Package: epimdr 0.6-5

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

Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/book/9783319974866>. 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>.

Authors:Ottar N. Bjornstad [aut, cre]

epimdr_0.6-5.tar.gz
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epimdr_0.6-5.tgz(r-4.4-any)epimdr_0.6-5.tgz(r-4.3-any)
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epimdr.pdf |epimdr.html✨
epimdr/json (API)

# Install 'epimdr' in R:
install.packages('epimdr', repos = c('https://objornstad.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/objornstad/epimdr/issues

Datasets:
  • Icelandflu - Monthly incidence of influenza-like illness in Iceland between 1980 and 2009.
  • SH9 - Daily measures of malaria infected mice.
  • black - Black's measles seroprevalence data.
  • burnett - Burnett's Parasitoid-Host data.
  • ccs - UK measles CCS data.
  • cholera - Dacca cholera death data.
  • dalziel - Measles incidence across 40 US cities
  • ebola - Sierra-Leone Ebola 2015 data.
  • ferrari - Ferrari et al. 2005 outbreak data.
  • filipendula - Filipendula rust data.
  • fiv - FIV infection in cats.
  • flu - Boarding school influenza data.
  • gm - Defoliated by gypsy moth each in northeast US 1975-2002.
  • gonnet - De et al. 2004 gonorrhea contact matrix
  • gra - Euthamia graminifolia rust data.
  • litter - Bordetella bronchiseptica in rabbit kittens.
  • magono - Massachusetts gonorrhea data.
  • meas - Bi-weekly measles incidence in London from 1944-65.
  • mossong - POLYMOD contact-rate data by Age.
  • niamey - Weekly measles incidence from 2003-04 in Niamey, Niger.
  • niamey_daily - Day of appearance of each measles case from 2003-04 outbreak in Niamey, Niger.
  • pagiard - Weekly incidence of giardia in Pennsylvania between 2006 and 2014.
  • paili - Weekly deaths from Influenza-like illness in Pennsylvania between 1972 and 1998.
  • palymes - Weekly incidence of Lymes disease in Pennsylvania between 2006 and 2014.
  • pameasle - Weekly incidence of measles in Pennsylvania between 1928 and 1969.
  • pertcop - Weekly whooping cough incidence from 1900-1937 in Copenhagen, Denmark.
  • peru - Rubella in Peru data.
  • rabbit - Rabbit _Bordetella brochiseptica_ data.
  • rabies - Raccoon rabies data.
  • silene2 - Antler smut on wild campion.
  • tydiphtheria - Weekly incidence of diphtheria in Philadelphia between 1914 and 1947.
  • tymeasles - Weekly incidence of measles in Philadelphia between 1914 and 1947.
  • tyscarlet - Weekly incidence of scarlet fever in Philadelphia between 1914 and 1947.
  • tywhooping - Weekly incidence of whooping cough in Philadelphia between 1925 and 1947.
  • usflu - US 1975/76 ILI data.

On CRAN:

1.64 score 44 scripts 249 downloads 32 exports 32 dependencies

Last updated 5 years agofrom:1c01406a95. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:BarabasiAlbertchainSIRcoyneflowFieldgillespieintegrandpcllik.cbllik.pcMay.appNBNetworkSIRorv.appr0funretrospecringlatticeSEIR.appseirmodseirmod2SEIRS.appsim.cbSimTsirSimTsir2SIR.appsiragemodsirmodsirwmodsivmodtauTSIR.appTSIRllyapTSIRlyapWattsStrogatz

Dependencies:base64encbslibcachemclicommonmarkcrayondeSolvedigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclemagrittrmemoisemimepolsplinepromisesR6rappdirsRcpprlangsassshinysourcetoolswithrxtable

Readme and manuals

Help Manual

Help pageTopics
Function to generate a Barabasi-Albert networkBarabasiAlbert
Black's measles seroprevalence data.black
Burnett's Parasitoid-Host data.burnett
UK measles CCS data.ccs
Gradient-function for the chain-SIR modelchainSIR
Dacca cholera death data.cholera
Gradient-function for Coyne et al's rabies modelcoyne
Measles incidence across 40 US citiesdalziel
Sierra-Leone Ebola 2015 data.ebola
Ferrari et al. 2005 outbreak data.ferrari
Filipendula rust data.filipendula
FIV infection in cats.fiv
FlowfieldflowField
Boarding school influenza data.flu
Gillespie exact algorithmgillespie
Defoliated by gypsy moth each in northeast US 1975-2002.gm
De et al. 2004 gonorrhea contact matrixgonnet
Euthamia graminifolia rust data.gra
Monthly incidence of influenza-like illness in Iceland between 1980 and 2009.Icelandflu
Auxillary function used by llik.pcintegrandpc
Bordetella bronchiseptica in rabbit kittens.litter
Negative log-likelihood function for the chain-binomial modelllik.cb
Function to estimate parameters for the picewise-constant catalytic modelllik.pc
Massachusetts gonorrhea data.magono
Launch a shiny-app simulating May's Parasitoid-host Model modelMay.app
Bi-weekly measles incidence in London from 1944-65.meas
POLYMOD contact-rate data by Age.mossong
The Nicholson-Bailey modelNB
Function to simulate an epidemic on a networknetSIR NetworkSIR
Weekly measles incidence from 2003-04 in Niamey, Niger.niamey
Day of appearance of each measles case from 2003-04 outbreak in Niamey, Niger.niamey_daily
Launch a shiny-app to study outbreak-response vaccination campaignsorv.app
Weekly incidence of giardia in Pennsylvania between 2006 and 2014.pagiard
Weekly deaths from Influenza-like illness in Pennsylvania between 1972 and 1998.paili
Weekly incidence of Lymes disease in Pennsylvania between 2006 and 2014.palymes
Weekly incidence of measles in Pennsylvania between 1928 and 1969.pameasle
Weekly whooping cough incidence from 1900-1937 in Copenhagen, Denmark.pertcop
Rubella in Peru data.peru
Function to plot an object of class CMplot.cm
Function to plot a netSIR objectplot.netSIR
Function to calculate R0 from a contact matrixr0fun
Rabbit _Bordetella brochiseptica_ data.rabbit
Raccoon rabies data.rabies
Function to predict efficacy of outbreak-response vaccination campaignretrospec
Function to generate a ring latticeringlattice
Launch a shiny-app simulating the seasonal SEIR modelSEIR.app
Gradient-function for the SEIR modelseirmod
Gradient-function for the forced SEIR modelseirmod2
Launch a shiny-app simulating the SEIRS modelSEIRS.app
Daily measures of malaria infected mice.SH9
Antler smut on wild campion.silene2
Function to simulate the chain-binomial modelsim.cb
Function to simulate the stochastic TSIRSimTsir
Function to simulate the seasonally-forced TSIRSimTsir2
Launch a shiny-app simulating the SIR modelSIR.app
Gradient-function for the age-structured SIR model with possibly heterogeneous mixingsiragemod
Gradient-function for the SIR modelsirmod
Gradient-function for the SIRWS modelsirwmod
Gradient-function for the SIR model with outbreak-response vaccinationsivmod
Function to calculate the degree distribution for an object of class CMsummary.cm
Function to summarize a netSIR objectsummary.netSIR
Gillespie tau-leap algorithmtau
Launch a shiny-app simulating TSIR modelTSIR.app
Function to calculate the local Lyapunov exponents for the TSIRTSIRllyap
Function to do Lyapunov exponent calculations from a TSIR simulationTSIRlyap
Weekly incidence of diphtheria in Philadelphia between 1914 and 1947.tydiphtheria
Weekly incidence of measles in Philadelphia between 1914 and 1947.tymeasles
Weekly incidence of scarlet fever in Philadelphia between 1914 and 1947.tyscarlet
Weekly incidence of whooping cough in Philadelphia between 1925 and 1947.tywhooping
US 1975/76 ILI data.usflu
Function to generate a Watts-Strogats networkWattsStrogatz