Model param updates #596
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Model param updates #596
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* added python script for estimating Rt * replaced r iteration comparison script with py script * added Rt timeline plot to iteration comparison script and updated batch file * commented channels det vs no det * cleanup Rt estimation script * removed not used R files * removed rfiles from batch and shell files (commented out seroprevalence plot and fitting script) * added py epyestim script for LL data * moved argument specification to function call * updated requirements txt * bugfixes
added extract_sample_param.py
Region specific LoS in ICU (recovery_time_crit)
* reformated prevalence script and revised seroprevalence calculation * use time-varying N and shift seroprevalence by 14 days * removed prevalence calculation from emodls and added det channels to observed output for postprocessing, also return N_All * added function to calculate prevalence, seroprevalence and IFR * edited param - trajectory plotter * removed prevalence func call in load_sim_data and added back to prevalence script to allow modyfing 'ems' argument
added yaml files with mean sample parameters for testing, edited readme
updated population (IL, catchment, and EMS_1) with civis CO-EST2019-A…
…hicago into model_param_updates
activating ki_multiplier_12 with date 12/20/2020
small updates to campus model
Added negative log-likelihood assignment function
no message
bugfix on if statement when to generate postprocessing batch files
…-default yaml is used for spatial model
bugfix in overflow_probabiliies.py
…hicago into model_param_updates
Change data_comparison fields
… in IL, removed region-specificity as not required
…ugfix define d_Sym parameter
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Jan 14, 2021
…alf of d_Sym (not region specific)
…hicago into model_param_updates
…customized depending on fit
…a_comparison_spatial.py
…ion population as in main yaml
…ink to population source and recovery rate As parameter
bugfixes spatial yaml and updated readme
…hicago into model_param_updates # Conflicts: # README.md # experiment_configs/spatial_EMS_experiment.yaml
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Adding several of the model structure and parameters updates. The different parameter changes might affect each other and having the structures all implemented with the option to switch it on or off will facilitate more systematic simulations to determine the best fit and most reliable model.
new parameter in the master yaml file:
dSym_dAsP_ratioreduced_infectious_Asrecovery_time_postcritfraction_deadinstead ofcfrfraction_dead_change1- 9fraction_critical_change1- 10d_Sym_change1- 8d_Sys_incr1- 8new parameter in the spatial yaml file:
recovery_time_hosp_change1recovery_time_hosp_change_time_1