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 12 days ago

12.32 score 176 stars 28 dependents 1.9k scripts 10k downloads

mstate - 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 4 days ago

12.13 score 11 stars 55 dependents 322 scripts 7.7k downloads

EpiEstim - 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 6 months ago

12.08 score 95 stars 7 dependents 1.1k scripts 1.4k downloads

incidence - 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 7 months ago

outbreak

12.05 score 58 stars 12 dependents 504 scripts 1.8k 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 19 hours ago

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp

11.88 score 120 stars 210 scripts 1.2k downloads

AMR - 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

11.87 score 92 stars 6 dependents 171 scripts 2.3k downloads

pomp - 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 12 days ago

abcb-splinedifferential-equationsdynamical-systemsiterated-filteringlikelihoodlikelihood-freemarkov-chain-monte-carlomarkov-modelmathematical-modellingmeasurement-errorparticle-filtersequential-monte-carlosimulation-based-inferencesobol-sequencestate-spacestatistical-inferencestochastic-processestime-seriesopenblas

11.69 score 114 stars 4 dependents 1.3k scripts 2.5k downloads

EpiModel - 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 23 days ago

agent-based-modelingepidemicsepidemiologyinfectious-diseasesnetwork-graphcpp

11.42 score 249 stars 315 scripts 971 downloads

COVID19 - COVID-19 Data Hub

Unified datasets for a better understanding of COVID-19.

Last updated 3 days ago

2019-ncovcoronaviruscovid-19covid-datacovid19-data

11.08 score 252 stars 265 scripts 752 downloads

SimInf - 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 22 days ago

data-drivenepidemiologyhigh-performance-computingmarkov-chainmathematical-modellinggslopenmp

10.09 score 35 stars 224 scripts 516 downloads

socialmixr - 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 3 months ago

9.94 score 38 stars 1 dependents 230 scripts 590 downloads

odin - ODE Generation and Integration

Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.

Last updated 8 months ago

infrastructure

9.74 score 106 stars 2 dependents 290 scripts 881 downloads

Epi - 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 1 months ago

9.58 score 4 stars 11 dependents 708 scripts 8.2k downloads

nhanesA - 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 1 months ago

nhanes

9.34 score 57 stars 239 scripts 2.0k downloads

cholera - 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

9.33 score 136 stars 95 scripts 471 downloads

surveillance - Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

Last updated 4 months ago

cpp

9.25 score 11 stars 3 dependents 440 scripts 1.6k downloads

malariaAtlas - 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 7 months ago

databasemalariaopendataraster

9.10 score 44 stars 3 dependents 118 scripts 668 downloads

epicontacts - 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 1 months ago

outbreak

8.86 score 15 stars 2 dependents 112 scripts 704 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 23 days ago

data-accessdata-packageepidemiologyepiverseprobability-distribution

8.85 score 33 stars 1 dependents 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

8.80 score 8 stars 2 dependents 61 scripts 662 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 7 months ago

8.65 score 59 stars 210 scripts 795 downloads

epiworldR - 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 8 hours ago

abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelcppopenmp

8.27 score 9 stars 1 dependents 58 scripts 547 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

outbreaker2 - 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 5 months ago

cpp

8.16 score 31 stars 1 dependents 100 scripts 317 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 14 days ago

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

8.15 score 13 stars 35 scripts 273 downloads

epiR - Tools for the Analysis of Epidemiological Data

Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

Last updated 21 days ago

7.90 score 10 dependents 672 scripts 9.9k 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

7.83 score 16 stars 224 downloads

epidatr - Client for Delphi's 'Epidata' API

The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.

Last updated 3 months ago

7.79 score 5 stars 114 scripts 268 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 14 days ago

colombiaepidemiological-surveillanceepiversepublic-health

7.75 score 43 stars 251 downloads

cmprsk - 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 9 months ago

fortran

7.72 score 3 stars 63 dependents 608 scripts 15k downloads

popEpi - 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 20 days ago

adjust-estimatesage-adjustingdirect-adjustingepidemiologyindirect-adjustingsurvival

7.68 score 8 stars 1 dependents 118 scripts 1.0k downloads

incidence2 - 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 3 months ago

7.57 score 17 stars 1 dependents 103 scripts 833 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 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

nosoi - A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

Last updated 1 months ago

7.20 score 7 stars 30 scripts 378 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 213 downloads

epikit - 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 15 days ago

6.30 score 10 stars 2 dependents 22 scripts 925 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.

Last updated 16 days ago

data-packageepidemiologyepiverse

5.92 score 2 stars 2 dependents 251 downloads

epigrowthfit - Nonlinear Mixed Effects Models of Epidemic Growth

Maximum likelihood estimation of nonlinear mixed effects models of epidemic growth using Template Model Builder ('TMB'). Enables joint estimation for collections of disease incidence time series, including time series that describe multiple epidemic waves. Supports a set of widely used phenomenological models: exponential, logistic, Richards (generalized logistic), subexponential, and Gompertz. Provides methods for interrogating model objects and several auxiliary functions, including one for computing basic reproduction numbers from fitted values of the initial exponential growth rate. Preliminary versions of this software were applied in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.

Last updated 3 days ago

cppopenmp

5.78 score 9 stars 45 scripts 145 downloads

EpiContactTrace - Epidemiological Tool for Contact Tracing

Routines for epidemiological contact tracing and visualisation of network of contacts.

Last updated 4 months ago

cpp

5.74 score 11 stars 42 scripts 523 downloads

dde - 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 5 months ago

5.72 score 15 stars 35 scripts 321 downloads

contactdata - 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 3 months ago

demographicsepidemiologysocial-sciences

5.65 score 9 stars 11 scripts 370 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 30 days ago

deathshealth-datainfectious-diseaseslifeexpectancy

5.48 score 4 stars 572 downloads

epidm - 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 6 months ago

5.14 score 13 stars 273 downloads

denguedatahub - A Tidy Format Datasets of Dengue by Country

Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.

Last updated 7 days ago

openjdk

5.12 score 11 stars 34 scripts 234 downloads

o2geosocial - 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 8 months ago

baysian-inferencemarkov-chain-monte-carlotransmission-chain-reconstructioncpp

4.90 score 8 stars 5 scripts 315 downloads

diyar - Record Linkage and Epidemiological Case Definitions in 'R'

An R package for iterative and batched record linkage, and applying epidemiological case definitions. 'diyar' can be used for deterministic and probabilistic record linkage, or multistage record linkage combining both approaches. It features the implementation of nested match criteria, and mechanisms to address missing data and conflicting matches during stepwise record linkage. Case definitions are implemented by assigning records to groups based on match criteria such as person or place, and overlapping time or duration of events e.g. sample collection dates or periods of hospital stays. Matching records are assigned a unique group ID. Index and duplicate records are removed or further analyses as required.

Last updated 2 months ago

4.77 score 6 stars 33 scripts 359 downloads

epiworldRShiny - 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 8 hours ago

abmagent-based-modelingcovid-19epidemic-simulationsepidemiologynetscinetwork-analysisshinyappsshinydashboardsimulation-modeling

4.23 score 4 scripts 607 downloads

covid19dbcand - 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 11 months ago

datasetdbparserdrugbankdrugbank-database

3.48 score 3 stars 6 scripts 191 downloads

authoritative - Parse and Deduplicate Author Names

Utilities to parse authors fields from DESCRIPTION files and general purpose functions to deduplicate names in database, beyond the specific case of R package authors.

Last updated 16 days ago

3.00 score

excessmort - 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 7 months ago

4.30 score 20 stars 599 downloads

deSolve - 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

12.01 score 11 stars 422 dependents 8.0k scripts 46k downloads

epitrix - 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 downloads

TransPhylo - 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 1 years ago

cpp

8.43 score 61 stars 74 scripts 215 downloads

coronavirus - 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 495 downloads

coarseDataTools - 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

8.01 score 9 stars 8 dependents 34 scripts 1.1k downloads

etm - 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

7.97 score 13 dependents 110 scripts 4.4k downloads

epitools - Epidemiology Tools

Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.

Last updated 5 years ago

6.73 score 2 stars 12 dependents 768 scripts 9.7k downloads

SpatialEpi - 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 827 downloads

earlyR - 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 207 downloads

inctools - 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 288 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 11 months ago

biasepidemiologysensitivity-analysisstatistics

6.45 score 12 stars 1 dependents 39 scripts 542 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 537 downloads

mem - 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 428 downloads

epiflows - 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 1 years ago

outbreak

6.16 score 18 stars 20 scripts 285 downloads

covid19italy - 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 193 downloads

epiphy - Analysis of Plant Disease Epidemics

A toolbox to make it easy to analyze plant disease epidemics. It provides a common framework for plant disease intensity data recorded over time and/or space. Implemented statistical methods are currently mainly focused on spatial pattern analysis (e.g., aggregation indices, Taylor and binary power laws, distribution fitting, SADIE and 'mapcomp' methods). See Laurence V. Madden, Gareth Hughes, Franck van den Bosch (2007) <doi:10.1094/9780890545058> for further information on these methods. Several data sets that were mainly published in plant disease epidemiology literature are also included in this package.

Last updated 1 years ago

cpp

6.05 score 15 stars 37 scripts 236 downloads

epitweetr - 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 345 downloads

R0 - Estimation of R0 and Real-Time Reproduction Number from Epidemics

Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.

Last updated 1 years ago

5.87 score 4 stars 184 scripts 501 downloads

outbreaks - 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

5.65 score 51 stars 290 scripts 898 downloads

trending - 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 255 downloads

covid19.analytics - Load and Analyze Live Data from the COVID-19 Pandemic

Load and analyze updated time series worldwide data of reported cases for the Novel Coronavirus Disease (COVID-19) from different sources, including the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) data repository <https://github.com/CSSEGISandData/COVID-19>, "Our World in Data" <https://github.com/owid/> among several others. The datasets reporting the COVID-19 cases are available in two main modalities, as a time series sequences and aggregated data for the last day with greater spatial resolution. Several analysis, visualization and modelling functions are available in the package that will allow the user to compute and visualize total number of cases, total number of changes and growth rate globally or for an specific geographical location, while at the same time generating models using these trends; generate interactive visualizations and generate Susceptible-Infected-Recovered (SIR) model for the disease spread.

Last updated 3 years ago

covid19covid19-datancov2019sars-cov-2

5.52 score 33 stars 20 scripts 350 downloads

EpiSignalDetection - Signal Detection Analysis

Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. The package includes: - Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see 'Population' variable). This project was funded by the European Centre for Disease Prevention and Control.

Last updated 6 years ago

5.43 score 16 stars 17 scripts 237 downloads

epiDisplay - 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

5.39 score 1 stars 2 dependents 760 scripts 5.4k downloads

covid19us - 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 320 downloads

covid19sf - 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 193 downloads

riskCommunicator - G-Computation to Estimate Interpretable Epidemiological Effects

Estimates flexible epidemiological effect measures including both differences and ratios using the parametric G-formula developed as an alternative to inverse probability weighting. It is useful for estimating the impact of interventions in the presence of treatment-confounder-feedback. G-computation was originally described by Robbins (1986) <doi:10.1016/0270-0255(86)90088-6> and has been described in detail by Ahern, Hubbard, and Galea (2009) <doi:10.1093/aje/kwp015>; Snowden, Rose, and Mortimer (2011) <doi:10.1093/aje/kwq472>; and Westreich et al. (2012) <doi:10.1002/sim.5316>.

Last updated 2 years ago

4.88 score 4 stars 19 scripts 431 downloads

EpiReport - Epidemiological Report

Drafting an epidemiological report in 'Microsoft Word' format for a given disease, similar to the Annual Epidemiological Reports published by the European Centre for Disease Prevention and Control. Through standalone functions, it is specifically designed to generate each disease specific output presented in these reports and includes: - Table with the distribution of cases by Member State over the last five years; - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, by month, over the past five years; - Trend plot with the trend and number of cases at the European Union / European Economic Area level, by month, over the past five years; - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level. Two types of datasets can be used: - The default dataset of dengue 2015-2019 data; - Any dataset specified as described in the vignette.

Last updated 4 years ago

4.84 score 11 stars 14 scripts 304 downloads

EpiILM - 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 4 years ago

fortran

4.80 score 6 stars 21 scripts 253 downloads

nbTransmission - Naive Bayes Transmission Analysis

Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.

Last updated 1 years ago

4.45 score 4 stars 14 scripts 267 downloads

bets.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 downloads

epitab - 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 233 downloads

EpiCurve - 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 375 downloads

CovidMutations - 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 4 years ago

4.30 score 4 stars 6 scripts 181 downloads

shinySIR - Interactive Plotting for Mathematical Models of Infectious Disease Spread

Provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ordinary differential equation (ODE) models (such as the SIR, SIRS, and SIS models), or create their own. This latter flexibility allows 'shinySIR' to be applied to simple ODEs from any discipline. The package is a useful teaching tool as students can visualize how changing different parameters can impact model dynamics, with minimal knowledge of coding in R. The built-in models are inspired by those featured in Keeling and Rohani (2008) <doi:10.2307/j.ctvcm4gk0> and Bjornstad (2018) <doi:10.1007/978-3-319-97487-3>.

Last updated 9 months ago

4.10 score 14 stars 18 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 1 years ago

4.00 score 2 stars 5 scripts 273 downloads

covid19swiss - 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 212 downloads

RSurveillance - Design and Analysis of Disease Surveillance Activities

A range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (<https://www.fp7-risksur.eu/sites/default/files/documents/Deliverables/RISKSUR_%28310806%29_D6.24.pdf>). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: <http://epitools.ausvet.com.au>.

Last updated 5 years ago

3.98 score 64 scripts 225 downloads

epimdr2 - Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"

Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (ISBN: 978-3-031-12055-8) <https://link.springer.com/book/9783031120558>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the Coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.

Last updated 2 years ago

3.98 score 19 stars 675 downloads

EpiForsk - Code Sharing at the Department of Epidemiological Research at Statens Serum Institut

This is a collection of assorted functions and examples collected from various projects. Currently we have functionalities for simplifying overlapping time intervals, Charlson comorbidity score constructors for Danish data, getting frequency for multiple variables, getting standardized output from logistic and log-linear regressions, sibling design linear regression functionalities a method for calculating the confidence intervals for functions of parameters from a GLM, Bayes equivalent for hypothesis testing with asymptotic Bayes factor, and several help functions for generalized random forest analysis using 'grf'.

Last updated 12 months ago

epidemiology

3.95 score 139 downloads

covid19br - 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 394 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 299 downloads

EpiILMCT - 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 256 downloads

tsiR - 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 5 years ago

difference-equationsepidemic-modelepidemicsinfectious-diseasemodel-fittingsir-model

3.59 score 7 stars 28 scripts 263 downloads

memapp - 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 533 downloads

powerSurvEpi - Power and Sample Size Calculation for Survival Analysis of Epidemiological Studies

Functions to calculate power and sample size for testing main effect or interaction effect in the survival analysis of epidemiological studies (non-randomized studies), taking into account the correlation between the covariate of the interest and other covariates. Some calculations also take into account the competing risks and stratified analysis. This package also includes a set of functions to calculate power and sample size for testing main effect in the survival analysis of randomized clinical trials and conditional logistic regression for nested case-control study.

Last updated 4 years ago

3.36 score 1 dependents 77 scripts 888 downloads

trendeval - 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 177 downloads

colmozzie - 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 155 downloads

EpiStats - Tools for Epidemiologists

Provides set of functions aimed at epidemiologists. The package includes commands for measures of association and impact for case control studies and cohort studies. It may be particularly useful for outbreak investigations including univariable analysis and stratified analysis. The functions for cohort studies include the CS(), CSTable() and CSInter() commands. The functions for case control studies include the CC(), CCTable() and CCInter() commands. References - Cornfield, J. 1956. A statistical problem arising from retrospective studies. In Vol. 4 of Proceedings of the Third Berkeley Symposium, ed. J. Neyman, 135-148. Berkeley, CA - University of California Press. Woolf, B. 1955. On estimating the relation between blood group disease. Annals of Human Genetics 19 251-253. Reprinted in Evolution of Epidemiologic Ideas Annotated Readings on Concepts and Methods, ed. S. Greenland, pp. 108-110. Newton Lower Falls, MA Epidemiology Resources. Gilles Desve & Peter Makary, 2007. 'CSTABLE Stata module to calculate summary table for cohort study' Statistical Software Components S456879, Boston College Department of Economics. Gilles Desve & Peter Makary, 2007. 'CCTABLE Stata module to calculate summary table for case-control study' Statistical Software Components S456878, Boston College Department of Economics.

Last updated 1 years ago

2.91 score 82 scripts 470 downloads

epibasix - Elementary Epidemiological Functions for Epidemiology and Biostatistics

Contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity). Appropriate print and summary statements are also written to facilitate interpretation wherever possible. Source code is commented throughout to facilitate modification. The target audience includes advanced undergraduate and graduate students in epidemiology or biostatistics courses, and clinical researchers.

Last updated 6 years ago

2.04 score 22 scripts 344 downloads

corona - Coronavirus ('Rona') Data Exploration

Manipulate and view coronavirus data and other societally relevant data at a basic level.

Last updated 4 years ago

1.70 score 1 scripts 177 downloads

covid19france - 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 171 downloads

epinet - 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 306 downloads

argo - 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 306 downloads

modelSSE - Modelling Infectious Disease Superspreading from Contact Tracing Data

Comprehensive analytical tools are provided to characterize infectious disease superspreading from contact tracing surveillance data. The underlying theoretical frameworks of this toolkit include branching process with transmission heterogeneity (Lloyd-Smith et al. (2005) <doi:10.1038/nature04153>), case cluster size distribution (Nishiura et al. (2012) <doi:10.1016/j.jtbi.2011.10.039>, Blumberg et al. (2014) <doi:10.1371/journal.ppat.1004452>, and Kucharski and Althaus (2015) <doi:10.2807/1560-7917.ES2015.20.25.21167>), and decomposition of reproduction number (Zhao et al. (2022) <doi:10.1371/journal.pcbi.1010281>).

Last updated 1 years ago

1.00 score 214 downloads

epicasting - Ewnet: An Ensemble Wavelet Neural Network for Forecasting and Epicasting

Method and tool for generating time series forecasts using an ensemble wavelet-based auto-regressive neural network architecture. This method provides additional support of exogenous variables and also generates confidence interval. This package provides EWNet model for time series forecasting based on the algorithm by Panja, et al. (2022) and Panja, et al. (2023) <arXiv:2206.10696> <doi:10.1016/j.chaos.2023.113124>.

Last updated 2 years ago

1.00 score 263 downloads

endtoend - 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 197 downloads