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.
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data-accessdata-packageepidemiologyepiverseprobability-distribution
9.67 score 37 stars 1 dependents 168 scripts 290 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.
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datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
8.39 score 11 stars 2 dependents 89 scripts 567 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>.
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branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction
7.74 score 10 stars 28 scripts 189 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.
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epidemiologyepiverselinelistoutbreaks
7.69 score 11 stars 46 scripts 192 downloads
readepi - Read Data from Relational Database Management Systems and Health Information Systems
Import Data from Relational Database Management Systems (RDBMS) and Health Information Systems ('HIS'). The current version of the package supports importing data from RDBMS including 'MS SQL', 'MySQL', 'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and 'SORMAS'.
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data-importepidemiologyepiversehealth-information-systems
7.64 score 6 stars 11 scripts 8.3k 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.
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decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccination
7.63 score 18 stars 63 scripts
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>.
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epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp
7.44 score 15 stars 58 scripts 297 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, and generates a comprehensive report detailing the outcomes of each cleaning task.
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data-cleaningepidemiologyepiverse
7.40 score 12 stars 44 scripts 311 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>.
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case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
7.26 score 15 stars 61 scripts 274 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>).
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disease-transmissionepidemiologyepiverse
7.17 score 5 stars 30 scripts 222 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.
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epidemiologyepiversevaccine-effectiveness
6.75 score 16 stars 13 scripts 183 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.
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colombiaepidemiological-surveillanceepiversepublic-health
6.44 score 44 stars 28 scripts 10 downloads
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.
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climatecolombiadata-packagedemographicsmaps
6.28 score 13 stars 21 scripts 212 downloads
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.
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data-packageepidemiologyepiverse
6.10 score 3 stars 2 dependents 5 scripts 310 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>).
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colombiadecision-supportdemographicsepiverseoutbreak-analysissdg-3spatio-temporal-analysisvector-borne-diseases
5.89 score 13 stars 10 scripts 277 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.
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r-programming
4.26 score 4 stars 1 dependents 3 scripts 270 downloads