Files in JMacDonaldPhD/Epidemics
Inference For Epidemics (one line, title case)
.Rbuildignore
.gitignore
2.RData
CPP Compatibility between machines
DESCRIPTION
ESS_200_vs_1000
ESS_sec_200_vs_1000
Epidemics.Rproj
Graphs/Bad_Observation.png
Graphs/Better_Observation.png
Graphs/ESS_200_vs_1000
Graphs/ESS_sec_200_vs_1000
Graphs/Enough_Infectious_Process_Obs.jpeg
Graphs/Many_Centered_Runs.png
Graphs/Not_Enough_Epidemic_Process_Obs.jpeg
Graphs/Not_Enough_Infectious_Process_Obs.jpeg
Graphs/PM_MCMC_ESS10.jpeg
Graphs/PM_MCMC_PosteriorSamples10.jpeg
Graphs/PM_MCMC_SIS1.jpeg
Graphs/PM_MCMC_SIS2.jpeg
Graphs/PM_MCMC_SIS3.jpeg
Graphs/PM_MCMC_SIS4.jpeg
Graphs/PM_MCMC_SIS5.jpeg
Graphs/R0highvsR0low.jpeg
Graphs/SIStestEpidemic.jpeg
Graphs/VarOfEpidemicIncreasingN.jpeg
Graphs/VarOfEpidemicIncreasingR0.jpeg
Graphs/beta_rep_vs_random.jpeg
Graphs/beta_rep_vs_random_1000.jpeg
Graphs/fsMCMC_ESS10.jpeg
Graphs/fsMCMC_PosteriorSamples10.jpeg
Graphs/fsMCMCmixing.jpeg
Graphs/gamma_rep_vs_random.jpeg
Graphs/gamma_rep_vs_random_1000.jpeg
IS_ESS_Increasing_panel_no.RData
NAMESPACE
Notebooks/Household_SIS_Inference.Rmd
Notebooks/Household_SIS_Inference.nb.html
Notebooks/Particle Filtering for Epidemic Modelling.Rmd
Notebooks/Particle Filtering for Epidemic Modelling.nb.html
Notebooks/Single Particle MCMC to make inference on SIS Panel Data.Rmd
Notebooks/Single Particle MCMC to make inference on SIS Panel Data.nb.html
Notebooks/fsMCMC
Notebooks/fsMCMC, using Non-centered simulation-based proposals to estimate likelihoods.Rmd
Notebooks/fsMCMC, using Non-centered simulation-based proposals to estimate likelihoods.nb.html
Notebooks/fsMCMC,-using-Non-centered-simulation-based-proposals-to-estimate-likelihoods.html
Notebooks/fsMCMC,-using-Non-centered-simulation-based-proposals-to-estimate-likelihoods.pdf
Notebooks/fsMCMC: using Non-centered simulation-based proposals to estimate likelihoods.Rmd
PM_MCMC_SIS 960 960
R/ASIS_MCMC.R
R/AdaptiveSIR_PM-MCMC.R
R/AdaptiveSIS_PM-MCMC.R
R/Centered_MCMC.R
R/Counting_Transitions.R
R/Data.R
R/Deterministic_Epidemic_Solutions .R
R/Deterministic_Gillespie.R
R/Epidemic_GIllespie.R
R/Epidemic_Simulation.R
R/Epidemic_fsMCMC_seed.R
R/Epidemics.R
R/General_Epidemic_Simulation.R
R/Importance Sampler.R
R/Infectious_Disease_Gillespie.R
R/Kernels.R
R/Leftovers/ASIS_MCMC.R
R/Leftovers/Counting_Transitions.R
R/Leftovers/Deterministic_Epidemic_Solutions .R
R/Leftovers/Deterministic_Gillespie.R
R/Leftovers/Epidemic_GIllespie.R
R/Leftovers/Epidemic_Simulation.R
R/Leftovers/Epidemic_fsMCMC_seed.R
R/Leftovers/event.epidemics.R
R/Leftovers/fsMCMC.epidemics.R
R/Leftovers/fsMCMC_sim.R
R/Likelihood_Calculations.R
R/MCMC_Output.R
R/Non-Centered_MCMC.R
R/PM-MCMCpanelExperiment.R
R/Partially_ Non-Centered_MCMC.R
R/Psuedo_Marginal_MCMC.R
R/RWMEpidemics.R
R/RcppExports.R
R/SIR_Gillespie.R
R/SIR_PM-MCMC.R
R/SIR_PM-MCMCexperiment1.R
R/SIRfsMCMCexperiment.R
R/SIS_Gillespie.R
R/SIS_PM-MCMC.R
R/SIS_deterministic.R
R/SIS_fsMCMC.R
R/SIS_fsMCMC_new.R
R/SIS_gillespies.R
R/SISfsMCMC_blockedIndependenceSampler.R
R/SISpanelExperiment.R
R/Sellke_Epidemic_Construction.R
R/Sequential Importance Sampler.R
R/adaptiveSISfsMCMC.R
R/blockSamplesSIRfsMCMC.R
R/dHyperGeom.R
R/fsMCMC_SIS.R
R/oneParticlePM_SIS.R
R/oneParticlePM_SIS_beta.R
R/panel_data.R
R/panel_data_epidemics.R
R/plot.epidemic.R
R/possible_transitions.R
R/simplified_gillespies.R
R/state.R
R/state_table.R
R/transitionData.R
Results/ExploringSISPMresults.R
Results/ExploringSISfsMCMCresults.R
Results/IS_ESS_Increasing_panel_no.Rdata
Results/IS_ESS_Increasing_panel_no.rds
Results/IS_optimal_results.csv
Results/PMnoSimsExperiment.Rdata
Results/RWM_optimal_results.csv
Results/SIRPMnoSimsExperiment.Rdata
Results/SIRPMnoSimsExperiment5Panels.Rdata
Results/SIRfsMCMCnoPanelsExperiment.Rdata
Results/SISIncreasingPanels.RData
Results/SIS_PMnoSimsExperiment.Rdata
Results/Variability-big_epidemic.csv
Results/bigRuns_SISIncreasingPanels.Rdata
Results/finalRunParameters.RData
Results/fsMCMC200Results.RData
Results/fsMCMC200Results.rds
Results/test_panelSample.RData
Results/test_panelSample.rds
Rprof.out
Scripts/Boundary Hitting SIS.R
Scripts/Deterministic_Epidemic_Solutions_Results.R
Scripts/Effect_Epidemic_Variability_PM_MCMC.R
Scripts/Epidemic Profile Likelihoods.R
Scripts/Epidemic_Variability_R0_N.R
Scripts/ExperimentingWithAdaptiveSISfsMCMC.R
Scripts/Household Kernel.R
Scripts/IS_Performance.R
Scripts/LongRunSISExperiment.R
Scripts/MCMC_results.R
Scripts/No_Kernel_vs_Kernel.R
Scripts/PM-fsMCMC_200.R
Scripts/PMSIRExperiment1.R
Scripts/PMSISexperiemnt.R
Scripts/Plotting_fsMCMC_results.R
Scripts/PsuedoMarginalResults.R
Scripts/SIS_panelDataInvestigation.R
Scripts/Simle_Centered_Results.R
Scripts/Simulating_Panel_Data_Example.R
Scripts/Testing PM-MCMC.R
Scripts/Testing SIS.R
Scripts/Testing fsMCMC.R
Scripts/Testing_Centered_MCMC.R
Scripts/Testing_Epidemics.R
Scripts/Testing_reduce_MCMC.R
Scripts/Variability in fsMCMC Boxplots.R
Scripts/Variability_fsMCMC_sampling.R
Scripts/Varying_no_observations.R
Scripts/benchmarking/Profiling_Epidemics_Package.R
Scripts/benchmarking/benchmarking_Gillespies.R
Scripts/benchmarking/profilingSISGIllespie.R
Scripts/check_typeC.cpp
Scripts/fsMCMCResults.R
Scripts/simdata1000_centered.R
Scripts/simdata1000_noncentered.R
Scripts/simdata200_centered.R
Scripts/simdata200_noncentered.R
Scripts/simdata500_centered.R
Scripts/simdata500_noncentered.R
Scripts/simulated_datasets.R
Scripts/testC.cpp
Whiteboard Notes/Sellke(1).jpeg
Whiteboard Notes/Sellke(2).jpeg
beta_rep_vs_random.jpeg
beta_rep_vs_random_1000.jpeg
data/Contact_Epidemic.rda
data/Contact_Epidemic2.rda
data/Epidemic1.rda
data/Epidemic2.rda
data/Epidemic3.rda
data/Epidemic4.rda
data/Homo_HighPop_HighR0.rda
data/Homo_HighPop_LowR0.rda
data/Homo_HighPop_MedR0.rda
data/Homo_LowPop_HighR0.rda
data/Homo_LowPop_LowR0.rda
data/Homo_LowPop_MedR0.rda
data/Homo_MedPop_HighR0.rda
data/Homo_MedPop_LowR0.rda
data/Homo_MedPop_MedR0.rda
data/Variability.rda
data/bad_sample_200.rda
data/big_epidemic.rda
data/simdata1000.rda
data/simdata200.rda
data/simdata500.rda
data/test_epidemic.rda
data/toy_epidemic.rda
finalRunParameters - SIS Experiment
fsMCMC.epidemics Profile
fsMCMC_PosteriorSamples10.jpeg
fsMCMCmixing.jpeg
gamma_rep_vs_random.jpeg
gamma_rep_vs_random_1000.jpeg
man/Contact_Kernel.Rd
man/Epidemic_fsMCMC.Rd
man/General_Epidemic_Process.Rd
man/Homo_HighPop_HighR0.Rd
man/Homo_HighPop_LowR0.Rd
man/Homo_HighPop_MedR0.Rd
man/Homo_LowPop_HighR0.Rd
man/Homo_LowPop_LowR0.Rd
man/Homo_LowPop_MedR0.Rd
man/Homo_MedPop_HighR0.Rd
man/Homo_MedPop_LowR0.Rd
man/Homo_MedPop_MedR0.Rd
man/Homogeneous_Kernel.Rd
man/IP_t.Rd
man/Infectious_Disease_Gillespie.Rd
man/MCMCplots.Rd
man/NonCentered_MCMC.Rd
man/PM_MCMCexperiment.Rd
man/PNC.Algorithm.Rd
man/Pseudo_Marginal_MCMC.Rd
man/RWMSampler.Rd
man/SIR_Gillespie.Rd
man/SIR_PM_MCMCexperiment1.Rd
man/SIR_PseudoMarginalMCMC.Rd
man/SIR_fsMCMC_blockedIS.Rd
man/SIRfsMCMCexperiment1.Rd
man/SIS_Gillespie.Rd
man/SIS_PseudoMarginalMCMC.Rd
man/SIS_fsMCMC.Rd
man/SIS_fsMCMC_beta.Rd
man/SIS_fsMCMC_blockedIS.Rd
man/SIS_fsMCMC_oneProposal.Rd
man/SIS_y_soln.Rd
man/SISfsMCMCexperiment.Rd
man/adaptiveSIR_PseudoMarginalMCMC.Rd
man/adaptiveSIRfsMCMC7_blockedIS.Rd
man/adaptiveSIS_PseudoMarginalMCMC.Rd
man/adaptiveSISfsMCMC.Rd
man/adaptiveSISfsMCMC7_blockedIS.Rd
man/dHyperGeom.Rd
man/epidemicImportanceSampler.Rd
man/epidemic_loglikelihood.Rd
man/fsMCMC_SIS.Rd
man/heterogeneousSIR_Gillespie.Rd
man/homogeneousPanelDataSIR_Gillespie.Rd
man/homogeneousPanelDataSIR_GillespieEU.Rd
man/homogeneousPanelDataSIS_Gillespie.Rd
man/homogeneousPanelDataSIS_GillespieEU.Rd
man/homogeneousSIR_Gillespie.Rd
man/individualHomogeneousSIR_Gillespie.Rd
man/individualHomogeneousSIS_Gillespie.Rd
man/inf_time_proposal.Rd
man/interval_intersect.Rd
man/log_likelihood_rem.Rd
man/oneParticlePM_SIS.Rd
man/oneParticlePM_SIS_beta.Rd
man/panelDataSIR_Gillespie.Rd
man/panel_data_new.epidemics.Rd
man/pi_Y_given_X.Rd
man/plot.epidemic.Rd
man/possible_transitions.Rd
man/prod_part_inf.Rd
man/rates.Rd
man/relevant_rates.Rd
man/start_state.Rd
man/state.Rd
man/state_table.Rd
man/time_to_next_event.Rd
man/transitionData.Rd
man/which_event.Rd
simdata1000_noncentered.R
src/Epidemics.so
src/RcppExports.cpp
src/RcppExports.o
src/calling_c.cpp
src/calling_c.o
src/concat.cpp
src/concat.o
src/event_epidemicsC.cpp
src/event_epidemicsC.o
src/prod_likelihood_C.cpp
src/prod_likelihood_C.o
test_panelSample.RData
test_panelSample.rds
