Package: epireview 1.4.3

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]

epireview_1.4.3.tar.gz
epireview_1.4.3.zip(r-4.5)epireview_1.4.3.zip(r-4.4)epireview_1.4.3.zip(r-4.3)
epireview_1.4.3.tgz(r-4.5-any)epireview_1.4.3.tgz(r-4.4-any)epireview_1.4.3.tgz(r-4.3-any)
epireview_1.4.3.tar.gz(r-4.5-noble)epireview_1.4.3.tar.gz(r-4.4-noble)
epireview_1.4.3.tgz(r-4.4-emscripten)epireview_1.4.3.tgz(r-4.3-emscripten)
epireview.pdf |epireview.html✨
epireview/json (API)
NEWS

# 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 site:https://mrc-ide.github.io

On CRAN:

Conda:

6.72 score 30 stars 6 scripts 42 exports 56 dependencies

Last updated 2 months agofrom:5c9671a605 (on main). Checks:5 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winNOTEFeb 17 2025
R-4.5-macNOTEFeb 17 2025
R-4.5-linuxNOTEFeb 17 2025
R-4.4-winOKFeb 17 2025
R-4.4-macOKFeb 17 2025
R-4.3-winOKFeb 17 2025
R-4.3-macOKFeb 17 2025

Exports:article_column_typeassign_qa_scorecheck_column_typescheck_df_for_metacheck_ulimcolor_palettecountry_palettecustom_palettedelays_to_daysfilter_colsfilter_df_for_metameanfilter_df_for_metapropforest_plotforest_plot_delay_intforest_plot_doubling_timeforest_plot_incubation_periodforest_plot_infectious_periodforest_plot_r0forest_plot_rtforest_plot_serial_intervalget_incubation_periodget_key_columnsget_parameterinvert_inverse_paramsload_epidataload_epidata_rawmark_multiple_estimatesmodel_column_typeoutbreak_column_typeparam_pm_uncertaintyparameter_column_typeparameter_palettepretty_article_labelpriority_pathogensqa_questionsreorder_studiesreparam_gammashape_paletteshort_parameter_typetheme_epireviewupdate_article_infovalue_type_palette

Dependencies:bitbit64clicliprcolorspacecpp11crayondistcretedplyrepitrixfansifarvergenericsggforceggplot2gluegtablehmsisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpolyclipprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrrlangscalessodiumstringistringrsystemfontstibbletidyrtidyselecttweenrtzdbutf8vctrsviridisLitevroomwithr

epireview

Rendered fromepireview_overview.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-05-13
Started: 2023-06-19

load-filter-view-epidata

Rendered fromload-filter-view-epidata.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-05-13
Started: 2024-03-19

Readme and manuals

Help Manual

Help pageTopics
Define the column types for the article data framearticle_column_type
Assign quality assessment score to each articleassign_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-analysischeck_df_for_meta
Check upper limit of parameter valuescheck_ulim
Define a consistent color palette for use in figures. Palettes are currently defined for parameters and countries. Any other variable will return NULLcolor_palette
country_palette Functioncountry_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 meansfilter_df_for_metamean
Prepare parameter dataframe for meta analysis of proportionsfilter_df_for_metaprop
Basic forest plotforest_plot
Create forest plot for human delaysforest_plot_delay_int
Forest plot for doubling timeforest_plot_doubling_time
Create forest plot for incubation periodforest_plot_incubation_period
Create forest plot for infectious periodforest_plot_infectious_period
forest_plot_r0 functionforest_plot_r0
Generate a forest plot for effective reproduction number (Rt)forest_plot_rt
Create forest plot for serial intervalforest_plot_serial_interval
Subset the epidemiological parameter columns by parameter typeget_key_columns
retrieve all parameters of specified type or classget_parameter
Retrieve all incubation period parameters for a given pathogenget_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 dataload_epidata
Loads raw data for a particular pathogenload_epidata_raw
Ensure that each article gets a unique id across all tablesmake_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 studymark_multiple_estimates
model_column_typemodel_column_type
outbreak_column_typeoutbreak_column_type
Update parameter uncertainty columns in a data frameparam_pm_uncertainty
parameter_column_typeparameter_column_type
Define a consistent color palette for use in figuresparameter_palette
Make pretty labels for articlespretty_article_label
priority_pathogenspriority_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 valuereorder_studies
Reparameterize Gamma Distributionreparam_gamma
shape_palette functionshape_palette
Short labels parameters for use in figuresshort_parameter_type
Plotting theme for epireview A standard theme for figures in epireview.theme_epireview
Include key article information when DOI is missingupdate_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 plotsvalue_type_palette