upper limit of parameter values	check_ulim
Define a consistent color palette for use in figures. Palettes are currently defined for parameters and countries. Any other variable will return NULL	color_palette
country_palette Function	country_palette
Create a custom color palette.	custom_palette
This function converts delays in different units (hours, weeks, months) to days. It checks if all delays are in days and warns the user if not. It then converts hours to days by dividing by 24, weeks to days by multiplying by 7, and months to days by multiplying by 30.	delays_to_days
Intended for internal use only; setting desirable defaults for reading in data files.	epireview_read_file
Filter columns of a data frame based on specified conditions.	filter_cols
Prepare parameter dataframe for meta analysis of means	filter_df_for_metamean
Prepare parameter dataframe for meta analysis of proportions	filter_df_for_metaprop
Basic forest plot	forest_plot
Create forest plot for human delays	forest_plot_delay_int
Forest plot for doubling time	forest_plot_doubling_time
Create forest plot for incubation period	forest_plot_incubation_period
Create forest plot for infectious period	forest_plot_infectious_period
forest_plot_r0 function	forest_plot_r0
Generate a forest plot for effective reproduction number (Rt)	forest_plot_rt
Create forest plot for serial interval	forest_plot_serial_interval
Subset the epidemiological parameter columns by parameter type	get_key_columns
retrieve all parameters of specified type or class	get_parameter
Retrieve all incubation period parameters for a given pathogen	get_attack_rate get_cfr get_delays get_doubling_time get_generation_time get_genomic get_growth_rate get_incubation_period get_overdispersion get_relative_contribution get_reproduction_number get_risk_factors get_serial_interval get_seroprevalence get_specific
Inverts the values of selected parameters in a data frame. Sometimes parameters are reported in inverse form (e.g., a delay might be reported as per day instead of days). Here we carry out a very simple transformation to convert these to the correct form by inverting the parameter value and the uncertainty bounds. This may not be appropriate in all cases, and must be checked on a case-by-case basis. This function takes a data frame as input and inverts the values of selected parameters. The selected parameters are identified by the column 'inverse_param'. The function performs the following operations: • Inverts the parameter values of the selected parameters. • Swaps the upper and lower bounds of the selected parameters. • Inverts the uncertainty values of the selected parameters. • Updates the logical vector to indicate that the parameters are no longer inverted. • Does not change the unit of the parameters, as it remains the same as the original parameter.	invert_inverse_params
Retrieve pathogen-specific data	load_epidata
Loads raw data for a particular pathogen	load_epidata_raw
Ensure that each article gets a unique id across all tables	make_unique_id
Data on the articles identified and included in the systematic review of articles related to Marburg virus disease.	marburg_article
Dropdown menu options for model extractions in the systematic review of articles related to Marburg virus disease (MVD).	marburg_dropdown_models
Dropdown menu options for outbreak extractions in the systematic review of articles related to Marburg virus disease (MVD).	marburg_dropdown_outbreaks
Dropdown menu options for parameter extractions in the systematic review of articles related to Marburg virus disease (MVD).	marburg_dropdown_parameters
Data on the models identified in the systematic review of articles related to Marburg virus disease.	marburg_model
Data on the outbreaks identified in the systematic review of articles related to Marburg virus disease.	marburg_outbreak
Data on the parameters identified in the systematic review of articles related to Marburg virus disease.	marburg_parameter
Distinguish multiple estimates from the same study	mark_multiple_estimates
model_column_type	model_column_type
outbreak_column_type	outbreak_column_type
Update parameter uncertainty columns in a data frame	param_pm_uncertainty
parameter_column_type	parameter_column_type
Define a consistent color palette for use in figures	parameter_palette
Make pretty labels for articles	pretty_article_label
priority_pathogens	priority_pathogens
Quality assessment questionnaire This function returns the list of 7 questions used to assess quality of articles.	qa_questions
Reorder articles based on parameter value	reorder_studies
Reparameterize Gamma Distribution	reparam_gamma
shape_palette function	shape_palette
Short labels parameters for use in figures	short_parameter_type
Plotting theme for epireview A standard theme for figures in epireview.	theme_epireview
Include key article information when DOI is missing	update_article_info
Define a consistent shape palette for use in forest plots We map shape aesthetic to value type i.e., mean, median etc. This function defines a shape palette that can be used in forest plots	value_type_palette

Package: epireview 1.4.8

epireview: Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)