institutefordiseasemodeling / covid-health-systems Goto Github PK

These should all be non-zero and the number in the Q should be multiplied by the epi curve adjustment rate.

Currently, the default export path is

C:\Users\Brittany\Google Drive\COVID-19

Suggested:

c:\Users\public\Documents

List 3rd party licenses

See picture. Suggested addition to text: Something like

On initially installing Simul8 professional, the software will walk you through a tutorial. You may need to open and close the program a couple of times to avoid seeing these:

In the README.md file:

Next, you will need to download the model itself. You can access this from the GitHub repository here:

____________________________________. You will want to download the entire package and save into a convenient location on your computer. Leave all of the files in one folder location, so that when you export your results files from the model after it has run, they will be automatically available to the R script for analysis.

Anyone reading the readme has already found the repository.

When attempting to run with "Unlimited Beds", I get this message:

Simulation Object Data Item (gv ARef) not set
SET gv ARef.Replication = lv Replications
View this Visual Logic now?

If you choose "Ignore", every VL expression using gv ARef.<property> will raise this dialog.

Here is the Information Store

Button,
Current Work Item,0
Day Duration,1440
Graph Sync Interval,10800
LOOP I,2
LOOP J,8
Overhead Cost,0
Overhead Revenue,0
Results Collection Period,120960
ResultsFolder,..\..\output
ResultsName,DemoModelRun1
Simulation Time,0
TRACKER OPEN,1
TRACKER RUN,0
TRACKER RUNNING_SCENARIOS,Yes
TRACKER SCENARIOSET,1
TRACKER TOTALRUNSMAX,30
TRACKER TRIAL,1
Warm Up Period,0
gv ARef,
gv ARef2,H10 ICU
gv BalkDuration,24
gv Cap1,1
gv Cap2,0
gv Cap3,1
gv Cap4,0
gv DayNum,0
gv Epi Curve,4
gv Epi1,0
gv Epi2,1
gv Epi3,1
gv Epi4,0
gv Epi5,0
gv ICU Mortality,0.29
gv ICU Q Tolerance,6
gv KillSwitch,0
gv MaxQSize,600
gv Num ICUeligible,0
gv Num NonICU eligible,0
gv NumHospitals,10
gv NumTrials,5
gv Portion ICU,0.5
gv QRef,Q H10
gv QRef2,Q ICU10
gv Select RunSweep,No
gv SelectCapacity,1
gv SelectCrowding,1
gv SelectICU,5
gv SelectICUMort,1
gv SelectNursingLoss,2
gv SelectReferralTriage,4
gv SelectTriage,4
gv SelectWeeksOptions,1
gv SimWeeks,12
gv StartCount,2
gv StartRow,2
gv SweepPop,100000
gv TurnedAway,24
gv Unlimited,1
gv WeekNum,0

In the Simul8 model, under setting, the 'Current covid census' button is only available when you click run with limited beds. Need to add under run with unlimited beds as well.

I attempted to run the script without changing anything (under the assumption that DEMOMODELRUN1 was the default project name I saved), and got several errors on running the script.

NOTE: This was my first time installing R and RStudio on this client, so maybe a rerun will work...

First error was here

> #Load CSVs
> ASSUMPTIONS <- read.csv(paste("SS_R_TRIAL_ASSUMPTIONS_TRACKER_",INPUTSET,".csv",sep=""))
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'SS_R_TRIAL_ASSUMPTIONS_TRACKER_DEMOMODELRUN1.csv': No such file or directory

I did find this file in the same folder:

MODELSS_R_TRIAL_ASSUMPTIONS_TRACKER_DEMOMODELRUN1.csv

Which is clearly the right one...

The pre-loaded defaults are for a single hospital but "reset defaults" does not address this. It needs to

• reset hospital sheet
• reset threshold values
• clear inpatient census sheet

Change to mean with variation parameter with long tail (weibull?)

Currently, the docs suggest copying a file path from windows explorer for your export path.

If you do that and copy this path (for example):

C:\GitHub\covid-health-systems\model

You get the unexpected result of your model being exported here:

C:\GitHub\covid-health-systems

Suggested: Either enforce this in the export UI, or include a note in the documents about this, or both.

"catchment" --> portion of catchment
pop size = scale factor (multiply by 100k)
define scale factor as catchment pop
fix R script 10/100k --> 100/100k

When epi curves start at a historical date, want to be able to choose when in that curve the model actually starts.

Update VL to take individual CSVs for the model configuration. Should be able to still be configured within Simul8 as needed.