├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CI.yaml │ └── pkgdown.yaml ├── .gitignore ├── .lintr ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── C-generator.R ├── SEIR.R ├── SIR.R ├── SIS.R ├── SISe.R ├── SISe3.R ├── SISe3_sp.R ├── SISe_sp.R ├── SimInf-package.R ├── SimInf.R ├── SimInf_events.R ├── SimInf_individual_events.R ├── SimInf_model.R ├── abc.R ├── check_arguments.R ├── classes.R ├── degree.R ├── density_ratio.R ├── distance.R ├── distributions.R ├── edge_properties.R ├── init.R ├── lambert.R ├── match_compartments.R ├── mparse.R ├── n.R ├── openmp.R ├── package_skeleton.R ├── pfilter.R ├── plot.R ├── pmcmc.R ├── prevalence.R ├── print.R ├── punchcard.R ├── run.R ├── trajectory.R ├── u0.R ├── v0.R └── valid.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── cleanup ├── configure ├── configure.ac ├── data ├── events_SISe3.rda ├── nodes.rda └── u0_SISe3.rda ├── inst ├── CITATION └── include │ └── SimInf.h ├── logo ├── logo.png ├── logo.svg └── logo.tex ├── man-roxygen ├── C_code-slot.R ├── G-param.R ├── G-slot.R ├── S-param.R ├── S-slot.R ├── U-param.R ├── U-slot.R ├── U_sparse-slot.R ├── beta-end-param.R ├── beta-param.R ├── beta-section.R ├── compartments-param.R ├── data-param.R ├── end-param.R ├── epsilon-param.R ├── events-param.R ├── gamma-param.R ├── gdata-param.R ├── gdata-slot.R ├── index-param.R ├── init_model-param.R ├── ldata-param.R ├── ldata-slot.R ├── mparse-example.R ├── n_iterations-param.R ├── n_particles-param.R ├── obs_process-param.R ├── phi-param.R ├── plot-frame-param.R ├── plot-index-param.R ├── plot-legend-param.R ├── plot-lwd-param.R ├── plot-range-param.R ├── plot-type-param.R ├── plot-y-param.R ├── post-particle-param.R ├── post_gen-param.R ├── post_proposal-param.R ├── prevalence-formula-param.R ├── prevalence-index-param.R ├── prevalence-level-param.R ├── priors-param.R ├── priors-slot.R ├── start-param.R ├── thin-param.R ├── tspan-param.R ├── tspan-slot.R ├── u0-param.R ├── u0-slot.R ├── verbose-param-pmcmc.R └── verbose-param.R ├── man ├── C_code.Rd ├── SEIR-class.Rd ├── SEIR.Rd ├── SIR-class.Rd ├── SIR.Rd ├── SIS-class.Rd ├── SIS.Rd ├── SISe-class.Rd ├── SISe.Rd ├── SISe3-class.Rd ├── SISe3.Rd ├── SISe3_sp-class.Rd ├── SISe3_sp.Rd ├── SISe_sp-class.Rd ├── SISe_sp.Rd ├── SimInf.Rd ├── SimInf_abc-class.Rd ├── SimInf_events-class.Rd ├── SimInf_events.Rd ├── SimInf_individual_events-class.Rd ├── SimInf_model-class.Rd ├── SimInf_model.Rd ├── SimInf_pfilter-class.Rd ├── SimInf_pmcmc-class.Rd ├── abc.Rd ├── add_spatial_coupling_to_ldata.Rd ├── as.data.frame.SimInf_abc.Rd ├── as.data.frame.SimInf_events.Rd ├── as.data.frame.SimInf_individual_events.Rd ├── as.data.frame.SimInf_pmcmc.Rd ├── boxplot-SimInf_model-method.Rd ├── continue_abc.Rd ├── continue_pmcmc.Rd ├── distance_matrix.Rd ├── edge_properties_to_matrix.Rd ├── events.Rd ├── events_SEIR.Rd ├── events_SIR.Rd ├── events_SIS.Rd ├── events_SISe.Rd ├── events_SISe3.Rd ├── examples │ ├── abc.R │ └── pfilter.R ├── figures │ └── README-mparse-SIR-1.png ├── gdata-set.Rd ├── gdata.Rd ├── get_individuals.Rd ├── indegree.Rd ├── individual_events.Rd ├── lambertW0.Rd ├── ldata.Rd ├── length-SimInf_pmcmc-method.Rd ├── logLik-SimInf_pfilter-method.Rd ├── macros │ └── citations.Rd ├── mparse.Rd ├── n_compartments.Rd ├── n_generations.Rd ├── n_nodes.Rd ├── n_replicates.Rd ├── node_events.Rd ├── nodes.Rd ├── outdegree.Rd ├── package_skeleton.Rd ├── pairs-SimInf_model-method.Rd ├── pfilter.Rd ├── plot-SimInf_abc-method.Rd ├── plot-SimInf_events-method.Rd ├── plot-SimInf_individual_events-method.Rd ├── plot-SimInf_pfilter-method.Rd ├── plot-SimInf_pmcmc-method.Rd ├── plot.Rd ├── pmcmc.Rd ├── prevalence-SimInf_model-method.Rd ├── prevalence-SimInf_pfilter-method.Rd ├── prevalence-SimInf_pmcmc-method.Rd ├── prevalence.Rd ├── punchcard-set.Rd ├── run.Rd ├── select_matrix-set.Rd ├── select_matrix.Rd ├── set_num_threads.Rd ├── shift_matrix-set.Rd ├── shift_matrix.Rd ├── show-SimInf_abc-method.Rd ├── show-SimInf_events-method.Rd ├── show-SimInf_individual_events-method.Rd ├── show-SimInf_model-method.Rd ├── show-SimInf_pfilter-method.Rd ├── show-SimInf_pmcmc-method.Rd ├── summary-SimInf_abc-method.Rd ├── summary-SimInf_events-method.Rd ├── summary-SimInf_individual_events-method.Rd ├── summary-SimInf_model-method.Rd ├── summary-SimInf_pfilter-method.Rd ├── summary-SimInf_pmcmc-method.Rd ├── trajectory-SimInf_model-method.Rd ├── trajectory-SimInf_pfilter-method.Rd ├── trajectory-SimInf_pmcmc-method.Rd ├── trajectory.Rd ├── u0-set.Rd ├── u0.Rd ├── u0_SEIR.Rd ├── u0_SIR.Rd ├── u0_SIS.Rd ├── u0_SISe.Rd ├── u0_SISe3.Rd └── v0-set.Rd ├── src ├── Makevars.in ├── Makevars.win ├── SimInf-win.def ├── SimInf.c ├── SimInf_internal.h ├── init.c ├── misc │ ├── SimInf_LambertW.c │ ├── SimInf_abc.c │ ├── SimInf_arg.c │ ├── SimInf_distance_matrix.c │ ├── SimInf_forward_euler_linear_decay.c │ ├── SimInf_individual_events.c │ ├── SimInf_ldata.c │ ├── SimInf_local_spread.c │ ├── SimInf_openmp.c │ ├── SimInf_particle_filter.c │ ├── SimInf_trajectory.c │ ├── binheap.c │ └── kvec.h ├── models │ ├── SEIR.c │ ├── SIR.c │ ├── SIS.c │ ├── SISe.c │ ├── SISe3.c │ ├── SISe3_sp.c │ └── SISe_sp.c └── solvers │ ├── SimInf_solver.c │ ├── SimInf_solver_aem.c │ ├── SimInf_solver_mssm.c │ └── SimInf_solver_ssm.c ├── tests ├── SEIR.R ├── SIR.R ├── SIS.R ├── SISe.R ├── SISe3.R ├── SISe3_sp.R ├── SISe_sp.R ├── SimInf.R ├── SimInf_events.R ├── SimInf_model.R ├── abc-gdata.R ├── abc-ldata.R ├── abc.R ├── density_ratio.R ├── distributions.R ├── edge_properties.R ├── individual_events.R ├── lambert.R ├── ldata_sp.R ├── match_compartments.R ├── measures.R ├── mparse.R ├── package_skeleton.R ├── pfilter.R ├── phi.R ├── pmcmc.R ├── prevalence.R ├── punchcard.R ├── sample_select.R ├── solver_aem.R ├── trajectory.R ├── u0.R ├── util │ └── check.R └── v0.R └── vignettes ├── SimInf.Rnw ├── SimInf.bib ├── img ├── SIR.pdf ├── SIR.svg ├── SIR.tex ├── SISe3_sp.pdf ├── SISe3_sp.svg ├── SISe3_sp.tex ├── 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