Files in fintzij/augSIR

Estimation of stochastic SIR epidemic parameters via Bayesian data augmentation.

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/RcppExports.R R/SIRsimulation.R R/augSIR.R R/auxilliary_functions.R R/matrix_build_update.R R/metropolis_hastings_functions.R R/path_sampling_functions.R R/rjmcmc_functions.R

Read-and-delete-me

Simulation Journal/augSIR_simulations.aux

Simulation Journal/augSIR_simulations.dvi

Simulation Journal/augSIR_simulations.log

Simulation Journal/augSIR_simulations.pdf

Simulation Journal/augSIR_simulations.ps

Simulation Journal/augSIR_simulations.tex

Simulation Journal/corrected_likelihood_8_7_2015.log

Simulation Journal/corrected_likelihood_8_7_2015.tex

Thumbs.db

augSIR.Rproj

augSIR_log_10_0.1_0.1_4_1.txt

augSIR_log_10_0.2_0.1_4_1.txt

code_to_load_packages_on_cluster

log_10_0.1_0.1_4_1.txt

man/augSIR-package.Rd man/rcpp_hello_world.Rd

plots/sim1_BetaMu_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim1_trajecs_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim2_trajecs_b0.005_m0.5_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim3_BetaMu_b0.008_m1.2_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim3_Mu_b0.008_m1.2_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim3_beta_b0.008_m1.2_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim3_loglike_b0.008_m1.2_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim3_trajecs_b0.008_m1.2_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim_1_Beta_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim_1_Mu_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim_1_binomprob_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim_1_loglike_b0.005_m0.5_0.98_0.02_0_wpu_noMH_withinit.bmp

plots/sim_2_BetaMu_b0.005_m0.5_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim_2_Beta_b0.005_m0.5_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim_2_Mu_b0.005_m0.5_0.995_0.005_0_wpu_noMH_withinit.bmp

plots/sim_2_loglike_b0.005_m0.5_0.995_0.005_0_wpu_noMH_withinit.bmp

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.05_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.05_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.05_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.05_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.2_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.2_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.2_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.2_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.4_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.4_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.4_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__200_0.4_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.05_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.05_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.05_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.05_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.2_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.2_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.2_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.2_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.4_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.4_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.4_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__500_0.4_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.05_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.05_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.05_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.05_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.2_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.2_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.2_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.2_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.4_0.1_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.4_0.1_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.4_0.4_4_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Data/augSIR__50_0.4_0.4_8_1.Rdata

tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.05_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.05_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.05_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.05_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.2_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.2_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.2_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.2_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.4_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.4_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.4_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__200_0.4_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.05_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.05_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.05_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.05_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.2_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.2_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.2_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.2_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.4_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.4_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.4_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__500_0.4_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.05_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.05_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.05_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.05_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.2_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.2_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.2_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.2_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.4_0.1_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.4_0.1_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.4_0.4_4_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/Plots/augSIR__50_0.4_0.4_8_plot.pdf tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/convcomp_augSIR_reparMH.R tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/convcomp_stats_batch_reparMH.R tests/Experiments/Experiment series 1 - popsize_sampprob_censusInterval_R0_8_7_2015/process_exper1_results.R tests/Experiments/Experiment series 2 - Geweke simulations_fixed parameters_8_7_2015/convcomp_augSIR_geweke.R tests/Experiments/Experiment series 2 - Geweke simulations_fixed parameters_8_7_2015/convcomp_stats_batch_geweke.R

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/7_30_2015_fixed_params.tex

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/7_30_2015_reparameterized_model.log

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/7_30_2015_reparameterized_model.tex

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/Convergence experiment - populations size_/& binomial probability vs. mixing.tex

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/augSIR_simulations.aux

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/augSIR_simulations.dvi

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/augSIR_simulations.log

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/augSIR_simulations.pdf

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/augSIR_simulations.ps

tests/TESTS WITH WRONG LIKELIHOOD/augSIR simulation journal - bad likelihood simulations/exper_7_25_2015.tex

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_augSIR.R tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_250_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_250_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_250_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_25_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_25_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_25_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_500_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_500_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_500_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_50_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_50_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_augSIR_50_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_1000_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_1000_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_1000_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_100_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_100_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_100_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_250_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_250_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_250_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_25_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_25_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_500_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_500_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_500_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_50_0.2_0.5_1_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_50_0.2_0.5_1_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_plots_rjmcmc_50_0.2_0.5_1_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_rjmcmc.R

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_rjmcmc.sh

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 1 - effect of population size - augSIR vs rjmcmc/convcomp_stats_batch.R

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/Thumbs.db

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/convcomp_augSIR.R tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/convcomp_popsize_accepts.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/convcomp_popsize_results.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/convcomp_stats_batch.R tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_10_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_10_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_10_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_2_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_2_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_2_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_5_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - population size and binomial prob - assessing mixing/plots/convcomp_plots_augSIR_100_0.2_0.05_5_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 2 - 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tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/censusInterval_0.2/Results data/augSIR__200_0.05_10_1.Rdata

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tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/censusInterval_0.2/Results data/augSIR__50_0.25_5_1.Rdata

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tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/censusInterval_0.2/Results data/augSIR__50_0.25_5_3.Rdata

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/convcomp_augSIR.R tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/convcomp_stats_batch.R tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 3 - population size vs. mixing with fixed parameters/process_exper2_results.R

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/description.tex

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.aux

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.dvi

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.log

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.pdf

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.ps

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/MCMC procedure description/mcmc_descrip_reparam.tex

tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_4_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_4_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_4_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_8_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_8_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.1_8_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_4_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_4_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_4_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_8_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_8_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.05_0.4_8_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_4_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_4_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_4_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_8_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_8_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.1_8_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_4_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_4_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_4_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_8_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_8_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_150_0.2_0.4_8_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_300_0.05_0.1_4_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_300_0.05_0.1_4_2.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_300_0.05_0.1_4_3.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - reparameterized model/Plots/convcomp_plots_augSIR_300_0.05_0.1_8_1.pdf tests/TESTS WITH WRONG LIKELIHOOD/convergence_comp/Experiment series 4 - 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tests/convergence_comp/Experiment series 6 - Geweke test/Data files/augSIR__20_1_0.4_4_1.Rdata

tests/convergence_comp/Experiment series 6 - Geweke test/Data files/augSIR__20_1_0.4_8_1.Rdata

tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.05_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.05_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.2_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.2_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.5_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_0.5_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_1_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_10_1_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.05_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.05_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.2_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.2_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.5_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_0.5_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_1_0.4_4_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/Plots/convcomp_plots_augSIR_20_1_0.4_8_1.pdf tests/convergence_comp/Experiment series 6 - Geweke test/process_exper6_results.R

tests/convergence_comp/convcomp.sh

tests/convergence_comp/convcomp_augSIR.R tests/convergence_comp/convcomp_rjmcmc.R

tests/convergence_comp/convcomp_rjmcmc.sh

tests/convergence_comp/convcomp_rjmcmc_cluster_code.R

tests/convergence_comp/convcomp_run.sh

tests/convergence_comp/convcomp_stats_batch.R

tests/convergence_comp/convcomp_statsclust_run.sh

tests/eval.R tests/gibbsupdate_comparison.R

tests/jointdist_comparisons/infecprob_demeaned_sim1.png

tests/jointdist_comparisons/infecprob_demeaned_sim3.png

tests/jointdist_comparisons/infecprob_demeaned_sim4.png

tests/jointdist_comparisons/infecprob_sim1.png

tests/jointdist_comparisons/infecprob_sim3.png

tests/jointdist_comparisons/infecprob_sim4.png

tests/jointdist_comparisons/jointcomp.aux

tests/jointdist_comparisons/jointcomp.log

tests/jointdist_comparisons/jointcomp.pdf

tests/jointdist_comparisons/jointcomp.synctex.gz

tests/jointdist_comparisons/jointcomp.tex

tests/jointdist_comparisons/jointcomp_rjmcmc.R

tests/jointdist_comparisons/jointcomp_run.sh

tests/jointdist_comparisons/jointcomp_sim1.R

tests/jointdist_comparisons/jointcomp_sim1.sh

tests/jointdist_comparisons/jointcomp_sim2.R

tests/jointdist_comparisons/jointcomp_sim2.sh

tests/jointdist_comparisons/jointcomp_sim3.R

tests/jointdist_comparisons/jointcomp_sim3.sh

tests/jointdist_comparisons/jointcomp_sim4.R

tests/jointdist_comparisons/jointcomp_sim4.sh

tests/jointdist_comparisons/jointcomp_sim5.R

tests/jointdist_comparisons/jointcomp_sim5.sh

tests/jointdist_comparisons/jointcomp_sim6.R

tests/jointdist_comparisons/jointcomp_sim6.sh

tests/paramsim.R tests/pomp_comparison.R tests/pomp_intro.R

tests/profile/Rprof.out

tests/profile/augSIRprofile.out

tests/profile/augSIRprofile.pdf tests/profile/profile2.pdf

tests/results2.Rdata

tests/rjmcmc comparison/Thumbs.db

tests/rjmcmc comparison/augSIR_loglikelihood.png

tests/rjmcmc comparison/augSIR_rjmcmc_comp.png

tests/rjmcmc comparison/augSIR_trajecs.png

tests/rjmcmc comparison/rjmcmc.sh

tests/rjmcmc comparison/rjmcmc_cluster_code.R

tests/rjmcmc comparison/rjmcmc_loglikelihood.png

tests/rjmcmc comparison/rjmcmc_run.sh

tests/rjmcmc comparison/rjmcmc_trajecs.png

tests/rjmcmc_augSIR_jointcomp.R tests/rjmcmc_cluster_code.R tests/rjmcmc_comp.R tests/sample_calls.R tests/sample_calls[Conflict].R tests/sim_one_check.R tests/sim_recoveries.R tests/smallpop.R tests/testfb.R tests/testfb2.R tests/trajsim.R

fintzij/augSIR documentation built on May 16, 2019, 12:57 p.m.