epiparameter - Classes and Helper Functions for Working with Epidemiological Parameters

Classes and helper functions for loading, extracting, converting, manipulating, plotting and aggregating epidemiological parameters for infectious diseases. Epidemiological parameters extracted from the literature are loaded from the 'epiparameterDB' R package.

Last updated 24 days ago

data-accessdata-packageepidemiologyepiverseprobability-distribution

9.87 score 33 stars 1 dependents 105 scripts 211 downloads

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 2 months ago

datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data

8.86 score 8 stars 2 dependents 66 scripts 632 downloads

finalsize - 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 7 days ago

epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp

8.16 score 11 stars 46 scripts 288 downloads

cfr - 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 2 hours ago

case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3

8.15 score 13 stars 35 scripts 316 downloads

sivirep - 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 15 days ago

colombiaepidemiological-surveillanceepiversepublic-health

8.07 score 43 stars 21 scripts 251 downloads

vaccineff - 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 3 months ago

epidemiologyepiversevaccine-effectiveness

7.94 score 16 stars 13 scripts 197 downloads

simulist - 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 20 hours ago

epidemiologyepiverselinelistoutbreaks

7.79 score 9 stars 25 scripts 204 downloads

epidemics - 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 8 months ago

decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccinationcpp

7.55 score 8 stars 59 scripts

ColOpenData - 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 7 days ago

climatecolombiadata-packagedemographicsmaps

7.55 score 11 stars 17 scripts 616 downloads

epichains - 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 17 days ago

branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction

7.52 score 7 stars 7 scripts 226 downloads

cleanepi - 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 10 days ago

data-cleaningepidemiologyepiverse

7.40 score 9 stars 18 scripts 291 downloads

superspreading - Understand Individual-Level Variation in Infectious Disease Transmission

Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions ('Kremer et al.' (2021) <doi:10.1038/s41598-021-93578-x>), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct ('Kucharski et al.' (2020) <doi:10.1016/S1473-3099(20)30144-4>), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission ('Lloyd-Smith et al.' (2005) <doi:10.1038/nature04153>).

Last updated 23 days ago

disease-transmissionepidemiologyepiverse

7.06 score 4 stars 16 scripts 5 downloads

epiCo - 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 1 months ago

colombiadecision-supportdemographicsepiverseoutbreak-analysisspatio-temporal-analysisvector-borne-diseases

6.97 score 12 stars 8 scripts 238 downloads

serofoi - Bayesian Estimation of the Force of Infection from Serological Data

Estimating the force of infection from time varying, age varying, or constant serocatalytic models from population based seroprevalence studies using a bayesian framework, including data simulation functions enabling the generation of serological surveys based on this models. This tool also provides a flexible prior specification syntax for the force of infection and the seroreversion rate, as well as methods to assess model convergence and comparison criteria along with useful visualisation functions.

Last updated 21 hours ago

antibodiesbayesian-methodsepidemiologyepiverseserological-surveysstan-languagecpp

6.17 score 18 stars 10 scripts

epiparameterDB - 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 17 days ago

data-packageepidemiologyepiverse

5.92 score 2 stars 2 dependents 4 scripts 251 downloads

numberize - 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 4 months ago

r-programming

5.16 score 3 stars 1 dependents 1 scripts 635 downloads

readepi - 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 8 months ago

data-importepidemiologyepiversehealth-information-systems

5.08 score 6 stars 5 scripts

tracetheme - 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 10 months ago

4.18 score 1 stars 6 scripts