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EpiModel  

Mathematical Modeling of Infectious Disease Dynamics
View on CRAN: Click here


Download and install EpiModel package within the R console
Install from CRAN:
install.packages("EpiModel")

Install from Github:
library("remotes")
install_github("cran/EpiModel")

Install by package version:
library("remotes")
install_version("EpiModel", "2.5.0")



Attach the package and use:
library("EpiModel")
Maintained by
Samuel Jenness
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-04-08
Latest Update: 2023-06-20
Description:
Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact 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 API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, ).
How to cite:
Samuel Jenness (2013). EpiModel: Mathematical Modeling of Infectious Disease Dynamics. R package version 2.5.0, https://cran.r-project.org/web/packages/EpiModel. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.25 (2013-04-08 17:44), 0.95 (2014-01-23 20:29), 1.0.1 (2014-07-29 07:38), 1.0.2 (2014-08-30 09:19), 1.0 (2014-06-09 07:47), 1.1.1 (2014-11-02 09:17), 1.1.2 (2014-12-01 20:38), 1.1.3 (2015-01-18 06:43), 1.1.4 (2015-04-12 09:05), 1.1.6 (2015-05-16 09:44), 1.1 (2014-10-01 07:21), 1.2.0 (2015-07-08 00:42), 1.2.1 (2015-07-24 06:50), 1.2.2 (2015-11-03 11:59), 1.2.4 (2016-02-01 16:35), 1.2.5 (2016-03-09 23:12), 1.2.6 (2016-05-24 18:50), 1.2.7 (2016-07-30 00:34), 1.2.8 (2016-12-16 22:51), 1.3.0 (2017-03-13 21:14), 1.5.0 (2017-06-01 05:47), 1.6.0 (2018-01-24 22:22), 1.6.1 (2018-01-25 15:45), 1.6.5 (2018-04-10 10:31), 1.7.0 (2018-11-21 18:40), 1.7.2 (2018-12-18 17:40), 1.7.3 (2019-08-29 19:10), 1.7.5 (2020-01-07 22:50), 1.8.0 (2020-05-08 17:10), 2.0.2 (2020-08-05 11:52), 2.0.3 (2020-11-09 22:40), 2.0.5 (2021-05-15 20:50), 2.1.0 (2021-06-25 22:20), 2.2.0 (2021-11-09 22:20), 2.2.1 (2022-02-02 09:50), 2.3.0 (2022-07-19 05:30), 2.3.1 (2022-10-01 14:00), 2.3.2 (2023-02-17 00:30), 2.4.0 (2023-06-20 20:20)
Other packages that cited EpiModel R package
View EpiModel citation profile
Other R packages that EpiModel depends, imports, suggests or enhances
Complete documentation for EpiModel
Functions, R codes and Examples using the EpiModel R package
Some associated functions: EpiModel-package . InitErgmTerm.absdiffby . InitErgmTerm.absdiffnodemix . InitErgmTerm.fuzzynodematch . add_vertices . apportion_lr . arrivals.2g.net . arrivals.icm.bip . arrivals.icm . arrivals.net . as.data.frame.dcm . as.data.frame.icm . as.data.frame.netdx . as.network.transmat . as.phylo.transmat . auto_update_attr . brewer_ramp . check_attr_lengths . check_degdist_bal . color_tea . common_updater . comp_plot . control.dcm . control.icm . control.net . copy_datattr_to_nwattr . copy_nwattr_to_datattr . create_dat_object . create_scenario_list . crosscheck.dcm . crosscheck.icm . crosscheck.net . dcm.mods . dcm . deleteAttr . delete_attr . delete_vertices . departures.2g.net . departures.icm.bip . departures.icm . departures.net . discord_edgelist . dissolution_coefs . edgelist_censor . edges_correct . epi_trackers . epiweb . format_param . generate_random_params . geom_bands . get_args . get_attr_history . get_attr_prop . get_cumulative_edgelist . get_cumulative_edgelists_df . get_current_timestep . get_degree . get_edgelist . get_formula_term_attr . get_network . get_network_term_attr . get_nwparam . get_nwstats . get_param_set . get_partners . get_sims . get_transmat . get_vertex_attribute . icm . idgroup . increment_timestep . infection.2g.net . infection.icm.bip . infection.icm . infection.net . init.dcm . init.icm . init.net . init_status.icm . init_status.net . init_tergmLite . initialize.icm . initialize.net . is_active_posit_ids . is_active_unique_ids . make_stats_table . mcat . merge.icm . merge.netsim . modules.icm . modules.net . mutate_epi . net-accessor . netdx . netest . netsim . netsim_cond_msg . networkLite . networkLitemethods . network_initialize . nwupdate.net . param.dcm . param.icm . param.net . param.net_from_table . param_random . plot.dcm . plot.icm . plot.netdx . plot.netsim . plot.transmat . prevalence.icm.bip . prevalence.icm . prevalence.net . print.netdx . print_nwstats_table . process_out.net . record_attr_history . record_raw_object . recovery.2g.net . recovery.icm.bip . recovery.icm . recovery.net . resim_nets . saveout.dcm . saveout.icm . saveout.net . set_current_timestep . set_transmat . set_vertex_attribute . sim_nets_t1 . ssample . summary.dcm . summary.icm . summary.netest . summary.netsim . tedgelist_to_toggles . test_icm . test_net . toggles_to_diss_stats . trim_netest . truncate_sim . unique_id-tools . update_cumulative_edgelist . update_dissolution . update_list . update_params . update_unique_ids . use_scenario . verbose.dcm . verbose.icm . verbose.net . 
Some associated R codes: EpiModel-package.R . ErgmTerms.R . RcppExports.R . as.data.frame.R . dcm.R . dcm.inputs.R . dcm.mods.R . dendo.R . el_cuml.R . get.R . icm.R . icm.inputs.R . icm.mod.init.R . icm.mod.status.R . icm.mod.vital.R . icm.utils.R . initialize.R . merge.R . modules.icm.R . modules.net.R . net.accessor.R . net.helpers.R . net.inputs.R . net.mod.infection.R . net.mod.init.R . net.mod.nwupdate.R . net.mod.prevalence.R . net.mod.recovery.R . net.mod.simnet.R . net.mod.trackers.R . net.mod.updater.R . net.mod.vital.R . net.record.R . net.scenarios.R . net.utils.R . netdx.R . netest.R . netsim.R . netsim_checkpoint.R . network.R . networkLite.R . plot.R . print.R . saveout.R . shiny.R . summary.R . test.R . update.R . utils.R . verbose.R .  Full EpiModel package functions and examples
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