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 3 months ago
datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
8 stars 8.64 score 18 dependencies 1 dependentsepiparameter - Library of Epidemiological Parameters with Helper Functions and Classes
Library of epidemiological parameters for infectious diseases and a set of classes and helper functions.
Last updated 4 days ago
data-accessdata-packageepidemiologyepiverseprobability-distribution
32 stars 8.64 score 14 dependencies 1 dependentsfinalsize - 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 4 months ago
epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3
11 stars 8.20 score 4 dependenciescfr - 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 3 months ago
case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
13 stars 8.10 score 2 dependenciesepidemics - 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 4 months ago
decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccination
8 stars 7.82 score 9 dependenciesColOpenData - 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 10 days ago
climatecolombiadata-packagedemographicsmaps
7 stars 7.30 score 38 dependenciescleanepi - 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 days ago
data-cleaningepidemiologyepiverse
8 stars 7.03 score 41 dependenciesepiCo - 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 18 days ago
colombiadecision-supportdemographicsepiverseoutbreak-analysisspatio-temporal-analysisvector-borne-diseases
10 stars 6.88 score 107 dependenciesserofoi - Estimates the Force-of-Infection of a Given Pathogen from Population Based Seroprevalence Studies
Estimate time-varying Force-of-Infection of a given pathogen from population based seroprevalence studies using a bayesian framework.
Last updated 2 months ago
antibodiesbayesian-methodsepidemiologyepiverseserological-surveysstan-language
17 stars 6.83 score 95 dependenciesvaccineff - Estimate Vaccine Effectiveness Based on Different Study Designs
R package with tools for estimating vaccine effectiveness and vaccine related metrics.
Last updated 12 days ago
epidemiologyepiversevaccine-effectiveness
14 stars 6.67 score 39 dependenciesepichains - 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 5 days ago
branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction
6 stars 6.46 score 2 dependenciessuperspreading - Estimate Individual-Level Variation in Transmission
Implements functions to estimate individual-level variation in transmission.
Last updated 8 days ago
disease-transmissionepidemiologyepiverse
4 stars 6.03 score 4 dependenciesreadepi - 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 4 months ago
data-importepidemiologyepiversehealth-information-systems
6 stars 5.56 score 81 dependenciesnumberize - 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 2 months ago
r-programming
4 stars 5.28 score 0 dependencies 1 dependentssimulist - 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 1 days ago
epidemiologyepiverselinelistoutbreaks
5 stars 4.65 score 41 dependenciestracetheme - 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 6 months ago
1 stars 4.32 score 31 dependencies