Files in bbolker/McMasterPandemic
Pandemic Model

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CONTRIBUTING.md ChangeLog.md

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NAMESPACE

R/afuns.R R/ageify.R R/avail_for.R R/calibrate.R R/constructing_vectors.R R/data.R R/expandify.R R/flexmodel_calibrate.R R/flexmodel_convert.R R/flexmodel_parameters.R R/flexmodel_simulate.R R/flexstruc.R R/getters_for_devs.R R/globals.R R/impsamp.R R/kfuns.R R/methods.R R/models.R R/models_IP.R R/names_and_strings.R R/opt_info.R R/pkgname.R R/sim_funs.R R/specs.R R/structure.R R/testify.R R/tmb.R R/tmb_indices.R R/tmbutils.R R/topological_sort.R R/utils.R R/zzz.R README.md ROADMAP.md TODO.md

assets/architecture.drawio

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data/ONcalib.rda

data/ONcalib_2brks.rda

data/ONcalib_mob1_2020Jun01.rda

data/ONdata_2020Jun01.rda

data/mobility_comb.rda

dockerfile

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docs/articles/calibration.html

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dottarget.mk

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notes/indexing/tmb_data_struct.md notes/indexing/tmb_data_struct_v2.md notes/indexing/utilities.R notes/indexing/vaccine_model_structure.R notes/indexing/vax.md notes/indexing/vax_model_from_irena.R notes/loglin_spatial.R notes/ltcf.Rmd notes/midas_estimates.R notes/mlefit.R notes/nested_testify.R notes/ode.R

notes/outputs/testing_distrib.html

notes/phac_handover.md notes/pkg_versions.R notes/plot_caltest.R

notes/random.csv

notes/ratemat_vis.Rmd notes/refactor/refactor.Rmd

notes/refactor/refactor.bib

notes/refactor/refactor.pdf notes/reimplementation.md notes/renewal.md notes/run_DEoptim.R notes/run_caltest.R notes/run_caltest_1break.R notes/run_params_breaks.R notes/run_params_breaks_DE.R notes/run_params_mobility_DE.R notes/run_params_nobreak.R notes/selection_coefficient.rmd notes/sharcnet_kickoff.md

notes/sim_funs.cpp

notes/sim_funs_cpp.md notes/simcalib_plot.R notes/simcalib_tidy.R notes/simple.R notes/simple_spline_sim.R notes/simplify_macpan.md notes/simplots.R

notes/slow.csv

notes/sparse_benchmark.R

notes/spline.csv

notes/spline_calib.R notes/spline_compare.R notes/spline_fit.R notes/spline_fitplots.R notes/spline_forecast.R notes/spline_forecast_plot.R notes/spline_plots.R notes/spline_projection1.R notes/spline_projection2.R notes/spline_recalib.R notes/spline_recalib_compare.R notes/spline_shape_calib.R notes/spline_sim.R notes/spline_test_macpan.R notes/stable_tmb.md

notes/steve_TMB_do_step.cpp

notes/steve_test_TMB.R notes/stoch_forecasts.R notes/structure.md

notes/symptomatic.csv

notes/test.log

notes/test_TMB.R notes/test_calibration.R notes/test_calibreaks.R notes/test_exp.R notes/test_hosp.R notes/test_pps.R notes/test_sir.R notes/testify_calibration.R notes/testify_check.R notes/testify_funs.R notes/testify_makesim.R notes/testify_sim.R notes/testify_simreportplot.R notes/testify_testcatplot.R notes/testing.md notes/testing_distrib.Rmd notes/testing_flow.md notes/testing_flow_graph.R notes/testsim.R notes/testwt_N.R notes/time_series.Rmd notes/vacc_test.R notes/weekly_calibrations_work.md

ontario/.gitignore

ontario/Makefile

ontario/McMasterReport.Rnw

ontario/ON_june1.R ontario/ONepigrowthfit.R ontario/Ontario_Mobility.R ontario/Ontario_PH.R ontario/Ontario_calibration_setup.R ontario/Ontario_calibration_setup_nomake.R ontario/Ontario_current.R ontario/Ontario_splines.R ontario/README.md ontario/batchtools.R ontario/codegraph.R ontario/collect_spline_factorial.R ontario/comb_calib.R ontario/compare_calib.R ontario/de_pop.R ontario/epiestim.R ontario/epiestim_plot.R ontario/example.rmd ontario/git_push/example.pdf

ontario/git_push/ont_cal_factorial.RData

ontario/git_push/ont_cal_factorial_plot.Rout.pdf ontario/git_push/plot_spline_factorial.Rout.pdf ontario/mobility.R

ontario/nlipreamble.tex

ontario/ont_cal.R ontario/ont_cal_1brks.R ontario/ont_cal_2brks.R ontario/ont_cal_2brks_ndt.R ontario/ont_cal_H.R ontario/ont_cal_HD_2brks.R ontario/ont_cal_factorial.R ontario/ont_cal_factorial_plots.R ontario/ont_cal_factorial_plots.Rmd ontario/ont_cal_forecast.R ontario/ont_cal_mob1.R ontario/ont_cal_mob1_HD.R ontario/ont_cal_noICU.R ontario/ont_cal_noICU_1brks.R ontario/ont_cal_noICU_2brks.R ontario/ont_cal_noICU_2brks_prior.R ontario/ont_cal_spline1.R ontario/ont_cal_splinecomp.R ontario/ont_cal_splinecomp_plots.R ontario/ont_cal_splinemob1.R ontario/ont_cal_zeta.R ontario/ont_keep.R ontario/ont_single_var.R ontario/ont_spline_factorial.R ontario/ontario_ICU.Rmd ontario/ontario_calibration_report.Rmd ontario/ontario_clean.R ontario/ontario_de_cal.R ontario/ontario_nbfit.R ontario/ontario_quadmod.R ontario/plot_spline_factorial.R ontario/reference_mod_forecast.R refactor/benchmark_inplace.R refactor/coverage/coverage.R refactor/dependencies/dependency_visualization.R refactor/dependencies/function_locations.R refactor/hpc/comparison.R

refactor/hpc/setup.sh

refactor/no-anydate/find_dates.R refactor/optimization_ideas.md refactor/profiling/benchmark_sweep.R refactor/profiling/profvis_everything.R refactor/profiling/profvis_grepl.R refactor/profiling/profvis_specifics.R refactor/profiling/test.R refactor/test-autotest.R rename.md

sandbox/ON.short.breaks.RDS

sandbox/ON.short.spline.RDS

sandbox/ageify_workshop.R sandbox/break_tests.R

sandbox/calibrate_gif/animation.gif

sandbox/calibrate_gif/sims.R sandbox/calibrate_timeargs_reprex.R

sandbox/calibration_2021-06-18_ON.RDS

sandbox/demo_vaccination_switch.R sandbox/do_make_state_segfault.R sandbox/fix_stored_plot.R sandbox/forecast2.R sandbox/jaggy.R sandbox/kernel_test.R sandbox/odin.R

sandbox/ontario_vaccine.RDS

sandbox/ontario_vaccine_plot.R sandbox/reprex_flex_timevar_backcompatibility.R sandbox/run_sim_mre.R sandbox/run_sim_mre_tmb.R sandbox/sample_vaxify_sim.R sandbox/santaclara_ex.R

sandbox/sim.RData

sandbox/spline_tests.R sandbox/test_mob_breaks.R sandbox/threedosewane.R sandbox/time_varying_mre.R sandbox/time_varying_run_sim.R sandbox/tmb-sandbox/debug_stuff.R sandbox/tmb-sandbox/mre_tmb_obj_fun_nans.R sandbox/tmb-sandbox/opt_params_tmb.R sandbox/tmb-sandbox/tmb-condense-to-tmb.R sandbox/tmb_forecast.R sandbox/variant_demo.R sandbox/vaxify_demo.R sandbox/visNetwork.R

sandbox/yukon/PHAC_Yukon_brian.csv

sandbox/yukon/new_yukon/animation.gif

sandbox/yukon/new_yukon/fitted.mod.rda

sandbox/yukon/new_yukon/report_data_yukon_h_and_i.csv

sandbox/yukon/new_yukon/yukon_steve_lisa_works_reports_hosp_forecast.R

sandbox/yukon/report_data_yukon.csv

sandbox/yukon/report_data_yukon_h_and_i-1.csv

sandbox/yukon/report_data_yukon_h_and_i.csv

sandbox/yukon/report_data_yukon_hosp.csv

sandbox/yukon/yukon.R sandbox/yukon/yukon_steve_lisa.R sandbox/yukon/yukon_steve_lisa_forecast_V2.R

src/McMasterPandemic.cpp

vignettes/getting_started.Rnw

vignettes/model.rmd

vignettes/nlipreamble.tex

vignettes/testing_flow.rmd vignettes/vaxify_implementation.Rmd

weekly_calibrations/ONcalib_2021Aug02.rda

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bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.

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