linelist - Tagging and Validating Epidemiological Data
Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Last updated 1 days ago
datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
9.10 score 8 stars 3 dependents 66 scripts 660 downloadsepiparameter - Library of Epidemiological Parameters with Helper Functions and Classes
Library of epidemiological parameters for infectious diseases extracted from the literature, and a set of classes and helper functions for working with parameters.
Last updated 14 days ago
data-accessdata-packageepidemiologyepiverseprobability-distribution
8.91 score 33 stars 1 dependents 96 scriptscfr - Estimate Disease Severity and Case Ascertainment
Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.
Last updated 6 days ago
case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
8.18 score 13 stars 35 scripts 392 downloadsfinalsize - Calculate the Final Size of an Epidemic
Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) <doi:10.1007/s11538-012-9749-6>.
Last updated 6 months ago
epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp
8.18 score 11 stars 48 scripts 212 downloadssivirep - Data Wrangling and Automated Reports from 'SIVIGILA' Source
Data wrangling, pre-processing, and generating automated reports from Colombia's epidemiological surveillance system, 'SIVIGILA' <https://portalsivigila.ins.gov.co/>. It provides a customizable R Markdown template for analysis and automatic generation of epidemiological reports that can be adapted to local, regional, and national contexts. This tool offers a standardized and reproducible workflow that helps to reduce manual labor and potential errors in report generation, improving their efficiency and consistency.
Last updated 7 days ago
colombiaepidemiological-surveillanceepiversepublic-health
8.10 score 43 stars 21 scripts 284 downloadsvaccineff - Estimate Vaccine Effectiveness Based on Different Study Designs
Provides tools for estimating vaccine effectiveness and related metrics. The 'vaccineff_data' class manages key features for preparing, visualizing, and organizing cohort data, as well as estimating vaccine effectiveness. The results and model performance are assessed using the 'vaccineff' class.
Last updated 5 days ago
epidemiologyepiversevaccine-effectiveness
7.94 score 16 stars 13 scripts 90 downloadsepidemics - Composable Epidemic Scenario Modelling
A library of compartmental epidemic models taken from the published literature, and classes to represent affected populations, public health response measures including non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical interventions that affect disease transmissibility, vaccination regimes, and disease seasonality, which can be combined to compose epidemic scenario models.
Last updated 6 months ago
decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccinationcpp
7.60 score 8 stars 53 scriptsepichains - Simulating and Analysing Transmission Chain Statistics Using Branching Process Models
Provides methods to simulate and analyse the size and length of branching processes with an arbitrary offspring distribution. These can be used, for example, to analyse the distribution of chain sizes or length of infectious disease outbreaks, as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>.
Last updated 22 hours ago
branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction
7.53 score 7 stars 7 scripts 201 downloadscleanepi - Clean and Standardize Epidemiological Data
Cleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, ensuring seamless integration into existing workflows. Additionally, it generates a comprehensive report detailing the outcomes of each cleaning task.
Last updated 2 months ago
data-cleaningepidemiologyepiverse
7.35 score 8 stars 18 scripts 333 downloadsColOpenData - Download Colombian Demographic, Climate and Geospatial Data
Downloads wrangled Colombian socioeconomic, geospatial,population and climate data from DANE <https://www.dane.gov.co/> (National Administrative Department of Statistics) and IDEAM <https://ideam.gov.co> (Institute of Hydrology, Meteorology and Environmental Studies). It solves the problem of Colombian data being issued in different web pages and sources by using functions that allow the user to select the desired database and download it without having to do the exhausting acquisition process.
Last updated 1 months ago
climatecolombiadata-packagedemographicsmaps
7.31 score 8 stars 15 scripts 395 downloadsepiCo - Statistical and Viz Tools for Vector-Borne Diseases in Colombia
Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
Last updated 27 days ago
colombiadecision-supportdemographicsepiverseoutbreak-analysisspatio-temporal-analysisvector-borne-diseases
7.00 score 12 stars 7 scripts 181 downloadssimulist - Simulate Disease Outbreak Line List and Contacts Data
Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.
Last updated 2 months ago
epidemiologyepiverselinelistoutbreaks
6.44 score 5 stars 23 scriptsserofoi - Estimates the Force-of-Infection of a Given Pathogen from Population Based Seroprevalence Studies
Estimate time or age varying Force-of-Infection from population based seroprevalence studies using a bayesian framework.
Last updated 2 hours ago
antibodiesbayesian-methodsepidemiologyepiverseserological-surveysstan-languagecpp
6.24 score 17 stars 12 scriptssuperspreading - Estimate Individual-Level Variation in Transmission
Implements functions to estimate individual-level variation in transmission.
Last updated 1 months ago
disease-transmissionepidemiologyepiverse
6.13 score 4 stars 16 scriptsreadepi - Read Data from Health Information Systems
Data import from several health information systems ('HIS'). The current version of the package covers 'HIS' such as 'MS SQL', 'MySQL', and 'PostGRESQL' servers, 'REDCap', 'DHIS2' and 'Fingertips'.
Last updated 6 months ago
data-importepidemiologyepiversehealth-information-systems
5.26 score 6 stars 5 scriptsnumberize - Convert Words to Numbers in Multiple Languages
Converts written out numbers into their equivalent numbers. Supports numbers written out in English, French, or Spanish.
Last updated 1 months ago
r-programming
5.16 score 3 stars 1 dependents 1 scripts 749 downloadstracetheme - A 'ggplot2' Theme and Scale Using 'Epiverse-TRACE' Visual Style
A 'ggplot2' theme and scale using 'Epiverse-TRACE' visual style, colour scheme, and visualisation guidelines.
Last updated 8 months ago
4.32 score 1 stars 5 scriptsepiparameterDB - Database of Epidemiological Parameters
A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature.
Last updated 13 days ago
3.48 score 1 dependents 3 scriptsvaccineff - Estimate Vaccine Effectiveness Based on Different Study Designs
Provides tools for estimating vaccine effectiveness and related metrics. The 'vaccineff_data' class manages key features for preparing, visualizing, and organizing cohort data, as well as estimating vaccine effectiveness. The results and model performance are assessed using the 'vaccineff' class.
Last updated 12 days ago
3.26 score 12 scripts