adegenet - Exploratory Analysis of Genetic and Genomic Data
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
Last updated 2 months ago
12.60 score 182 stars 29 dependents 1.9k scripts 18k downloadsmstate - Data Preparation, Estimation and Prediction in Multi-State Models
Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Last updated 2 months ago
12.20 score 11 stars 57 dependents 322 scripts 8.7k downloadsincidence - 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 8 months ago
outbreak
12.06 score 58 stars 11 dependents 504 scripts 2.0k downloadsEpiEstim - Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Last updated 7 months ago
12.06 score 95 stars 7 dependents 1.0k scripts 1.4k downloads
EpiNow2 - Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.
Last updated 6 days ago
backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp
11.91 score 125 stars 210 scripts 934 downloadsAMR - Antimicrobial Resistance Data Analysis
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Last updated 2 days ago
amrantimicrobial-dataepidemiologymicrobiologysoftware
11.83 score 95 stars 6 dependents 182 scripts 1.7k downloadspomp - Statistical Inference for Partially Observed Markov Processes
Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Last updated 13 days ago
abcb-splinedifferential-equationsdynamical-systemsiterated-filteringlikelihoodlikelihood-freemarkov-chain-monte-carlomarkov-modelmathematical-modellingmeasurement-errorparticle-filtersequential-monte-carlosimulation-based-inferencesobol-sequencestate-spacestatistical-inferencestochastic-processestime-seriesopenblas
11.74 score 114 stars 4 dependents 1.3k scripts 3.0k downloadsEpiModel - Mathematical Modeling of Infectious Disease Dynamics
Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Last updated 2 months ago
agent-based-modelingepidemicsepidemiologyinfectious-diseasesnetwork-graphcpp
11.43 score 250 stars 315 scripts 1.0k downloads
COVID19 - COVID-19 Data Hub
Unified datasets for a better understanding of COVID-19.
Last updated 1 months ago
2019-ncovcoronaviruscovid-19covid-datacovid19-data
11.08 score 252 stars 265 scripts 703 downloadsSimInf - A Framework for Data-Driven Stochastic Disease Spread Simulations
Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.
Last updated 3 days ago
data-drivenepidemiologyhigh-performance-computingmarkov-chainmathematical-modellinggslopenmp
10.11 score 35 stars 227 scripts 527 downloadssocialmixr - Social Mixing Matrices for Infectious Disease Modelling
Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
Last updated 1 months ago
9.97 score 38 stars 1 dependents 227 scripts 654 downloads
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 2 months ago
data-accessdata-packageepidemiologyepiverseprobability-distribution
9.82 score 34 stars 1 dependents 102 scripts 191 downloadsEpi - Statistical Analysis in Epidemiology
Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.
Last updated 3 months ago
9.64 score 4 stars 11 dependents 708 scripts 9.3k downloadsnhanesA - NHANES Data Retrieval
Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/>.
Last updated 3 months ago
nhanes
9.37 score 59 stars 239 scripts 2.6k downloadscholera - Amend, Augment and Aid Analysis of John Snow's Cholera Map
Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.
Last updated 8 hours ago
choleradata-visualizationdatasetsepidemiologyjohn-snowpublic-healthtriangulation-delaunayvoronoivoronoi-polygons
9.34 score 134 stars 95 scripts 583 downloadsmalariaAtlas - An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Last updated 9 months ago
databasemalariaopendataraster
9.10 score 44 stars 3 dependents 118 scripts 729 downloadslinelist - 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 7 days ago
datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data
8.69 score 7 stars 2 dependents 61 scripts 447 downloadsepicontacts - Handling, Visualisation and Analysis of Epidemiological Contacts
A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Last updated 2 months ago
outbreak
8.68 score 15 stars 2 dependents 112 scripts 652 downloads
dbparser - Drugs Databases Parser
This tool is for parsing public drug databases such as 'DrugBank' XML database <https://go.drugbank.com/>. The parsed data are then returned in a proper 'R' object called 'dvobject'.
Last updated 9 months ago
8.47 score 59 stars 210 scripts 846 downloadsepiworldR - Fast Agent-Based Epi Models
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Last updated 13 hours ago
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelcppopenmp
8.35 score 9 stars 1 dependents 58 scripts 317 downloadsoutbreaker2 - Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Last updated 6 months ago
cpp
8.16 score 31 stars 1 dependents 101 scripts 294 downloadscfr - 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 1 months ago
case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
8.11 score 14 stars 35 scripts 406 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 2 months ago
epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp
8.11 score 11 stars 46 scripts 292 downloadspopEpi - Functions for Epidemiological Analysis using Population Data
Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.
Last updated 1 days ago
adjust-estimatesage-adjustingdirect-adjustingepidemiologyindirect-adjustingsurvival
8.01 score 8 stars 1 dependents 118 scripts 1.8k 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 1 months ago
colombiaepidemiological-surveillanceepiversepublic-health
8.00 score 42 stars 21 scripts 215 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 1 months ago
epidemiologyepiversevaccine-effectiveness
7.88 score 15 stars 13 scripts 156 downloadsincidence2 - Compute, Handle and Plot 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 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org>).
Last updated 4 months ago
7.64 score 17 stars 1 dependents 104 scripts 1.2k downloadsepichains - 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 21 days ago
branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction
7.48 score 7 stars 8 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, and generates a comprehensive report detailing the outcomes of each cleaning task.
Last updated 12 days ago
data-cleaningepidemiologyepiverse
7.39 score 8 stars 19 scripts 341 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 3 months ago
colombiadecision-supportdemographicsepiverseoutbreak-analysissdg-3spatio-temporal-analysisvector-borne-diseases
6.86 score 11 stars 8 scripts 190 downloadssuperspreading - 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 2 months ago
disease-transmissionepidemiologyepiverse
6.73 score 4 stars 158 downloadsepikit - 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.app/>.
Last updated 2 months ago
6.32 score 10 stars 2 dependents 22 scripts 1.0k downloadsdde - Solve Delay Differential Equations
Solves ordinary and delay differential equations, where the objective function is written in either R or C. Suitable only for non-stiff equations, the solver uses a 'Dormand-Prince' method that allows interpolation of the solution at any point. This approach is as described by Hairer, Norsett and Wanner (1993) <ISBN:3540604529>. Support is also included for iterating difference equations.
Last updated 6 months ago
6.20 score 15 stars 1 dependents 35 scripts 330 downloads
rplanes - Plausibility Analysis of Epidemiological Signals
Provides functionality to prepare data and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausibility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score.
Last updated 9 months ago
6.03 score 9 stars 171 downloadsepiparameterDB - 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 2 months ago
data-packageepidemiologyepiverse
5.92 score 2 stars 2 dependents 274 downloadsEpiContactTrace - Epidemiological Tool for Contact Tracing
Routines for epidemiological contact tracing and visualisation of network of contacts.
Last updated 6 months ago
cpp
5.74 score 11 stars 42 scripts 626 downloadscontactdata - Social Contact Matrices for 177 Countries
Data package for the supplementary data in Prem et al. (2017) <doi:10.1371/journal.pcbi.1005697> and Prem et al. <doi:10.1371/journal.pcbi.1009098>. Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.
Last updated 4 months ago
demographicsepidemiologysocial-sciences
5.65 score 9 stars 11 scripts 443 downloadsggsurveillance - Tools for Outbreak Investigation/Infectious Disease Surveillance
Create epicurves or epigantt charts in 'ggplot2'. Prepare data for visualisation or other reporting for infectious disease surveillance and outbreak investigation. Includes tidy functions to solve date based transformations for common reporting tasks, like (A) seasonal date alignment for respiratory disease surveillance, (B) date-based case binning based on specified time intervals like isoweek, epiweek, month and more, (C) automated detection and marking of the new year based on the date/datetime axis of the 'ggplot2'. An introduction on how to use epicurves can be found on the US CDC website (2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Last updated 1 months ago
epidemiologyinfectious-disease-surveillanceinfectious-diseasesoutbreaks
5.56 score 3 stars 1.6k downloads
hmsidwR - Health Metrics and the Spread of Infectious Diseases
A collection of datasets and supporting functions accompanying Health Metrics and the Spread of Infectious Diseases by Federica Gazzelloni (2024). This package provides data for health metrics calculations, including Disability-Adjusted Life Years (DALYs), Years of Life Lost (YLLs), and Years Lived with Disability (YLDs), as well as additional tools for analyzing and visualizing health data. Federica Gazzelloni (2024) <doi:10.5281/zenodo.10818338>.
Last updated 2 months ago
deathshealth-datainfectious-diseaseslifeexpectancy
5.26 score 3 stars 6 scripts 468 downloadsdenguedatahub - A Tidy Format Datasets of Dengue by Country
Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Last updated 2 months ago
openjdk
5.12 score 11 stars 34 scripts 243 downloadsepidm - UK Epidemiological Data Management
Contains utilities and functions for the cleaning, processing and management of patient level public health data for surveillance and analysis held by the UK Health Security Agency, UKHSA.
Last updated 8 months ago
5.07 score 13 stars 2 scripts 291 downloads
cercospoRa - Process Based Epidemiological Model for Cercospora Leaf Spot of Sugar Beet
Estimates sugar beet canopy closure with remotely sensed leaf area index and estimates when action might be needed to protect the crop from a Leaf Spot epidemic with a negative prognosis model based on published models.
Last updated 4 months ago
4.90 score 265 downloadsphylepic - Combined Visualisation of Phylogenetic and Epidemiological Data
A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
Last updated 3 months ago
genomicsgenomics-visualizationpublic-health
4.65 score 453 downloadsexcessmort - Excess Mortality
Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Last updated 16 days ago
4.60 score 20 stars 25 scripts 647 downloadsepiworldRShiny - A 'shiny' Wrapper of the R Package 'epiworldR'
R 'shiny' web apps for epidemiological Agent-Based Models. It provides a user-friendly interface to the Agent-Based Modeling (ABM) R package 'epiworldR' (Meyer et al., 2023) <DOI:10.21105/joss.05781>. Some of the main features of the package include the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Recovered (SIR), and Susceptible-Exposed-Infected-Recovered (SEIR) models. 'epiworldRShiny' provides a web-based user interface for running various epidemiological ABMs, simulating interventions, and visualizing results interactively.
Last updated 2 days ago
abmagent-based-modelingcovid-19epidemic-simulationsepidemiologynetscinetwork-analysisshinyappsshinydashboardsimulation-modeling
4.18 score 1 stars 4 scripts 448 downloadsdeSolve - Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')
Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.
Last updated 1 years ago
fortranopenblas
12.08 score 11 stars 427 dependents 8.0k scripts 54k downloadsepitrix - Small Helpers and Tricks for Epidemics Analysis
A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
Last updated 2 years ago
epidemiology
8.58 score 11 stars 5 dependents 231 scripts 494 downloadsTransPhylo - Inference of Transmission Tree from a Dated Phylogeny
Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) <doi:10.1093/molbev/msw275>.
Last updated 2 years ago
cpp
8.43 score 61 stars 74 scripts 234 downloadscoronavirus - The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Last updated 2 years ago
covid-19covid19covid19-datadataset
8.25 score 499 stars 716 scripts 554 downloadsetm - Empirical Transition Matrix
The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multi-state model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Last updated 3 years ago
openblascpp
8.09 score 13 dependents 110 scripts 5.7k downloadscoarseDataTools - Analysis of Coarsely Observed Data
Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.
Last updated 2 years ago
8.05 score 9 stars 8 dependents 34 scripts 1.2k downloadscmprsk - Subdistribution Analysis of Competing Risks
Estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of a competing risk, Ann. Stat. 16:1141-1154 <DOI:10.1214/aos/1176350951>, and Fine JP and Gray RJ (1999), A proportional hazards model for the subdistribution of a competing risk, JASA, 94:496-509, <DOI:10.1080/01621459.1999.10474144>.
Last updated 11 months ago
fortran
7.83 score 3 stars 63 dependents 608 scripts 20k downloadsepitools - Epidemiology Tools
Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.
Last updated 5 years ago
6.81 score 2 stars 13 dependents 768 scripts 11k downloadsSpatialEpi - Methods and Data for Spatial Epidemiology
Methods and data for cluster detection and disease mapping.
Last updated 2 years ago
cpp
6.68 score 31 stars 146 scripts 886 downloadsearlyR - Estimation of Transmissibility in the Early Stages of a Disease Outbreak
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.
Last updated 4 years ago
6.59 score 9 stars 96 scripts 250 downloadsinctools - Incidence Estimation Tools
Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) <doi:10.1097/EDE.0b013e3182576c07>.
Last updated 4 years ago
biomarkersbiostatisticsepidemiologyhivincidenceincidence-estimationincidence-inferenceinfectious-diseasesstatistics
6.51 score 6 stars 27 scripts 223 downloads
episensr - Basic Sensitivity Analysis of Epidemiological Results
Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", ('Springer', 2021).
Last updated 1 years ago
biasepidemiologysensitivity-analysisstatistics
6.48 score 13 stars 1 dependents 39 scripts 702 downloads
DSAIDE - Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)
Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Last updated 1 years ago
6.30 score 26 stars 22 scripts 539 downloadsmem - The Moving Epidemic Method
The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Last updated 2 years ago
influenzamem
6.24 score 14 stars 1 dependents 82 scripts 570 downloadsepiflows - Predicting Disease Spread from Flow Data
Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 2 years ago
outbreak
6.16 score 18 stars 20 scripts 297 downloadscovid19italy - The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.
Last updated 2 years ago
6.07 score 47 stars 25 scripts 255 downloadsepitweetr - Early Detection of Public Health Threats from 'Twitter' Data
It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (doi:10.2807/1560-7917.ES.2022.27.39.2200177).
Last updated 1 years ago
early-warning-systemsepidemic-surveillancelucenemachine-learningsignal-detectionsparktwitter
5.98 score 56 stars 86 scripts 325 downloadsoutbreaks - A Collection of Disease Outbreak Data
Empirical or simulated disease outbreak data, provided either as RData or as text files.
Last updated 2 years ago
5.81 score 51 stars 290 scripts 1.5k downloadstrending - Model Temporal Trends
Provides a coherent interface to multiple modelling tools for fitting trends along with a standardised approach for generating confidence and prediction intervals.
Last updated 2 years ago
5.58 score 8 stars 1 dependents 16 scripts 248 downloadsepiDisplay - Epidemiological Data Display Package
Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at '<https://medipe.psu.ac.th/epicalc/>'.
Last updated 3 years ago
5.46 score 1 stars 2 dependents 760 scripts 6.3k downloadscovid19us - Cases of COVID-19 in the United States
A wrapper around the 'COVID Tracking Project API' <https://covidtracking.com/api/> providing data on cases of COVID-19 in the US.
Last updated 3 years ago
5.25 score 63 stars 28 scripts 353 downloadscovid19sf - The Covid19 San Francisco Dataset
Provides a verity of summary tables of the Covid19 cases in San Francisco. Data source: San Francisco, Department of Public Health - Population Health Division <https://datasf.org/opendata/>.
Last updated 2 years ago
5.16 score 12 stars 12 scripts 251 downloadslinelistBayes - Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches
Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.
Last updated 11 months ago
openblascpp
5.00 score 4 stars 479 downloadsEpiILM - Spatial and Network Based Individual Level Models for Epidemics
Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Last updated 5 years ago
fortran
4.80 score 6 stars 21 scripts 345 downloadso2geosocial - Reconstruction of Transmission Chains from Surveillance Data
Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).
Last updated 10 months ago
baysian-inferencemarkov-chain-monte-carlotransmission-chain-reconstructioncpp
4.60 score 8 stars 5 scripts 264 downloadsbets.covid19 - The BETS Model for Early Epidemic Data
Implements likelihood inference for early epidemic analysis. BETS is short for the four key epidemiological events being modeled: Begin of exposure, End of exposure, time of Transmission, and time of Symptom onset. The package contains a dataset of the trajectory of confirmed cases during the coronavirus disease (COVID-19) early outbreak. More detail of the statistical methods can be found in Zhao et al. (2020) <arXiv:2004.07743>.
Last updated 5 years ago
2019-ncov
4.43 score 27 stars 2 scripts 215 downloadsepitab - Flexible Contingency Tables for Epidemiology
Builds contingency tables that cross-tabulate multiple categorical variables and also calculates various summary measures. Export to a variety of formats is supported, including: 'HTML', 'LaTeX', and 'Excel'.
Last updated 7 years ago
4.41 score 1 stars 17 scripts 265 downloadsEpiCurve - Plot an Epidemic Curve
Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Last updated 4 years ago
4.34 score 1 stars 22 scripts 516 downloadsCovidMutations - Mutation Analysis and Assay Validation Toolkit for COVID-19 (Coronavirus Disease 2019)
A feasible framework for mutation analysis and reverse transcription polymerase chain reaction (RT-PCR) assay evaluation of COVID-19, including mutation profile visualization, statistics and mutation ratio of each assay. The mutation ratio is conducive to evaluating the coverage of RT-PCR assays in large-sized samples<doi:10.20944/preprints202004.0529.v1>.
Last updated 5 years ago
4.30 score 4 stars 6 scripts 196 downloads
apisensr - Interface to 'episensr' for Sensitivity Analysis of Epidemiological Results
API for using 'episensr', Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. See <https://cran.r-project.org/package=episensr>.
Last updated 2 years ago
4.18 score 3 stars 5 scripts 332 downloadscovid19swiss - COVID-19 Cases in Switzerland and Principality of Liechtenstein
Provides a daily summary of the Coronavirus (COVID-19) cases in Switzerland cantons and Principality of Liechtenstein. Data source: Specialist Unit for Open Government Data Canton of Zurich <https://www.zh.ch/de/politik-staat/opendata.html>.
Last updated 4 years ago
4.00 score 8 scripts 214 downloadscovid19br - Brazilian COVID-19 Pandemic Data
Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Last updated 1 years ago
brazilcovid-19
3.90 score 4 stars 40 scripts 448 downloadstidyrates - Tidy Epidemiological Rates
Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, wrapping functions from the 'epitools' package.
Last updated 1 years ago
3.70 score 1 stars 166 downloads
epiCleanr - A Tidy Solution for Epidemiological Data
Offers a tidy solution for epidemiological data. It houses a range of functions for epidemiologists and public health data wizards for data management and cleaning.
Last updated 1 years ago
3.70 score 5 scripts 272 downloadsEpiILMCT - Continuous Time Distance-Based and Network-Based Individual Level Models for Epidemics
Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks. An overview of the implemented continuous-time individual level models for epidemics is given by Almutiry and Deardon (2019) <doi:10.1515/ijb-2017-0092>.
Last updated 5 years ago
bayesian-inferencedistanceepidemic-dataepidemicsinfectious-disease-modelskerneltypenetworkplotsfortran
3.65 score 6 stars 15 scripts 313 downloadstsiR - An Implementation of the TSIR Model
An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <https://doi:10.1371/0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <DOI: 10.1111/1467-9876.00187>.
Last updated 6 years ago
difference-equationsepidemic-modelepidemicsinfectious-diseasemodel-fittingsir-model
3.59 score 7 stars 28 scripts 272 downloadscovid19dbcand - Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format
Provides different datasets parsed from 'Drugbank' <https://www.drugbank.ca/covid-19> database using 'dbparser' package. It is a smaller version from 'dbdataset' package. It contains only information about COVID-19 possible treatment.
Last updated 12 months ago
datasetdbparserdrugbankdrugbank-database
3.48 score 3 stars 6 scripts 203 downloadsmemapp - The Moving Epidemic Method Web Application
The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week. 'memapp' is a web application created in the Shiny framework for the 'mem' R package.
Last updated 2 years ago
influenzamem
3.48 score 3 stars 2 scripts 438 downloadstrendeval - Evaluate Trending Models
Provides a coherent interface for evaluating models fit with the trending package. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 2 years ago
3.00 score 2 stars 7 scripts 180 downloadscolmozzie - Dengue Cases and Climate Variables in Colombo Sri Lanka
Weekly notified dengue cases and climate variables in Colombo district Sri Lanka from 2008/ week-52 to 2014/ week-21.
Last updated 6 years ago
3.00 score 2 stars 7 scripts 200 downloadsgenSEIR - Predict Epidemic Curves with Generalized SEIR Modeling
Performs generalized Susceptible-Exposed-Infected-Recovered (SEIR) modeling to predict epidemic curves. The method is described in Peng et al. (2020) <doi:10.1101/2020.02.16.20023465>.
Last updated 4 years ago
covid-19forecastnonlinear-optimizationseir-model
1.70 score 1 stars 197 downloadscorona - Coronavirus ('Rona') Data Exploration
Manipulate and view coronavirus data and other societally relevant data at a basic level.
Last updated 5 years ago
1.70 score 1 scripts 193 downloadscovid19france - Cases of COVID-19 in France
Imports and cleans 'opencovid19-fr' <https://github.com/opencovid19-fr/data> data on COVID-19 in France.
Last updated 5 years ago
1.70 score 4 scripts 198 downloadsepinet - Epidemic/Network-Related Tools
A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Last updated 1 years ago
1.30 score 20 scripts 381 downloadsargo - Accurate Estimation of Influenza Epidemics using Google Search Data
Augmented Regression with General Online data (ARGO) for accurate estimation of influenza epidemics in United States on national level, regional level and state level. It replicates the method introduced in paper Yang, S., Santillana, M. and Kou, S.C. (2015) <doi:10.1073/pnas.1515373112>; Ning, S., Yang, S. and Kou, S.C. (2019) <doi:10.1038/s41598-019-41559-6>; Yang, S., Ning, S. and Kou, S.C. (2021) <doi:10.1038/s41598-021-83084-5>.
Last updated 2 years ago
1.30 score 2 stars 7 scripts 360 downloadsendtoend - Transmissions and Receptions in an End to End Network
Computes the expectation of the number of transmissions and receptions considering an End-to-End transport model with limited number of retransmissions per packet. It provides theoretical results and also estimated values based on Monte Carlo simulations. It is also possible to consider random data and ACK probabilities.
Last updated 6 years ago
1.00 score 2 scripts 200 downloads