EpiModel: Mathematical Modeling of Infectious Disease

Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic agent-based 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 easy API for extending these templates to address novel scientific research aims.

Author
Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Emily Beylerian [ctb], Skye Bender-deMoll [ctb], Kevis Weiss [ctb]
Date of publication
2016-07-30 00:34:06
Maintainer
Samuel Jenness <samuel.m.jenness@emory.edu>
License
GPL-3
Version
1.2.7
URLs

View on CRAN

Man pages

as.data.frame.dcm
Extract Model Data for Deterministic Compartmental Models
as.data.frame.icm
Extract Model Data for Stochastic Models
as.network.transmat
Converts transmat infection tree into a network object
as.phylo.transmat
Convert transmat infection tree into a phylo object
bipvals
Vertex Attributes for Bipartite Network
births.icm
Births: icm Module
births.net
Births: netsim Module
brewer_ramp
RColorBrewer Color Ramp for EpiModel Plots
calc_eql
Calculate Equilibrium for Infection Prevalence
check_bip_degdist
Check Degree Distribution for Bipartite Target Statistics
color_tea
Creates a TEA Variable for Infection Status for 'ndtv'...
comp_plot
Plot Compartment Diagram for Epidemic Models
control.dcm
Control Settings for Deterministic Compartmental Models
control.icm
Control Settings for Stochastic Individual Contact Models
control.net
Control Settings for Stochastic Network Models
copy_toall_attr
Copies Vertex Attributes in Formation Formula to attr List
crosscheck.dcm
Cross Checking of Inputs for Deterministic Compartmental...
crosscheck.icm
Cross Checking of Inputs for Stochastic Individual Contact...
crosscheck.net
Cross Checking of Inputs for Stochastic Network Models
dcm
Deterministic Compartmental Models
dcm.mods
Deterministic Compartmental Model Functions
deaths.icm
Deaths: icm Module
deaths.net
Deaths: netsim Module
deleteAttr
Delete Elements from Attribute List
discord_edgelist
Discordant Edgelist from NetworkDynamic Object
dissolution_coefs
Dissolution Coefficients for Stochastic Network Models
edgelist_censor
Table of Edge Censoring
edgelist_meanage
Mean Age of Partnerships over Time
edges_correct
Adjustment for the Edges Coefficient with Changing Network...
EpiModel-package
Mathematical Modeling of Infectious Disease
epiweb
EpiModel Web
get_attr_prop
Proportional Table of Vertex Attributes
get_degree
Get Individual Degree from Network or Edgelist
get_formula_terms
Outputs Formula Terms into a Character Vector
get_network
Extract networkDynamic Object from Network Epidemic Model
get_nwparam
Extract Network Model Parameters
get_nwstats
Extract Network Statistics from Network Epidemic Model
get_prev.icm
Get Epidemic Output from icm Model
get_prev.net
Get Epidemic Output from netsim Model
get_sims
Extract Network Simulations
get_transmat
Extract Transmissions Matrix from Network Epidemic Model
icm
Stochastic Individual Contact Models
idmode
Mode Numbers for Bipartite Network
infection.icm
Primary Infection Module for icm
infection.net
Primary Infection Module for netsim
init.dcm
Initial Conditions for Deterministic Compartmental Models
initialize.icm
Initialization: icm Module
initialize.net
Initialization: netsim Module
init.icm
Initial Conditions for Stochastic Individual Contact Models
init.net
Initial Conditions for Stochastic Network Models
init_pids
Persistent ID Initialization
init_status.icm
Disease Status Initialization Module for icm
init_status.net
Disease Status Initialization Module for netsim
mcat
Write Out Test Progress to Console
merge.icm
Merge Data across Stochastic Individual Contact Model...
merge.netsim
Merge Model Simulations Across netsim Objects
modeids
ID Numbers for Bipartite Network
modules.icm
Modules for Stochastic Individual Contact Models
modules.net
Modules for Stochastic Network Models
mutate_epi
Add New Epidemiology Variables
netdx
Dynamic Network Model Diagnostics
netest
Dynamic Network Model Estimation
netsim
Stochastic Network Models
param.dcm
Epidemic Parameters for Deterministic Compartmental Models
param.icm
Epidemic Parameters for Stochastic Individual Contact Models
param.net
Epidemic Parameters for Stochastic Network Models
plot.dcm
Plot Data from a Deterministic Compartmental Epidemic Model
plot.icm
Plot Data from a Stochastic Individual Contact Epidemic Model
plot.netdx
Plot Dynamic Network Model Diagnostics
plot.netsim
Plot Data from a Stochastic Network Epidemic Model
plot.transmat
Plot transmat infection tree in one of several styles
recovery.icm
Recovery: icm Module
recovery.net
Recovery: netsim Module
resim_nets
Resimulate Dynamic Network at Time 2+
saveout.dcm
Save dcm Data to Output List Format
saveout.icm
Save icm Data to Output List Format
saveout.net
Save netsim Data to Output List Format
sim_nets
Simulate Dynamic Network at Time 1
split_bip
Update Attribute Values for a Bipartite Network
ssample
Stable Sampling Function
summary.dcm
Summary Model Statistics
summary.icm
Summary Model Statistics
summary.netest
Summary for Network Model Fit
summary.netsim
Summary Model Statistics
test_icm
Test the Model Output from a Stochastic Individual Contact...
test_net
Test the Model Output from a Network Model
transco
Obtain Transparent Colors
update_dissolution
Adjust Dissolution Component of Network Model Fit
update_nwattr
Updates Vertex Attributes for Incoming Vertices
verbose.dcm
Progress Print Module for Deterministic Compartmental Models
verbose.icm
Progress Print Module for Stochastic Individual Contact...
verbose.net
Progress Print Module for Stochastic Network Models

Files in this package

EpiModel
EpiModel/inst
EpiModel/inst/shiny
EpiModel/inst/shiny/epidcm
EpiModel/inst/shiny/epidcm/ui.R
EpiModel/inst/shiny/epidcm/server.R
EpiModel/inst/shiny/epiicm
EpiModel/inst/shiny/epiicm/ui.R
EpiModel/inst/shiny/epiicm/server.R
EpiModel/inst/shiny/epinet
EpiModel/inst/shiny/epinet/ui.R
EpiModel/inst/shiny/epinet/server.R
EpiModel/inst/shiny/epinet/www
EpiModel/inst/shiny/epinet/www/style.css
EpiModel/inst/doc
EpiModel/inst/doc/Intro.R
EpiModel/inst/doc/Intro.Rmd
EpiModel/inst/doc/Intro.html
EpiModel/tests
EpiModel/tests/testthat
EpiModel/tests/testthat/test-utils.R
EpiModel/tests/testthat/test-shiny.R
EpiModel/tests/testthat/test-newicm.R
EpiModel/tests/testthat/test-icm-long.R
EpiModel/tests/testthat/test-netvary.R
EpiModel/tests/testthat/test-transmat-dendo.R
EpiModel/tests/testthat/test-get.R
EpiModel/tests/testthat/test-netoffset.R
EpiModel/tests/testthat/test-netattr.R
EpiModel/tests/testthat/test-merge.R
EpiModel/tests/testthat/test-dcm-long.R
EpiModel/tests/testthat/test-netsim-parallel.R
EpiModel/tests/testthat/test-netest.R
EpiModel/tests/testthat/test-dcm.R
EpiModel/tests/testthat/test-newdcm.R
EpiModel/tests/testthat/test-newnet.R
EpiModel/tests/testthat/test-net-long.R
EpiModel/tests/testthat/test-netrestart.R
EpiModel/tests/testthat/test-print.R
EpiModel/tests/testthat/test-netsim.R
EpiModel/tests/testthat/test-dcm-dede.R
EpiModel/tests/testthat/test-netpids.R
EpiModel/tests/testthat/test-netdx.R
EpiModel/tests/testthat/test-icm.R
EpiModel/tests/test-all.R
EpiModel/NAMESPACE
EpiModel/NEWS
EpiModel/R
EpiModel/R/saveout.R
EpiModel/R/dcm.mods.R
EpiModel/R/utils.R
EpiModel/R/net.mod.simnet.R
EpiModel/R/netest.R
EpiModel/R/icm.mod.init.R
EpiModel/R/print.r
EpiModel/R/icm.mod.status.R
EpiModel/R/plot.R
EpiModel/R/param.R
EpiModel/R/control.R
EpiModel/R/net.mod.vital.R
EpiModel/R/icm.mod.vital.R
EpiModel/R/netdx.R
EpiModel/R/modules.icm.R
EpiModel/R/get.R
EpiModel/R/dendo.R
EpiModel/R/dcm.R
EpiModel/R/netsim.R
EpiModel/R/net.mod.status.R
EpiModel/R/net.mod.init.R
EpiModel/R/init.R
EpiModel/R/shiny.R
EpiModel/R/test.R
EpiModel/R/icm.utils.R
EpiModel/R/verbose.R
EpiModel/R/crosscheck.R
EpiModel/R/as.data.frame.R
EpiModel/R/net.utils.R
EpiModel/R/modules.net.R
EpiModel/R/summary.R
EpiModel/R/icm.R
EpiModel/R/merge.R
EpiModel/R/EpiModel-package.r
EpiModel/R/net.mod.getprev.R
EpiModel/vignettes
EpiModel/vignettes/Intro.Rmd
EpiModel/MD5
EpiModel/build
EpiModel/build/vignette.rds
EpiModel/DESCRIPTION
EpiModel/man
EpiModel/man/get_degree.Rd
EpiModel/man/infection.icm.Rd
EpiModel/man/get_prev.icm.Rd
EpiModel/man/edgelist_censor.Rd
EpiModel/man/bipvals.Rd
EpiModel/man/plot.transmat.Rd
EpiModel/man/crosscheck.icm.Rd
EpiModel/man/mutate_epi.Rd
EpiModel/man/get_attr_prop.Rd
EpiModel/man/get_network.Rd
EpiModel/man/initialize.icm.Rd
EpiModel/man/check_bip_degdist.Rd
EpiModel/man/saveout.net.Rd
EpiModel/man/plot.netdx.Rd
EpiModel/man/saveout.icm.Rd
EpiModel/man/netdx.Rd
EpiModel/man/init.icm.Rd
EpiModel/man/color_tea.Rd
EpiModel/man/saveout.dcm.Rd
EpiModel/man/plot.dcm.Rd
EpiModel/man/plot.netsim.Rd
EpiModel/man/icm.Rd
EpiModel/man/get_prev.net.Rd
EpiModel/man/plot.icm.Rd
EpiModel/man/get_formula_terms.Rd
EpiModel/man/transco.Rd
EpiModel/man/summary.dcm.Rd
EpiModel/man/merge.netsim.Rd
EpiModel/man/as.phylo.transmat.Rd
EpiModel/man/discord_edgelist.Rd
EpiModel/man/update_dissolution.Rd
EpiModel/man/param.dcm.Rd
EpiModel/man/deaths.net.Rd
EpiModel/man/summary.netest.Rd
EpiModel/man/births.net.Rd
EpiModel/man/netsim.Rd
EpiModel/man/init.dcm.Rd
EpiModel/man/test_icm.Rd
EpiModel/man/sim_nets.Rd
EpiModel/man/init_status.net.Rd
EpiModel/man/merge.icm.Rd
EpiModel/man/modules.icm.Rd
EpiModel/man/init_pids.Rd
EpiModel/man/crosscheck.dcm.Rd
EpiModel/man/verbose.net.Rd
EpiModel/man/comp_plot.Rd
EpiModel/man/resim_nets.Rd
EpiModel/man/deaths.icm.Rd
EpiModel/man/dcm.Rd
EpiModel/man/births.icm.Rd
EpiModel/man/as.data.frame.dcm.Rd
EpiModel/man/brewer_ramp.Rd
EpiModel/man/dissolution_coefs.Rd
EpiModel/man/param.icm.Rd
EpiModel/man/deleteAttr.Rd
EpiModel/man/init_status.icm.Rd
EpiModel/man/as.data.frame.icm.Rd
EpiModel/man/modules.net.Rd
EpiModel/man/get_transmat.Rd
EpiModel/man/control.net.Rd
EpiModel/man/epiweb.Rd
EpiModel/man/split_bip.Rd
EpiModel/man/get_sims.Rd
EpiModel/man/calc_eql.Rd
EpiModel/man/netest.Rd
EpiModel/man/summary.icm.Rd
EpiModel/man/modeids.Rd
EpiModel/man/copy_toall_attr.Rd
EpiModel/man/crosscheck.net.Rd
EpiModel/man/control.icm.Rd
EpiModel/man/summary.netsim.Rd
EpiModel/man/control.dcm.Rd
EpiModel/man/update_nwattr.Rd
EpiModel/man/ssample.Rd
EpiModel/man/EpiModel-package.Rd
EpiModel/man/verbose.dcm.Rd
EpiModel/man/recovery.net.Rd
EpiModel/man/initialize.net.Rd
EpiModel/man/edges_correct.Rd
EpiModel/man/get_nwstats.Rd
EpiModel/man/param.net.Rd
EpiModel/man/idmode.Rd
EpiModel/man/recovery.icm.Rd
EpiModel/man/verbose.icm.Rd
EpiModel/man/mcat.Rd
EpiModel/man/dcm.mods.Rd
EpiModel/man/as.network.transmat.Rd
EpiModel/man/infection.net.Rd
EpiModel/man/test_net.Rd
EpiModel/man/edgelist_meanage.Rd
EpiModel/man/get_nwparam.Rd
EpiModel/man/init.net.Rd