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.

AuthorSamuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Emily Beylerian [ctb], Skye Bender-deMoll [ctb], Kevin Weiss [ctb]
Date of publication2017-03-13 21:14:09
MaintainerSamuel Jenness <samuel.m.jenness@emory.edu>
LicenseGPL-3
Version1.3.0
http://epimodel.org/

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

Functions

as.data.frame.dcm Man page
as.data.frame.icm Man page
as.data.frame.netsim Man page
as.network.transmat Man page
as.phylo.transmat Man page
bipvals Man page
births.icm Man page
births.net Man page
brewer_ramp Man page
calc_eql Man page
check_bip_degdist Man page
color_tea Man page
comp_plot Man page
comp_plot.dcm Man page
comp_plot.icm Man page
comp_plot.netsim Man page
control.dcm Man page
control.icm Man page
control.net Man page
copy_toall_attr Man page
crosscheck.dcm Man page
crosscheck.icm Man page
crosscheck.net Man page
dcm Man page
dcm.mods Man page
deaths.icm Man page
deaths.net Man page
deleteAttr Man page
discord_edgelist Man page
dissolution_coefs Man page
edgelist_censor Man page
edgelist_meanage Man page
edges_correct Man page
EpiModel Man page
EpiModel-package Man page
epiweb Man page
get_attr_prop Man page
get_degree Man page
get_formula_terms Man page
get_network Man page
get_nwparam Man page
get_nwstats Man page
get_prev.icm Man page
get_prev.net Man page
get_sims Man page
get_transmat Man page
icm Man page
idmode Man page
infection.icm Man page
infection.net Man page
init.dcm Man page
initialize.icm Man page
initialize.net Man page
init.icm Man page
init.net Man page
init_pids Man page
init_status.icm Man page
init_status.net Man page
is.transmat Man page
mcat Man page
merge.icm Man page
merge.netsim Man page
modeids Man page
mod_SI_1g_cl Man page
mod_SI_1g_op Man page
mod_SI_2g_cl Man page
mod_SI_2g_op Man page
mod_SIR_1g_cl Man page
mod_SIR_1g_op Man page
mod_SIR_2g_cl Man page
mod_SIR_2g_op Man page
mod_SIS_1g_cl Man page
mod_SIS_1g_op Man page
mod_SIS_2g_cl Man page
mod_SIS_2g_op Man page
modules.icm Man page
modules.net Man page
mutate_epi Man page
netdx Man page
netest Man page
netsim Man page
param.dcm Man page
param.icm Man page
param.net Man page
plot.dcm Man page
plot.icm Man page
plot.netdx Man page
plot.netsim Man page
plot.transmat Man page
recovery.icm Man page
recovery.net Man page
resim_nets Man page
saveout.dcm Man page
saveout.icm Man page
saveout.net Man page
sim_nets Man page
split_bip Man page
ssample Man page
summary.dcm Man page
summary.icm Man page
summary.netest Man page
summary.netsim Man page
test_icm Man page
test_net Man page
transco Man page
transmat Man page
update_dissolution Man page
update_nwattr Man page
verbose.dcm Man page
verbose.icm Man page
verbose.net Man page

Files

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-mutate.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

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