Files in cmhoove14/LEMMAABMv4
COVID ABM

.Rbuildignore

.gitignore

Analysis/Calibrate/41-Best-Replicates-Comp-Obs.html

Analysis/Calibrate/41-Best-Replicates-Comp-Obs4.html

Analysis/Calibrate/41-Best-Replicates-Comp-Obs5.html

Analysis/Calibrate/41-Best-Replicates-Comp-Obs6.html

Analysis/Calibrate/Manual_calibration_log.md

Analysis/Calibrate/b12-LHS_Array_Calibrate.sh

Analysis/Calibrate/b20-LHS_NLLs_Array.sh

Analysis/Calibrate/b24-LHS_Best_Replicate.sh

Analysis/Calibrate/b31-ABC-Sim-Sums-Array.sh

Analysis/Calibrate/b40-Replicate-Best-100.sh

Analysis/Calibrate2/Calibrate2_README

Analysis/Debug/01-Prep-Par-Inputs-Debug.R Analysis/Debug/02-Prep-Data-Inputs-Debug.R Analysis/Debug/10-Time-Run-Debug.R Analysis/Debug/ABM_V4_debug.R Analysis/SF_Synth_Pop_check.Rmd Analysis/Safegraph/Devices/SF_CTs_safegraph_devices.R Analysis/Safegraph/Devices/SF_CTs_safegraph_devices2021.R Analysis/Safegraph/Devices/SF_safegraph_devices_analyze.R Analysis/Safegraph/Devices/parse_safegraph_devices.R

Analysis/Safegraph/Devices/parse_safegraph_devices.sh

Analysis/Safegraph/Devices/parse_safegraph_devices2021.sh

Analysis/Safegraph/Movement/parse_safegraph_SF_CBGs.R

Analysis/Safegraph/Movement/parse_safegraph_SF_CBGs.sh

Analysis/Safegraph/Movement/parse_safegraph_SF_CensTracts.R

Analysis/Safegraph/Movement/parse_safegraph_SF_CensTracts.sh

Analysis/Safegraph/Movement/parse_safegraph_SF_CensTracts2021.sh

Analysis/Safegraph/Movement/safegraph_cbg_mvmt_process.R Analysis/Safegraph/Movement/safegraph_ct_mvmt_process.R Analysis/Safegraph/Visitors/process_sf_CT_visitors.R Analysis/Safegraph/Visitors/process_sf_CT_visitors2021.R Analysis/Safegraph/Visitors/process_sf_visitors.R Analysis/Safegraph/Visitors/safegraph_sf_visitors.R

Analysis/Safegraph/Visitors/sf_visitors.sh

Analysis/Safegraph/Visitors/sf_visitors2021.sh

Analysis/Validate/01-Prep-Par-Inputs-Validate.R Analysis/Validate/02-Prep-Data-Inputs-Validate.R Analysis/Validate/10-Validation-Runs.R Analysis/Validate/20-Plot-Validation-Sims.R

Analysis/Validate/b10-Validation-Runs.sh

Analysis/Vax_Scenarios/00-Vax-Scenarios-Prep.R Analysis/Vax_Scenarios/01-Prep-Par-Inputs-Vax-Scenarios.R Analysis/Vax_Scenarios/10-Vaccination-Runs.R Analysis/Vax_Scenarios/20-Plot-Vax-Sims.R Analysis/Vax_Scenarios/Vax_Scenarios_Report.Rmd

Analysis/Vax_Scenarios/b10-Vaccination-Runs.sh

Analysis/synthetic-pop.R

DESCRIPTION

LEMMAABMv4.Rproj

LICENSE

NAMESPACE

Plots/Hosps_CalVal.jpg

Plots/Hosps_CalVal2.jpg

Plots/Hosps_CalVal3.jpg

Plots/Init_Calibrate_Best_Hosps.jpg

Plots/Init_Calibrate_ConfCases.jpg

Plots/Init_Calibrate_Hosps.jpg

Plots/Init_Calibrate_Hosps_beta01.jpg

Plots/Init_Calibrate_Hosps_beta02.jpg

Plots/Inputs/expected_infected_visitors_by_hpi_quartile.jpg

Plots/Inputs/hpi_Jan2021_cum_prev_rate_corr.jpg

Plots/Inputs/safegraph_percent_home_work_behavior.jpg

Plots/LHS_Calibration/Fits1/Outcome_Zs_PRCC.jpg

Plots/LHS_Calibration/Fits1/Outcome_fits_PRCC.jpg

Plots/LHS_Calibration/Fits1/best10_confirmed.jpg

Plots/LHS_Calibration/Fits1/best10_test_pct.jpg

Plots/LHS_Calibration/Fits1/case_race_fit_scatter.jpg

Plots/LHS_Calibration/Fits1/case_race_sims_best.jpg

Plots/LHS_Calibration/Fits1/case_race_z_scatter.jpg

Plots/LHS_Calibration/Fits1/ct_case_fit_scatter.jpg

Plots/LHS_Calibration/Fits1/ct_case_z_scatter.jpg

Plots/LHS_Calibration/Fits1/ct_cases_sims_best.jpg

Plots/LHS_Calibration/Fits1/dths_fit_scatter.jpg

Plots/LHS_Calibration/Fits1/dths_race_fit_scatter.jpg

Plots/LHS_Calibration/Fits1/dths_race_sims_best.jpg

Plots/LHS_Calibration/Fits1/dths_race_z_scatter.jpg

Plots/LHS_Calibration/Fits1/dths_sims_best.jpg

Plots/LHS_Calibration/Fits1/dths_z_scatter.jpg

Plots/LHS_Calibration/Fits1/hosp_sims_best.jpg

Plots/LHS_Calibration/Fits1/hosp_z_scatter.jpg

Plots/LHS_Calibration/Fits1/replicate_best_dths_10x.jpg

Plots/LHS_Calibration/Fits1/replicate_best_hosp_10x.jpg

Plots/LHS_Calibration/Fits2/Outcome_fits_PRCC.jpg

Plots/LHS_Calibration/Fits2/best10_confirmed.jpg

Plots/LHS_Calibration/Fits2/best10_test_pct.jpg

Plots/LHS_Calibration/Fits2/case_race_fit_scatter.jpg

Plots/LHS_Calibration/Fits2/case_race_sims_best.jpg

Plots/LHS_Calibration/Fits2/ct_case_fit_scatter.jpg

Plots/LHS_Calibration/Fits2/ct_cases_sims_best.jpg

Plots/LHS_Calibration/Fits2/dths_fit_scatter.jpg

Plots/LHS_Calibration/Fits2/dths_race_fit_scatter.jpg

Plots/LHS_Calibration/Fits2/dths_race_sims_best.jpg

Plots/LHS_Calibration/Fits2/dths_sims_best.jpg

Plots/LHS_Calibration/Fits2/first_wave_hosp.jpg

Plots/LHS_Calibration/Fits2/hosp_nll_scatter.jpg

Plots/LHS_Calibration/Fits2/hosp_sims_best.jpg

Plots/LHS_Calibration/Fits2/second_wave_hosp.jpg

Plots/LHS_Calibration/Fits_grizzlybear/Best_Fit2021-02-08Cases_race.jpg

Plots/LHS_Calibration/Fits_grizzlybear/Best_Fit2021-02-08Deaths.jpg

Plots/LHS_Calibration/Fits_grizzlybear/Best_Fit2021-02-08Deaths_race.jpg

Plots/LHS_Calibration/Fits_grizzlybear/Best_Fit2021-02-08Hospitalizations.jpg

Plots/Vax_Scenarios/vax_scenarios_short_hospitalizations.jpg

Plots/q_beta_red_multiplier_plot.jpg

R/ABMv4_contact.R R/ABMv4_debug.R R/ABMv4_fin.R R/Infection_Functions.R R/LEMMAABMv4-package.R R/Network_Mvmt_Functions.R R/RcppExports.R R/Testing_Functions.R R/Utils.R README.md

bash/Dec_Start_calibrate_bta.sh

bash/Dec_Start_vax65pS.sh

bash/Dec_Start_vaxessA.sh

bash/Dec_Start_vaxessS.sh

bash/Dec_Start_vaxgeoA.sh

bash/LHS_Calibration_Wynton/LHS2_NLLs_Array.sh

bash/LHS_Calibration_Wynton/LHS_Array_Calibrate2.sh

bash/LHS_Calibration_Wynton/LHS_Fits_Array.sh

bash/LHS_Calibration_Wynton/Same_Pars_100_runs.sh

bash/LHS_Calibration_Wynton/Short_30_runs.sh

bash/calibrate_bta01_04_sip01.sh

bash/calibrate_bta01_04_sip02.sh

bash/calibrate_bta01_04_sip025.sh

bash/calibrate_bta01_04_sip033.sh

bash/calibrate_bta01_04_sip05.sh

data/get/COVID_CA_get_latest.R data/get/Get_CA_HPI.R data/get/Get_PLACES.R data/get/Get_SF_geos.R

data/get/got/CA_SF_data2021-02-10.Rdata

data/get/got/CA_SF_data2021-02-16.Rdata

data/outputs/Test_Run_bta0.25_2021-01-29.rds

data/processed/Calibration_LHS.rds

data/processed/Calibration_LHS2_Wynton.rds

data/processed/Calibration_LHS_Wynton.rds

data/processed/LHS_Fits1_summary.rds

data/processed/SF_HPI.rds

data/processed/SF_PLACES.rds

data/processed/SF_agents_processed.rds

data/processed/SF_all_geos_sf.rds

data/processed/SF_cts_sf.rds

data/processed/Safegraph/SFCensTractsMvmt2020-01-01to2020-12-31.rds

data/processed/Safegraph/SFCensTractsMvmt2021-01-01to2021-02-13.rds

data/processed/Safegraph/SF_CTs_devices_sum2020-01-01to2020-12-31.rds

data/processed/Safegraph/SF_Visitors2020-01-01to2020-12-31.rds

data/processed/Safegraph/SF_Visitors2021-01-01to2021-02-13.rds

data/processed/Safegraph/SF_devices_sum2020-01-01to2020-12-31.rds

data/processed/Safegraph/SF_devices_sum2021-01-01to2021-02-13.rds

data/processed/Safegraph/SF_visitors_CTs_2020Processed.rds

data/processed/Safegraph/SF_visitors_CTs_2021Processed.rds

data/processed/Safegraph/safegraph_ct_mvmt_cdf_list_2020processed.rds

data/processed/Safegraph/safegraph_ct_mvmt_cdf_list_2021processed.rds

data/processed/Safegraph/sfgrph_devices_pct_home_cts_2020.rds

data/processed/Safegraph/sfgrph_devices_pct_home_cts_2021.rds

data/processed/data_inputs.rds

data/processed/data_inputs2020-12-15.rds

data/processed/data_inputs_Dec_Start.rds

data/processed/data_inputs_calibrate.rds

data/processed/data_inputs_debug.rds

data/processed/data_inputs_forecast_opt.rds

data/processed/data_inputs_forecast_pes.rds

data/processed/data_inputs_validate.rds

data/processed/input_pars.rds

data/processed/input_pars_Dec_start.rds

data/processed/input_pars_calibrate.rds

data/processed/input_pars_debug.rds

data/processed/input_pars_validate.rds

data/processed/input_pars_vax.rds

data/processed/obs_summaries_for_ABC.Rdata

data/processed/sim_summaries_for_ABC.rds

data/processed/vax65p_scenario.rds

data/processed/vax_forecast_opt.rds

data/processed/vax_forecast_pes.rds

data/processed/vax_scenarios_short.Rdata

data/processed/vaxessA_scenario.rds

data/processed/vaxessS_scenario.rds

data/processed/vaxgeoA_scenario.rds

man/GetCTVisit.Rd man/GetCTVisit_cpp.Rd man/adapt_site_fx.Rd man/covid_abm_v4.Rd man/covid_abm_v4_contact.Rd man/covid_abm_v4_debug.Rd man/foi_infect.Rd man/get_contacts.Rd man/grapes-not-in-grapes.Rd man/next_state.Rd man/other_location.Rd man/p_mort.Rd man/p_sevsymp.Rd man/p_symp.Rd man/q_prob_fx.Rd man/sac_location.Rd man/scl_wrk_loc.Rd man/sum.inf.Rd man/t_asymp.Rd man/t_latent.Rd man/t_msymp.Rd man/t_mtosev.Rd man/t_presymp.Rd man/t_sevsymp.Rd man/t_til_nxt.Rd man/test_probs_fx.Rd man/test_probs_pub_fx.Rd man/test_probs_pvt_fx.Rd man/tests0.Rd man/unpack_list.Rd man/visitors_to_agents.Rd man/worker_location.Rd

src/C_funx.cpp

src/C_funx.o

src/LEMMAABMv4.so

src/Makevars

src/RcppExports.cpp

src/RcppExports.o

cmhoove14/LEMMAABMv4 documentation built on Nov. 1, 2021, 10:23 p.m.

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cmhoove14/LEMMAABMv4
COVID ABM

Files in cmhoove14/LEMMAABMv4
COVID ABM

R Package Documentation

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cmhoove14/LEMMAABMv4 COVID ABM

Files in cmhoove14/LEMMAABMv4 COVID ABM

R Package Documentation

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cmhoove14/LEMMAABMv4
COVID ABM

Files in cmhoove14/LEMMAABMv4
COVID ABM