sitrep - Report Templates and Helper Functions for Applied Epidemiology

A meta-package that loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including 'epitabulate' (for epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for epidemiological utilities), and 'apyramid' (for age-sex pyramids). Simply load 'sitrep' to access all functions from the ecosystem.

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epidemiologymsfoutbreaksreport-generator

8.00 score 45 stars 7 scripts 211 downloads

epikit - Miscellaneous Helper Tools for Epidemiologists

Contains tools for formatting inline code, renaming redundant columns, aggregating age categories, adding survey weights, finding the earliest date of an event, plotting z-curves, generating population counts and formatting proportions with confidence intervals. This is part of the 'R4Epis' project <https://r4epi.github.io/sitrep/>.

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6.65 score 10 stars 2 dependents 24 scripts 1.0k downloads

epidict - Epidemiology Data Dictionaries and Random Data Generators

The 'R4EPIs' project <https://r4epi.github.io/sitrep/> seeks to provide a set of standardized tools for analysis of outbreak and survey data in humanitarian aid settings. This package currently provides standardized data dictionaries from Medecins Sans Frontieres Operational Centre Amsterdam for outbreak scenarios (Acute Jaundice Syndrome, Cholera, Diphtheria, Measles, Meningitis) and surveys (Retrospective mortality and access to care, Malnutrition, Vaccination coverage and Event Based Surveillance) - as described in the following <https://scienceportal.msf.org/assets/standardised-mortality-surveys?utm_source=chatgpt.com>. In addition, a data generator from these dictionaries is provided. It is also possible to read in any Open Data Kit format data dictionary.

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6.21 score 3 stars 1 dependents 3 scripts 231 downloads

apyramid - Visualize Population Pyramids Aggregated by Age

Provides a quick method for visualizing non-aggregated line-list or aggregated census data stratified by age and one or two categorical variables (e.g. gender and health status) with any number of values. It returns a 'ggplot' object, allowing the user to further customize the output. This package is part of the 'R4Epis' project <https://r4epis.netlify.app/>.

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6.19 score 20 stars 1 dependents 52 scripts 797 downloads

matchmaker - Flexible Dictionary-Based Cleaning

Provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the 'RECON' (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

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5.08 score 8 stars 1 dependents 9 scripts 508 downloads

epitabulate - Tables for Epidemiological Analysis

Produces tables for descriptive epidemiological analysis. These tables include attack rates, case fatality ratios, and mortality rates (with appropriate confidence intervals), with additional functionality to calculate Mantel-Haenszel odds, risk, and incidence rate ratios. The methods implemented follow standard epidemiological approaches described in Rothman et al. (2008, ISBN:978-0-19-513554-2). This package is part of the 'R4EPIs' project <https://R4EPI.github.io/sitrep/>.

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4.98 score 8 stars 1 dependents 3 scripts 224 downloads