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epimdr (version 0.6-5)

Functions and Data for "Epidemics: Models and Data in R"

Description

Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) . 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 .

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Version

Install

install.packages('epimdr')

Monthly Downloads

298

Version

0.6-5

License

GPL-3

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Repository

https://github.com/objornstad/epimdr

Homepage

https://www.springer.com/gp/book/9783319974866

Maintainer

Ottar Bjornstad

Last Published

January 25th, 2020

Functions in epimdr (0.6-5)

Function to generate a Barabasi-Albert network

Gillespie exact algorithm

Burnett's Parasitoid-Host data.

Monthly incidence of influenza-like illness in Iceland between 1980 and 2009.

UK measles CCS data.

Function to generate a Watts-Strogats network

Black's measles seroprevalence data.

Daily measures of malaria infected mice.

Launch a shiny-app simulating the SEIRS model

Function to simulate the stochastic TSIR

Function to calculate the local Lyapunov exponents for the TSIR

Function to do Lyapunov exponent calculations from a TSIR simulation

Boarding school influenza data.

Defoliated by gypsy moth each in northeast US 1975-2002.

Launch a shiny-app simulating the SIR model

Function to simulate the seasonally-forced TSIR

De et al. 2004 gonorrhea contact matrix

The Nicholson-Bailey model

Function to simulate the chain-binomial model

Weekly whooping cough incidence from 1900-1937 in Copenhagen, Denmark.

Euthamia graminifolia rust data.

Rubella in Peru data.

Sierra-Leone Ebola 2015 data.

Launch a shiny-app simulating May's Parasitoid-host Model model

Gradient-function for Coyne et al's rabies model

Ferrari et al. 2005 outbreak data.

Gradient-function for the age-structured SIR model with possibly heterogeneous mixing

POLYMOD contact-rate data by Age.

Auxillary function used by llik.pc

Weekly incidence of scarlet fever in Philadelphia between 1914 and 1947.

Negative log-likelihood function for the chain-binomial model

Function to plot an object of class CM

Function to plot a netSIR object

Function to estimate parameters for the picewise-constant catalytic model

Weekly measles incidence from 2003-04 in Niamey, Niger.

Function to predict efficacy of outbreak-response vaccination campaign

Raccoon rabies data.

Launch a shiny-app simulating TSIR model

Function to simulate an epidemic on a network

Function to calculate R0 from a contact matrix

Measles incidence across 40 US cities

Gradient-function for the SIR model with outbreak-response vaccination

Function to calculate the degree distribution for an object of class CM

Bordetella bronchiseptica in rabbit kittens.

Weekly incidence of whooping cough in Philadelphia between 1925 and 1947.

Gradient-function for the SIR model

Weekly incidence of giardia in Pennsylvania between 2006 and 2014.

Weekly deaths from Influenza-like illness in Pennsylvania between 1972 and 1998.

Rabbit Bordetella brochiseptica data.

Launch a shiny-app simulating the seasonal SEIR model

Weekly incidence of Lymes disease in Pennsylvania between 2006 and 2014.

Gradient-function for the SIRWS model

Weekly incidence of measles in Pennsylvania between 1928 and 1969.

Gradient-function for the chain-SIR model

Dacca cholera death data.

Filipendula rust data.

FIV infection in cats.

Gradient-function for the forced SEIR model

Antler smut on wild campion.

Massachusetts gonorrhea data.

Weekly incidence of measles in Philadelphia between 1914 and 1947.

Weekly incidence of diphtheria in Philadelphia between 1914 and 1947.

US 1975/76 ILI data.

Bi-weekly measles incidence in London from 1944-65.

Gradient-function for the SEIR model

Gillespie tau-leap algorithm

Launch a shiny-app to study outbreak-response vaccination campaigns

Function to summarize a netSIR object

Function to generate a ring lattice

Day of appearance of each measles case from 2003-04 outbreak in Niamey, Niger.