incidence - Compute, Handle, Plot and Model Incidence of Dated Events

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Last updated 3 months ago

outbreak

12.13 score 58 stars 11 packages 534 scripts 2.2k downloads

aweek - Convert Dates to Arbitrary Week Definitions

Which day a week starts depends heavily on the either the local or professional context. This package is designed to be a lightweight solution to easily switching between week-based date definitions.

Last updated 4 years ago

date-formattingdatesepidemiologytimeseriesweek

7.88 score 17 stars 15 packages 118 scripts 1.7k 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 calculating proportions with confidence intervals. This is part of the 'R4Epis' project <https://r4epis.netlify.com>.

Last updated 2 years ago

6.33 score 9 stars 2 packages 22 scripts 1.2k 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/>.

Last updated 2 years ago

6.12 score 20 stars 1 packages 44 scripts 880 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.

Last updated 5 years ago

5.43 score 9 stars 2 packages 9 scripts 451 downloads

epidict - Epidemiology data dictionaries and random data generators

The 'R4EPIs' project <https://R4epis.netlify.com> 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 MSF OCA for four outbreak scenarios (Acute Jaundice Syndrome, Cholera, Measles, Meningitis) and three surveys (Retrospective mortality and access to care, Malnutrition, and Vaccination coverage). In addition, a data generator from these dictionaries is provided.

Last updated 2 years ago

4.13 score 3 stars 1 packages 5 scripts

sitrep - Report templates and helper functions for applied epidemiology

Report templates and helper functions for applied epidemiology

Last updated 2 years ago

epidemiologymsfoutbreaksreport-generator

4.08 score 40 stars 9 scripts

epitabulate - Tables for Epidemiological Analysis

Produces tables for descriptive epidemiological analysis. These tables describe counts of variables in either line-list or survey data (with appropriate confidence intervals), with additional functionality to calculate odds, risk, and incidence rate ratios directly from a linelist across several variables. This package is part of the 'R4EPIs' project <https://R4epis.netlify.com>.

Last updated 2 years ago

3.38 score 8 stars 1 packages 3 scripts