├── .gitignore ├── R ├── makeFigure1_data.R ├── makeFigure3_results.R ├── makeFigure4_infections.R ├── makeFigure5_datasources.R ├── makeFigureS1_distributions.R ├── makeFigureS2_varyingdists.R ├── makeFigureS5_separateseries.R ├── makeFigureS9TableS9_MCMC.R ├── makeTable1_params.R ├── processNZData.R ├── supportLoadOutputs.R ├── updatedFigure3.R ├── updatedTable1.R ├── utilCheckPMHH.R ├── utilCheckPMMHCasesOnly.R ├── utilCheckPMMHWastewaterOnly.R └── utilPlotFilterResults.R ├── data ├── README.md ├── borderWorkerInfections.csv ├── cases.csv ├── dist_esr_onset.csv ├── dist_ww_shedding.csv ├── raw │ ├── covid-case-counts-moh.csv │ ├── sites.csv │ ├── ww_data_all.csv │ └── ww_national.csv └── wastewater.csv ├── outputs ├── curvewiseests │ ├── Feb2022PeakR_final_curvewise 2.txt │ ├── Feb2022PeakR_final_curvewise.txt │ └── July2022PeakCases_final_curvewise.txt ├── filter │ ├── example.csv │ └── example_rawdata.csv ├── fullposterior │ ├── casesonly.csv │ ├── casesonly_rawdata.csv │ ├── final.csv │ ├── final_alpha2e9.csv │ ├── final_alpha2e9_rawdata.csv │ ├── final_alpha4e9.csv │ ├── final_alpha4e9_rawdata.csv │ ├── final_earlyreporting.csv │ ├── final_earlyreporting_rawdata.csv │ ├── final_earlyshedding.csv │ ├── final_earlyshedding_rawdata.csv │ ├── final_fastgentime.csv │ ├── final_fastgentime_rawdata.csv │ ├── final_latereporting.csv │ ├── final_latereporting_rawdata.csv │ ├── final_lateshedding.csv │ ├── final_lateshedding_rawdata.csv │ ├── final_rawdata.csv │ ├── final_slowgentime.csv │ ├── final_slowgentime_rawdata.csv │ ├── updates.csv │ ├── updates_rawdata.csv │ ├── wastewateronly.csv │ └── wastewateronly_rawdata.csv ├── pmmh.nosync │ └── final │ │ ├── final_diagnostics │ │ ├── period1.txt │ │ ├── period1_pairs.png │ │ └── period1_trace.png │ │ ├── final_period1_chainno1_acceptanceprobs.csv │ │ ├── final_period1_chainno1_allparamlogliks.csv │ │ ├── final_period1_chainno1_logliks.csv │ │ ├── final_period1_chainno1_retainedparams.csv │ │ ├── final_period1_chainno2_acceptanceprobs.csv │ │ ├── final_period1_chainno2_allparamlogliks.csv │ │ ├── final_period1_chainno2_logliks.csv │ │ ├── final_period1_chainno2_retainedparams.csv │ │ ├── final_period1_chainno3_acceptanceprobs.csv │ │ ├── final_period1_chainno3_allparamlogliks.csv │ │ ├── final_period1_chainno3_logliks.csv │ │ ├── final_period1_chainno3_retainedparams.csv │ │ ├── final_period1_chainno4_acceptanceprobs.csv │ │ ├── final_period1_chainno4_allparamlogliks.csv │ │ ├── final_period1_chainno4_logliks.csv │ │ ├── final_period1_chainno4_retainedparams.csv │ │ ├── final_period1_chainno5_acceptanceprobs.csv │ │ ├── final_period1_chainno5_allparamlogliks.csv │ │ ├── final_period1_chainno5_logliks.csv │ │ ├── final_period1_chainno5_retainedparams.csv │ │ ├── final_period1_chainno6_acceptanceprobs.csv │ │ ├── final_period1_chainno6_allparamlogliks.csv │ │ ├── final_period1_chainno6_logliks.csv │ │ ├── final_period1_chainno6_retainedparams.csv │ │ ├── final_period1_chainno7_acceptanceprobs.csv │ │ ├── final_period1_chainno7_allparamlogliks.csv │ │ ├── final_period1_chainno7_logliks.csv │ │ ├── final_period1_chainno7_retainedparams.csv │ │ ├── final_period1_chainno8_acceptanceprobs.csv │ │ ├── final_period1_chainno8_allparamlogliks.csv │ │ ├── final_period1_chainno8_logliks.csv │ │ ├── final_period1_chainno8_retainedparams.csv │ │ ├── final_period1_mmhopts.json │ │ ├── final_period2_chainno1_acceptanceprobs.csv │ │ ├── final_period2_chainno1_allparamlogliks.csv │ │ ├── final_period2_chainno1_logliks.csv │ │ ├── final_period2_chainno1_retainedparams.csv │ │ ├── final_period2_chainno2_acceptanceprobs.csv │ │ ├── final_period2_chainno2_allparamlogliks.csv │ │ ├── final_period2_chainno2_logliks.csv │ │ ├── final_period2_chainno2_retainedparams.csv │ │ ├── final_period2_chainno3_acceptanceprobs.csv │ │ ├── final_period2_chainno3_allparamlogliks.csv │ │ ├── final_period2_chainno3_logliks.csv │ │ ├── final_period2_chainno3_retainedparams.csv │ │ ├── final_period2_chainno4_acceptanceprobs.csv │ │ ├── final_period2_chainno4_allparamlogliks.csv │ │ ├── final_period2_chainno4_logliks.csv │ │ ├── final_period2_chainno4_retainedparams.csv │ │ ├── final_period2_chainno5_acceptanceprobs.csv │ │ ├── final_period2_chainno5_allparamlogliks.csv │ │ ├── final_period2_chainno5_logliks.csv │ │ ├── final_period2_chainno5_retainedparams.csv │ │ ├── final_period2_chainno6_acceptanceprobs.csv │ │ ├── final_period2_chainno6_allparamlogliks.csv │ │ ├── final_period2_chainno6_logliks.csv │ │ ├── final_period2_chainno6_retainedparams.csv │ │ ├── final_period2_chainno7_acceptanceprobs.csv │ │ ├── final_period2_chainno7_allparamlogliks.csv │ │ ├── final_period2_chainno7_logliks.csv │ │ ├── final_period2_chainno7_retainedparams.csv │ │ ├── final_period2_chainno8_acceptanceprobs.csv │ │ ├── final_period2_chainno8_allparamlogliks.csv │ │ ├── final_period2_chainno8_logliks.csv │ │ ├── final_period2_chainno8_retainedparams.csv │ │ ├── final_period2_mmhopts.json │ │ ├── final_period3_chainno1_acceptanceprobs.csv │ │ ├── final_period3_chainno1_allparamlogliks.csv │ │ ├── final_period3_chainno1_logliks.csv │ │ ├── final_period3_chainno1_retainedparams.csv │ │ ├── final_period3_chainno2_acceptanceprobs.csv │ │ ├── final_period3_chainno2_allparamlogliks.csv │ │ ├── final_period3_chainno2_logliks.csv │ │ ├── final_period3_chainno2_retainedparams.csv │ │ ├── final_period3_chainno3_acceptanceprobs.csv │ │ ├── final_period3_chainno3_allparamlogliks.csv │ │ ├── final_period3_chainno3_logliks.csv │ │ ├── final_period3_chainno3_retainedparams.csv │ │ ├── final_period3_chainno4_acceptanceprobs.csv │ │ ├── final_period3_chainno4_allparamlogliks.csv │ │ ├── final_period3_chainno4_logliks.csv │ │ ├── final_period3_chainno4_retainedparams.csv │ │ ├── final_period3_chainno5_acceptanceprobs.csv │ │ ├── final_period3_chainno5_allparamlogliks.csv │ │ ├── final_period3_chainno5_logliks.csv │ │ ├── final_period3_chainno5_retainedparams.csv │ │ ├── final_period3_chainno6_acceptanceprobs.csv │ │ ├── final_period3_chainno6_allparamlogliks.csv │ │ ├── final_period3_chainno6_logliks.csv │ │ ├── final_period3_chainno6_retainedparams.csv │ │ ├── final_period3_chainno7_acceptanceprobs.csv │ │ ├── final_period3_chainno7_allparamlogliks.csv │ │ ├── final_period3_chainno7_logliks.csv │ │ ├── final_period3_chainno7_retainedparams.csv │ │ ├── final_period3_chainno8_acceptanceprobs.csv │ │ ├── final_period3_chainno8_allparamlogliks.csv │ │ ├── final_period3_chainno8_logliks.csv │ │ ├── final_period3_chainno8_retainedparams.csv │ │ ├── final_period3_mmhopts.json │ │ ├── final_period4_chainno1_acceptanceprobs.csv │ │ ├── final_period4_chainno1_allparamlogliks.csv │ │ ├── final_period4_chainno1_logliks.csv │ │ ├── final_period4_chainno1_retainedparams.csv │ │ ├── final_period4_chainno2_acceptanceprobs.csv │ │ ├── final_period4_chainno2_allparamlogliks.csv │ │ ├── final_period4_chainno2_logliks.csv │ │ ├── final_period4_chainno2_retainedparams.csv │ │ ├── final_period4_chainno3_acceptanceprobs.csv │ │ ├── final_period4_chainno3_allparamlogliks.csv │ │ ├── final_period4_chainno3_logliks.csv │ │ ├── final_period4_chainno3_retainedparams.csv │ │ ├── final_period4_chainno4_acceptanceprobs.csv │ │ ├── final_period4_chainno4_allparamlogliks.csv │ │ ├── final_period4_chainno4_logliks.csv │ │ ├── final_period4_chainno4_retainedparams.csv │ │ ├── final_period4_chainno5_acceptanceprobs.csv │ │ ├── final_period4_chainno5_allparamlogliks.csv │ │ ├── final_period4_chainno5_logliks.csv │ │ ├── final_period4_chainno5_retainedparams.csv │ │ ├── final_period4_chainno6_acceptanceprobs.csv │ │ ├── final_period4_chainno6_allparamlogliks.csv │ │ ├── final_period4_chainno6_logliks.csv │ │ ├── final_period4_chainno6_retainedparams.csv │ │ ├── final_period4_chainno7_acceptanceprobs.csv │ │ ├── final_period4_chainno7_allparamlogliks.csv │ │ ├── final_period4_chainno7_logliks.csv │ │ ├── final_period4_chainno7_retainedparams.csv │ │ ├── final_period4_chainno8_acceptanceprobs.csv │ │ ├── final_period4_chainno8_allparamlogliks.csv │ │ ├── final_period4_chainno8_logliks.csv │ │ ├── final_period4_chainno8_retainedparams.csv │ │ ├── final_period4_mmhopts.json │ │ ├── final_period5_chainno1_acceptanceprobs.csv │ │ ├── final_period5_chainno1_allparamlogliks.csv │ │ ├── final_period5_chainno1_logliks.csv │ │ ├── final_period5_chainno1_retainedparams.csv │ │ ├── final_period5_chainno2_acceptanceprobs.csv │ │ ├── final_period5_chainno2_allparamlogliks.csv │ │ ├── final_period5_chainno2_logliks.csv │ │ ├── final_period5_chainno2_retainedparams.csv │ │ ├── final_period5_chainno3_acceptanceprobs.csv │ │ ├── final_period5_chainno3_allparamlogliks.csv │ │ ├── final_period5_chainno3_logliks.csv │ │ ├── final_period5_chainno3_retainedparams.csv │ │ ├── final_period5_chainno4_acceptanceprobs.csv │ │ ├── final_period5_chainno4_allparamlogliks.csv │ │ ├── final_period5_chainno4_logliks.csv │ │ ├── final_period5_chainno4_retainedparams.csv │ │ ├── final_period5_chainno5_acceptanceprobs.csv │ │ ├── final_period5_chainno5_allparamlogliks.csv │ │ ├── final_period5_chainno5_logliks.csv │ │ ├── final_period5_chainno5_retainedparams.csv │ │ ├── final_period5_chainno6_acceptanceprobs.csv │ │ ├── final_period5_chainno6_allparamlogliks.csv │ │ ├── final_period5_chainno6_logliks.csv │ │ ├── final_period5_chainno6_retainedparams.csv │ │ ├── final_period5_chainno7_acceptanceprobs.csv │ │ ├── final_period5_chainno7_allparamlogliks.csv │ │ ├── final_period5_chainno7_logliks.csv │ │ ├── final_period5_chainno7_retainedparams.csv │ │ ├── final_period5_chainno8_acceptanceprobs.csv │ │ ├── final_period5_chainno8_allparamlogliks.csv │ │ ├── final_period5_chainno8_logliks.csv │ │ ├── final_period5_chainno8_retainedparams.csv │ │ └── final_period5_mmhopts.json ├── results │ ├── SuppFig_5.png │ ├── figure1_data.png │ ├── figure3_results.png │ ├── figure4_infections.png │ ├── figureMCMC_period1_pairs.png │ ├── figureMCMC_period1_trace.png │ ├── figureMCMC_period2_pairs.png │ ├── figureMCMC_period2_trace.png │ ├── figureMCMC_period3_pairs.png │ ├── figureMCMC_period3_trace.png │ ├── figureMCMC_period4_pairs.png │ ├── figureMCMC_period4_trace.png │ ├── figureMCMC_period5_pairs.png │ ├── figureMCMC_period5_trace.png │ ├── figureS1_distributions.png │ ├── figureS2_gentime.png │ ├── figureS2_reporting.png │ ├── figureS2_shedding.png │ ├── misc │ │ ├── genTimeDist.csv │ │ ├── infToRepDist.csv │ │ └── infToShedDist.csv │ ├── modeldiagram.pptx │ ├── table1_params_final.csv │ ├── tableMCMC_period1.csv │ ├── tableMCMC_period2.csv │ ├── tableMCMC_period3.csv │ ├── tableMCMC_period4.csv │ └── tableMCMC_period5.csv └── updates │ ├── 2023only.png │ ├── fullseries.png │ ├── parametertable.csv │ ├── parametertableformatted.png │ └── readme.md ├── readme.md ├── resultsCurvewiseEsts.jl ├── resultsFullPosterior.jl ├── resultsFullPosteriorUpdated.jl ├── resultsOtherText.jl ├── resultsPMMH.jl ├── resultsTestingShifts.jl ├── runFilterExample.jl ├── runPMMHExample.jl ├── src ├── PMMH.jl ├── covidParticleFilter.jl ├── covidParticleFilterWithCumulativeInfections.jl ├── estimateLikelihoods.jl ├── getOpts.jl ├── loadNZData.jl ├── predictObservations.jl ├── processPMMHResults.jl ├── processResults.jl ├── runCurvewiseEstimates.jl ├── runFullPosterior.jl └── supportFuncs.jl └── usefulscripts ├── choosingPriors.jl ├── installPackages.jl ├── likelihoodHeatmaps.jl └── misc.jl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nicsteyn2/NZWastewaterModelling/HEAD/.gitignore -------------------------------------------------------------------------------- /R/makeFigure1_data.R: -------------------------------------------------------------------------------- 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