Mathematical Modeling of Infectious Disease Dynamics


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Documentation for package ‘EpiModel’ version 2.0.5

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EpiModel-package Mathematical Modeling of Infectious Disease Dynamics
absdiffby Definition for absdiffby ERGM Term
absdiffnodemix Definition for absdiffnodemix ERGM Term
add_attr Functions to Access and Edit the Master List Object in Network Models
add_control Functions to Access and Edit the Master List Object in Network Models
add_epi Functions to Access and Edit the Master List Object in Network Models
add_init Functions to Access and Edit the Master List Object in Network Models
add_param Functions to Access and Edit the Master List Object in Network Models
append_attr Functions to Access and Edit the Master List Object in Network Models
append_core_attr Functions to Access and Edit the Master List Object in Network Models
apportion_lr Apportion Least-Remainder Method
as.data.frame.dcm Extract Model Data for Deterministic Compartmental Models
as.data.frame.icm Extract Model Data for Stochastic Models
as.data.frame.netdx Extract Timed Edgelists netdx Objects
as.data.frame.netsim 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
check_degdist_bal Check Degree Distribution for Balance in Target Statistics
color_tea Creates a TEA Variable for Infection Status for 'ndtv' Animations
comp_plot Plot Compartment Diagram for Epidemic Models
comp_plot.dcm Plot Compartment Diagram for Epidemic Models
comp_plot.icm Plot Compartment Diagram for Epidemic Models
comp_plot.netsim 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
dcm Deterministic Compartmental Models
dissolution_coefs Dissolution Coefficients for Stochastic Network Models
edgelist_censor Table of Edge Censoring
EpiModel Mathematical Modeling of Infectious Disease Dynamics
epiweb EpiModel Web
generate_random_params Generate Values for Random Parameters
geom_bands ggplot2 geom for Quantile Bands
get_args Get Arguments from EpiModel Parameterization Functions
get_attr Functions to Access and Edit the Master List Object in Network Models
get_attr_list Functions to Access and Edit the Master List Object in Network Models
get_control Functions to Access and Edit the Master List Object in Network Models
get_control_list Functions to Access and Edit the Master List Object in Network Models
get_degree Get Individual Degree from Network or Edgelist
get_epi Functions to Access and Edit the Master List Object in Network Models
get_epi_list Functions to Access and Edit the Master List Object in Network Models
get_formula_term_attr Outputs ERGM Formula Attributes into a Character Vector
get_init Functions to Access and Edit the Master List Object in Network Models
get_init_list Functions to Access and Edit the Master List Object in Network Models
get_network Extract networkDynamic and network Objects from Network Simulations
get_network_term_attr Outputs ERGM Formula Attributes into a Character Vector
get_nwstats Extract Network Statistics from netsim or netdx Object
get_param Functions to Access and Edit the Master List Object in Network Models
get_param_list Functions to Access and Edit the Master List Object in Network Models
get_posit_ids Convert Unique identifiers from/to Positional identifiers
get_sims Extract Network Simulations
get_transmat Extract Transmissions Matrix from Network Epidemic Model
get_unique_ids Convert Unique identifiers from/to Positional identifiers
icm Stochastic Individual Contact Models
init.dcm Initial Conditions for Deterministic Compartmental Models
init.icm Initial Conditions for Stochastic Individual Contact Models
init.net Initial Conditions for Stochastic Network Models
InitErgmTerm.absdiffby Definition for absdiffby ERGM Term
InitErgmTerm.absdiffnodemix Definition for absdiffnodemix ERGM Term
is.transmat Extract Transmissions Matrix from Network Epidemic Model
merge.icm Merge Data across Stochastic Individual Contact Model Simulations
merge.netsim Merge Model Simulations Across netsim Objects
modules.icm Modules for Stochastic Individual Contact Models
modules.net Modules for Stochastic Network Models
mutate_epi Add New Epidemiology Variables
net-accessor Functions to Access and Edit the Master List Object in Network Models
netdx Dynamic Network Model Diagnostics
netest Dynamic Network Model Estimation
netsim Stochastic Network Models
nwupdate.net Dynamic Network Updates
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
param_random Create a Value Sampler for Random Parameters
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
set_attr Functions to Access and Edit the Master List Object in Network Models
set_control Functions to Access and Edit the Master List Object in Network Models
set_epi Functions to Access and Edit the Master List Object in Network Models
set_init Functions to Access and Edit the Master List Object in Network Models
set_param Functions to Access and Edit the Master List Object in Network Models
set_transmat Save Transmission Matrix
summary.dcm Summary Model Statistics
summary.icm Summary Model Statistics
summary.netsim Summary Model Statistics
transmat Extract Transmissions Matrix from Network Epidemic Model
truncate_sim Truncate Simulation Time Series
unique_id-tools Convert Unique identifiers from/to Positional identifiers
update_dissolution Adjust Dissolution Component of Network Model Fit
update_params Update Model Parameters for Stochastic Network Models