Provides an assortment of statistical methods. Surveillance is a R package which authorizes to model and monitor time series of counts and continuous-time point processes of epidemic phenomena, and offers a multitude of methods for visualization, likelihood inference and simulation of endemic-epidemic models. The package also includes features to perform the regression-oriented modeling of spatiotemporal epidemic data.
Offers a method for evaluate time-varying instantaneous reproduction numbers from incidence time series. EpiEstim is a R package that relies on knowledge of the serial interval distribution but is able to directly incorporate uncertainty in serial interval distribution estimates. It can also detect changes in the reproduction number. Additionally, the package implements the Wallinga and Teunis method to facilitate comparison.
Assists in modelling the world-wide spread of epidemics for human transmissible diseases. GLEaMviz offers extensive flexibility in the design of the compartmental model and scenario setup. It offers three types of visualization highlighting: (i) the spread of the infection on a zoomable 2D map, (ii) the spread of the infection on an interactive 3D globe, and (iii) the structure of the airport network that influences the notion of distance.
Feigns numerous models of contact networks, viral transmission, phylogenetic and sequence evolution, data (sub)sampling, and real-world data perturbations. FAVITES is able to find people with increased risk of onward transmission. It can assist public health officials to optimize spending their limited budgets for targeted prevention or treatment. This tool allows to mimic conditions similar to epidemic and pick the best method/threshold tailored to a situation.
Allows estimation of a climate-driven mosquito-borne viral suitability index. MVSE is a program able to determine a suitability index based on a climate-driven mathematical expression for the basic reproductive number of a well established mathematical model for the transmission dynamics of mosquito-borne viruses. For instance, this tool can be used for studying a mosquito-borne viral suitability index.
Implements an illustrative epidemic model including host demography and risk structure. This approach consists of stochastic susceptible, infected and recovered (SIR) network model, where infection spreads across a network of nodes that are clustered into three distinct regions. This model demonstrates the management improvements that can be achieved by combining optimal control theory (OCT) with both open-loop and model predictive control (MPC).
Assists in simulating mathematical models of infectious disease. Kendrick was developed to simplify the creation of epidemiological models through a unified Domain-Specific Language for epidemiology that can support a variety of modelling and simulation approaches used in the field. This method can capture both deterministic models expressed as a set of ordinary differential equations (ODEs) and demographic-stochastic models.
Simulates the epidemiology of various diseases and the social processes that drives diseases in South Africa. MicroCOSM includes features for understanding socio-economic and racial inequality in health outcomes in South Africa. It can serve for assessing the potential impact of strategies to reduce these inequalities. Moreover, it is able to simulate HIV testing in different conditions such as in prison.
Offers a R package for procuring a way to construct, solve, and view mathematical models related with infectious disease. EpiModel permits users to simulate epidemic models for both pedagogical and research purposes. It proposes three classes of epidemic models (deterministic compartmental models, stochastic individual contact models, stochastic network models) and three infectious disease types (susceptible-infectious, susceptible-infectious-recovered, and susceptible-infectious-susceptible) which can be extended.
Assists users in the creation and use of spatial and temporal models for emerging infectious diseases. STEM is an application that includes models to aid in understanding and potentially preventing the spread of such diseases. This method also facilitates the development of advanced mathematical models, the creation of flexible models involving multiple populations (species) and interactions between diseases, and the understanding of epidemiology.
Provides flexible model fitting for epidemiological data analysis models. Epifit intends to fit variety models such as Cox regression or linear models as well as some models which expressed likelihood across negative binomial, gamma and Weibull distributions. The software also contains some functionalities of data handling including the possibility to create a person-years table from event, time and covariate data.
Compiles a combination of epidemic/network-related tools. Epinet is a R package that can generate contact networks to simulate the transmission of diseases. It includes features to perform bayesian inference on network and epidemic parameters. Moreover, the package allows users to convert the obtained transmission tree in Newick format or to generate posterior samples of an object.
Assists users in large epidemic spread simulations. epiDMS is an epidemic simulation data management system software. It includes (i) the storage and indexing of large-ensemble simulation data sets and the corresponding models and (ii) the search and analysis of ensemble simulation data sets to enable ensemble-based decision support. This application also provides parameterized queries and other interactive user interfaces to enable decision-makers with minimal experience to explore large-ensemble simulations.
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