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COVID_19.sas
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/* SAS Program COVID_19
Cleveland Clinic and SAS Collaboarion
These models are only as good as their inputs.
Input values for this type of model are very dynamic and may need to be evaluated across wide ranges and reevaluated as the epidemic progresses.
This work is currently defaulting to values for the population studied in the Cleveland Clinic and SAS collaboration.
You need to evaluate each parameter for your population of interest.
*/
/* directory path for files: COVID_19.sas (this file), libname store */
%let homedir = /Local_Files/covid-19-sas/ccf;
/* the storage location for the MODEL_FINAL table and other output tables - when &ScenarioSource=BATCH */
libname store "&homedir.";
/* Depending on which SAS products you have and which releases you have these options will turn components of this code on/off */
%LET HAVE_SASETS = YES; /* YES implies you have SAS/ETS software, this enable the PROC MODEL methods in this code. Without this the Data Step SIR model still runs */
%LET HAVE_V151 = NO; /* YES implies you have products verison 15.1 (latest) and switches PROC MODEL to PROC TMODEL for faster execution */
/* User Interface Switches - these are used if you using the code within SAS Visual Analytics UI */
%LET ScenarioSource = BATCH;
%macro EasyRun(Scenario,IncubationPeriod,InitRecovered,RecoveryDays,doublingtime,Population,KnownAdmits,
SocialDistancing,ISOChangeDate,ISOChangeEvent,SocialDistancingChange,
MarketSharePercent,Admission_Rate,ICUPercent,VentPErcent,FatalityRate,
plots=no,N_DAYS=365,DiagnosedRate=1.0,E=0,SIGMA=3,DAY_ZERO='13MAR2020'd,BETA_DECAY=0.0,
ECMO_RATE=0.03,DIAL_RATE=0.05,HOSP_LOS=7,ICU_LOS=9,VENT_LOS=10,ECMO_LOS=6,DIAL_LOS=11);
DATA INPUTS;
FORMAT
Scenario $200.
IncubationPeriod BEST12.
InitRecovered BEST12.
RecoveryDays BEST12.
doublingtime BEST12.
Population BEST12.
KnownAdmits BEST12.
SocialDistancing BEST12.
ISOChangeDate $200.
ISOChangeEvent $200.
SocialDistancingChange $50.
MarketSharePercent BEST12.
Admission_Rate BEST12.
ICUPercent BEST12.
VentPErcent BEST12.
FatalityRate BEST12.
plots $3.
N_DAYS BEST12.
DiagnosedRate BEST12.
E BEST12.
SIGMA BEST12.
DAY_ZERO DATE9.
BETA_DECAY BEST12.
ECMO_RATE BEST12.
DIAL_RATE BEST12.
HOSP_LOS BEST12.
ICU_LOS BEST12.
VENT_LOS BEST12.
ECMO_LOS BEST12.
DIAL_LOS BEST12.
;
LABEL
Scenario = "Scenario Name"
IncubationPeriod = "Average Days between Infection and Hospitalization"
InitRecovered = "Number of Recovered (Immune) Patients on Day 0"
RecoveryDays = "Average Days Infectious"
doublingtime = "Baseline Infection Doubling Time (No Social Distancing)"
Population = "Regional Population"
KnownAdmits = "Number of Admitted Patients in Hospital of Interest on Day 0"
SocialDistancing = "Initial Social Distancing (% Reduction from Normal)"
ISOChangeDate = "Dates of Change in Social Distancing"
ISOChangeEvent = "Event label associated with ISOChangeDate"
SocialDistancingChange = "Social Distancing Change (% Reduction from Normal)"
MarketSharePercent = "Anticipated Share (%) of Regional Hospitalized Patients"
Admission_Rate = "Percentage of Infected Patients Requiring Hospitalization"
ICUPercent = "Percentage of Hospitalized Patients Requiring ICU"
VentPErcent = "Percentage of Hospitalized Patients Requiring Ventilators"
FatalityRate = "Percentage of Hospitalized Patients who will Die"
plots = "Display Plots (Yes/No)"
N_DAYS = "Number of Days to Project"
DiagnosedRate = "Hospitalization Rate Reduction (%) for Underdiagnosis"
E = "Number of Exposed Patients on Day 0"
SIGMA = "Days Exposed before Infected"
DAY_ZERO = "Date of the First COVID-19 Case"
BETA_DECAY = "Daily Reduction (%) of Beta"
ECMO_RATE = "Percentage of Hospitalized Patients Requiring ECMO"
DIAL_RATE = "Percentage of Hospitalized Patients Requiring Dialysis"
HOSP_LOS = "Average Hospital Length of Stay"
ICU_LOS = "Average ICU Length of Stay"
VENT_LOS = "Average Ventilator Length of Stay"
ECMO_LOS = "Average ECMO Length of Stay"
DIAL_LOS = "Average Dialysis Length of Stay"
;
Scenario = "&Scenario.";
IncubationPeriod = &IncubationPeriod.;
InitRecovered = &InitRecovered.;
RecoveryDays = &RecoveryDays.;
doublingtime = &doublingtime.;
Population = &Population.;
KnownAdmits = &KnownAdmits.;
SocialDistancing = &SocialDistancing.;
ISOChangeDate = "&ISOChangeDate.";
ISOChangeEvent = "&ISOChangeEvent.";
SocialDistancingChange = "&SocialDistancingChange.";
MarketSharePercent = &MarketSharePercent.;
Admission_Rate = &Admission_Rate.;
ICUPercent = &ICUPercent.;
VentPErcent = &VentPErcent.;
FatalityRate = &FatalityRate.;
plots = "&plots.";
N_DAYS = &N_DAYS.;
DiagnosedRate = &DiagnosedRate.;
E = &E.;
SIGMA = &SIGMA.;
DAY_ZERO = &DAY_ZERO.;
BETA_DECAY = &BETA_DECAY.;
ECMO_RATE = &ECMO_RATE.;
DIAL_RATE = &DIAL_RATE.;
HOSP_LOS = &HOSP_LOS.;
ICU_LOS = &ICU_LOS.;
VENT_LOS = &VENT_LOS.;
ECMO_LOS = &ECMO_LOS.;
DIAL_LOS = &DIAL_LOS.;
RUN;
%IF &ScenarioSource = UI %THEN %DO;
/* this session is only used for reading the SCENARIOS table in the global caslib when the UI is running the scenario */
%LET PULLLIB=&CASSource.;
%END;
%ELSE %DO;
%LET PULLLIB=store;
%END;
/* create an index, ScenarioIndex for this run by incrementing the max value of ScenarioIndex in SCENARIOS dataset */
%IF %SYSFUNC(exist(&PULLLIB..scenarios)) %THEN %DO;
PROC SQL noprint; select max(ScenarioIndex) into :ScenarioIndex_Base from &PULLLIB..scenarios where ScenarioSource="&ScenarioSource."; quit;
/* this may be the first ScenarioIndex for the ScenarioSource - catch and set to 0 */
%IF &ScenarioIndex_Base = . %THEN %DO; %LET ScenarioIndex_Base = 0; %END;
%END;
%ELSE %DO; %LET ScenarioIndex_Base = 0; %END;
%LET ScenarioIndex = %EVAL(&ScenarioIndex_Base + 1);
/* store all the macro variables that set up this scenario in SCENARIOS dataset */
DATA SCENARIOS;
set sashelp.vmacro(where=(scope='EASYRUN'));
if name in ('SQLEXITCODE','SQLOBS','SQLOOPS','SQLRC','SQLXOBS','SQLXOPENERRS','SCENARIOINDEX_BASE','PULLLIB') then delete;
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
STAGE='INPUT';
RUN;
DATA INPUTS;
set INPUTS;
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
label ScenarioIndex="Unique Scenario ID";
RUN;
/* Calculate Parameters form Macro Inputs Here - these are repeated as comments at the start of each model phase below */
* calculated parameters used in model post-processing;
%LET HOSP_RATE = %SYSEVALF(&Admission_Rate. * &DiagnosedRate.);
%LET ICU_RATE = %SYSEVALF(&ICUPercent. * &DiagnosedRate.);
%LET VENT_RATE = %SYSEVALF(&VentPErcent. * &DiagnosedRate.);
* calculated parameters used in models;
%LET I = %SYSEVALF(&KnownAdmits. /
&MarketSharePercent. /
(&Admission_Rate. * &DiagnosedRate.));
%LET GAMMA = %SYSEVALF(1 / &RecoveryDays.);
%IF &SIGMA. <= 0 %THEN %LET SIGMA = 0.00000001;
%LET SIGMAINV = %SYSEVALF(1 / &SIGMA.);
%LET BETA = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &SocialDistancing.));
%LET R_T = %SYSEVALF(&BETA. / &GAMMA. * &Population.);
%IF %sysevalf(%superq(SocialDistancingChange)=,boolean)=0 %THEN %DO;
%LET sdchangetitle=Adjust R0 (Date / Event / R0 / Social Distancing):;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
%LET SocialDistancingChange&j = %scan(&SocialDistancingChange.,&j,:);
%LET BETAChange&j = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &&SocialDistancingChange&j));
%LET R_T_Change&j = %SYSEVALF(&&BETAChange&j / &GAMMA. * &Population.);
%LET ISOChangeDate&j = %scan(&ISOChangeDate.,&j,:);
%LET ISOChangeEvent&j = %scan(&ISOChangeEvent.,&j,:);
%LET sdchangetitle = &sdchangetitle. (%sysfunc(INPUTN(&&ISOChangeDate&j., date10.), date9.) / &&ISOChangeEvent&j / %SYSFUNC(round(&&R_T_Change&j,.01)) / %SYSEVALF(&&SocialDistancingChange&j.*100)%);
%END;
%END;
%ELSE %DO;
%LET sdchangetitle=No Adjustment to R0 over time;
%END;
DATA SCENARIOS;
set SCENARIOS sashelp.vmacro(in=i where=(scope='EASYRUN'));
if name in ('SQLEXITCODE','SQLOBS','SQLOOPS','SQLRC','SQLXOBS','SQLXOPENERRS','SCENARIOINDEX_BASE','PULLLIB','SDCHANGETITLE','J') then delete;
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
if i then STAGE='MODEL';
RUN;
/* Check to see if SCENARIOS (this scenario) has already been run before in SCENARIOS dataset */
%GLOBAL ScenarioExist;
%IF %SYSFUNC(exist(&PULLLIB..scenarios)) %THEN %DO;
PROC SQL noprint;
/* has this scenario been run before - all the same parameters and value - no more and no less */
select count(*) into :ScenarioExist from
(select t1.ScenarioIndex, t2.ScenarioIndex, t2.ScenarioSource, t2.ScenarioUser
from
(select *, count(*) as cnt
from work.SCENARIOS
where name not in ('SCENARIO','SCENARIOINDEX_BASE','SCENARIONAMEUNIQUE','SCENARIOINDEX','SCENARIOSOURCE','SCENARIOUSER','SCENPLOT','PLOTS')
group by ScenarioIndex, ScenarioSource, ScenarioUser) t1
join
(select * from &PULLLIB..SCENARIOS
where name not in ('SCENARIO','SCENARIOINDEX_BASE','SCENARIONAMEUNIQUE','SCENARIOINDEX','SCENARIOSOURCE','SCENARIOUSER','SCENPLOT','PLOTS')) t2
on t1.name=t2.name and t1.value=t2.value and t1.STAGE=t2.STAGE
group by t1.ScenarioIndex, t2.ScenarioIndex, t2.ScenarioSource, t2.ScenarioUser, t1.cnt
having count(*) = t1.cnt)
;
QUIT;
%END;
%ELSE %DO;
%LET ScenarioExist = 0;
%END;
/* recall an existing scenario to SASWORK if it matched */
%GLOBAL ScenarioIndex_recall ScenarioSource_recall ScenarioUser_recall ScenarioNameUnique_recall ScenarioName_recall;
%IF &ScenarioExist = 0 %THEN %DO;
PROC SQL noprint; select max(ScenarioIndex) into :ScenarioIndex from work.SCENARIOS; QUIT;
%END;
/*%ELSE %IF &PLOTS. = YES %THEN %DO;*/
%ELSE %DO;
/* what was a ScenarioIndex value that matched the requested scenario - store that in ScenarioIndex_recall ... */
PROC SQL noprint; /* can this be combined with the similar code above that counts matching scenarios? */
select t2.ScenarioIndex, t2.ScenarioSource, t2.ScenarioUser, t2.ScenarioNameUnique, t2.ScenarioName into :ScenarioIndex_recall, :ScenarioSource_recall, :ScenarioUser_recall, :ScenarioNameUnique_recall, :ScenarioName_recall from
(select t1.ScenarioIndex, t2.ScenarioIndex, t2.ScenarioSource, t2.ScenarioUser, t2.ScenarioNameUnique, t2.ScenarioName
from
(select *, count(*) as cnt
from work.SCENARIOS
where name not in ('SCENARIO','SCENARIOINDEX_BASE','SCENARIONAMEUNIQUE','SCENARIOINDEX','SCENARIOSOURCE','SCENARIOUSER','SCENPLOT','PLOTS')
group by ScenarioIndex) t1
join
(select * from &PULLLIB..SCENARIOS
where name not in ('SCENARIO','SCENARIOINDEX_BASE','SCENARIONAMEUNIQUE','SCENARIOINDEX','SCENARIOSOURCE','SCENARIOUSER','SCENPLOT','PLOTS')) t2
on t1.name=t2.name and t1.value=t2.value and t1.STAGE=t2.STAGE
group by t1.ScenarioIndex, t2.ScenarioIndex, t2.ScenarioSource, t2.ScenarioUser, t1.cnt
having count(*) = t1.cnt)
;
QUIT;
/* pull the current scenario data to work for plots below */
data work.MODEL_FINAL; set &PULLLIB..MODEL_FINAL; where ScenarioIndex=&ScenarioIndex_recall. and ScenarioSource="&ScenarioSource_recall." and ScenarioUser="&ScenarioUser_recall."; run;
%IF &HAVE_SASETS = YES AND %SYMEXIST(ISOChangeDate1) %THEN %DO;
data work.FIT_PRED; set &PULLLIB..FIT_PRED; where ScenarioIndex=&ScenarioIndex_recall. and ScenarioSource="&ScenarioSource_recall." and ScenarioUser="&ScenarioUser_recall."; run;
data work.FIT_PARMS; set &PULLLIB..FIT_PARMS; where ScenarioIndex=&ScenarioIndex_recall. and ScenarioSource="&ScenarioSource_recall." and ScenarioUser="&ScenarioUser_recall."; run;
%END;
%LET ScenarioIndex = &ScenarioIndex_recall.;
%END;
/* Prepare to create request plots from input parameter plots= */
%IF %UPCASE(&plots.) = YES %THEN %DO; %LET plots = YES; %END;
%ELSE %DO; %LET plots = NO; %END;
/*PROC TMODEL SEIR APPROACH*/
/* these are the calculations for variables used from above:
* calculated parameters used in model post-processing;
%LET HOSP_RATE = %SYSEVALF(&Admission_Rate. * &DiagnosedRate.);
%LET ICU_RATE = %SYSEVALF(&ICUPercent. * &DiagnosedRate.);
%LET VENT_RATE = %SYSEVALF(&VentPErcent. * &DiagnosedRate.);
* calculated parameters used in models;
%LET I = %SYSEVALF(&KnownAdmits. /
&MarketSharePercent. /
(&Admission_Rate. * &DiagnosedRate.));
%LET GAMMA = %SYSEVALF(1 / &RecoveryDays.);
%IF &SIGMA. <= 0 %THEN %LET SIGMA = 0.00000001;
%LET SIGMAINV = %SYSEVALF(1 / &SIGMA.);
%LET BETA = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &SocialDistancing.));
%LET R_T = %SYSEVALF(&BETA. / &GAMMA. * &Population.);
%IF %sysevalf(%superq(SocialDistancingChange)=,boolean)=0 %THEN %DO;
%LET sdchangetitle=Adjust R0 (Date / Event / R0 / Social Distancing):;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
%LET SocialDistancingChange&j = %scan(&SocialDistancingChange.,&j,:);
%LET BETAChange&j = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &&SocialDistancingChange&j));
%LET R_T_Change&j = %SYSEVALF(&&BETAChange&j / &GAMMA. * &Population.);
%LET ISOChangeDate&j = %scan(&ISOChangeDate.,&j,:);
%LET ISOChangeEvent&j = %scan(&ISOChangeEvent.,&j,:);
%LET sdchangetitle = &sdchangetitle. (%sysfunc(INPUTN(&&ISOChangeDate&j., date10.), date9.) / &&ISOChangeEvent&j / %SYSFUNC(round(&&R_T_Change&j,.01)) / %SYSEVALF(&&SocialDistancingChange&j.*100)%);
%END;
%END;
%ELSE %DO;
%LET sdchangetitle=No Adjustment to R0 over time;
%END;
*/
/* If this is a new scenario then run it */
%IF &ScenarioExist = 0 AND &HAVE_SASETS = YES %THEN %DO;
/*DATA FOR PROC TMODEL APPROACHES*/
DATA DINIT(Label="Initial Conditions of Simulation");
S_N = &Population. - (&I. / &DiagnosedRate.) - &InitRecovered.;
E_N = &E.;
I_N = &I. / &DiagnosedRate.;
R_N = &InitRecovered.;
*R0 = &R_T.;
/* prevent range below zero on each loop */
DO SIGMAfraction = 0.8 TO 1.2 BY 0.1;
SIGMAINV = 1/(SIGMAfraction*&SIGMA.);
SIGMAfraction = round(SIGMAfraction,.00001);
DO RECOVERYDAYSfraction = 0.8 TO 1.2 BY 0.1;
RECOVERYDAYS = RECOVERYDAYSfraction * &RecoveryDays;
RECOVERYDAYSfraction = round(RECOVERYDAYSfraction,.00001);
DO SOCIALDfraction = -.2 TO .2 BY 0.1;
SOCIALD = SOCIALDfraction + &SocialDistancing;
SOCIALDfraction = round(SOCIALDfraction,.00001);
IF SOCIALD >=0 and SOCIALD<=1 THEN DO;
GAMMA = 1 / RECOVERYDAYS;
BETA = ((2 ** (1 / &doublingtime.) - 1) + GAMMA) /
&Population. * (1 - SOCIALD);
R_T = BETA / GAMMA * &Population.;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
BETAChange&j = ((2 ** (1 / &doublingtime.) - 1) + GAMMA) /
&Population. * (1 - &&SocialDistancingChange&j);
R_T_Change&j = BETAChange&j / GAMMA * &Population.;
%END;
DO TIME = 0 TO &N_DAYS. by 1;
OUTPUT;
END;
END;
END;
END;
END;
RUN;
%IF &HAVE_V151 = YES %THEN %DO; PROC TMODEL DATA = DINIT NOPRINT; performance nthreads=4 bypriority=1 partpriority=1; %END;
%ELSE %DO; PROC MODEL DATA = DINIT NOPRINT; %END;
/* PARAMETER SETTINGS */
PARMS N &Population.;
BOUNDS 1 <= R_T <= 13;
%LET jmax = %SYSFUNC(countw(&SocialDistancingChange.,:));
RESTRICT R_T > 0 %DO j = 1 %TO &jmax; , R_T_Change&j > 0 %END;;
%IF &jmax = 0 %THEN %DO; BETA = BETA; %END;
%ELSE %DO;
%DO j = 1 %TO &jmax;
%LET j2 = %eval(&j + 1);
%IF &j = 1 %THEN %DO;
change_0 = (TIME < (&&ISOChangeDate&j - &DAY_ZERO));
%END;
%IF &j = &jmax %THEN %DO;
change_&j = (TIME >= (&&ISOChangeDate&j - &DAY_ZERO));
%END;
%ELSE %DO;
change_&j = ((TIME >= (&&ISOChangeDate&j - &DAY_ZERO.)) & (TIME < (&&ISOChangeDate&j2 - &DAY_ZERO.)));
%END;
%END;
BETA = change_0*R_T*GAMMA/N %DO j = 1 %TO &jmax; + change_&j*R_T_Change&j*GAMMA/N %END;;
%END;
/* DIFFERENTIAL EQUATIONS */
/* a. Decrease in healthy susceptible persons through infections: number of encounters of (S,I)*TransmissionProb*/
DERT.S_N = -BETA*S_N*I_N;
/* b. inflow from a. -Decrease in Exposed: alpha*e "promotion" inflow from E->I;*/
DERT.E_N = BETA*S_N*I_N - SIGMAINV*E_N;
/* c. inflow from b. - outflow through recovery or death during illness*/
DERT.I_N = SIGMAINV*E_N - GAMMA*I_N;
/* d. Recovered and death humans through "promotion" inflow from c.*/
DERT.R_N = GAMMA*I_N;
/* SOLVE THE EQUATIONS */
SOLVE S_N E_N I_N R_N / TIME=TIME OUT = TMODEL_SEIR_SIM;
by SIGMAfraction RECOVERYDAYSfraction SOCIALDfraction;
RUN;
QUIT;
/* use the center point of the ranges for the requested scenario inputs */
DATA TMODEL_SEIR;
FORMAT ModelType $30. DATE ADMIT_DATE DATE9.;
ModelType="SEIR with PROC (T)MODEL";
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
RETAIN LAG_S LAG_E LAG_I LAG_R LAG_N CUMULATIVE_SUM_HOSP CUMULATIVE_SUM_ICU CUMULATIVE_SUM_VENT CUMULATIVE_SUM_ECMO CUMULATIVE_SUM_DIAL Cumulative_sum_fatality
CUMULATIVE_SUM_MARKET_HOSP CUMULATIVE_SUM_MARKET_ICU CUMULATIVE_SUM_MARKET_VENT CUMULATIVE_SUM_MARKET_ECMO CUMULATIVE_SUM_MARKET_DIAL cumulative_Sum_Market_Fatality;
LAG_S = S_N;
LAG_E = E_N;
LAG_I = I_N;
LAG_R = R_N;
LAG_N = N;
SET TMODEL_SEIR_SIM(RENAME=(TIME=DAY) DROP=_ERRORS_ _MODE_ _TYPE_);
WHERE SIGMAfraction=1 and RECOVERYDAYSfraction=1 and SOCIALDfraction=0;
N = SUM(S_N, E_N, I_N, R_N);
SCALE = LAG_N / N;
/* START: Common Post-Processing Across each Model Type and Approach */
NEWINFECTED=LAG&IncubationPeriod(SUM(LAG(SUM(S_N,E_N)),-1*SUM(S_N,E_N)));
IF NEWINFECTED < 0 THEN NEWINFECTED=0;
HOSP = NEWINFECTED * &HOSP_RATE. * &MarketSharePercent.;
ICU = NEWINFECTED * &ICU_RATE. * &MarketSharePercent. * &HOSP_RATE.;
VENT = NEWINFECTED * &VENT_RATE. * &MarketSharePercent. * &HOSP_RATE.;
ECMO = NEWINFECTED * &ECMO_RATE. * &MarketSharePercent. * &HOSP_RATE.;
DIAL = NEWINFECTED * &DIAL_RATE. * &MarketSharePercent. * &HOSP_RATE.;
Fatality = NEWINFECTED * &FatalityRate * &MarketSharePercent. * &HOSP_RATE.;
MARKET_HOSP = NEWINFECTED * &HOSP_RATE.;
MARKET_ICU = NEWINFECTED * &ICU_RATE. * &HOSP_RATE.;
MARKET_VENT = NEWINFECTED * &VENT_RATE. * &HOSP_RATE.;
MARKET_ECMO = NEWINFECTED * &ECMO_RATE. * &HOSP_RATE.;
MARKET_DIAL = NEWINFECTED * &DIAL_RATE. * &HOSP_RATE.;
Market_Fatality = NEWINFECTED * &FatalityRate. * &HOSP_RATE.;
CUMULATIVE_SUM_HOSP + HOSP;
CUMULATIVE_SUM_ICU + ICU;
CUMULATIVE_SUM_VENT + VENT;
CUMULATIVE_SUM_ECMO + ECMO;
CUMULATIVE_SUM_DIAL + DIAL;
Cumulative_sum_fatality + Fatality;
CUMULATIVE_SUM_MARKET_HOSP + MARKET_HOSP;
CUMULATIVE_SUM_MARKET_ICU + MARKET_ICU;
CUMULATIVE_SUM_MARKET_VENT + MARKET_VENT;
CUMULATIVE_SUM_MARKET_ECMO + MARKET_ECMO;
CUMULATIVE_SUM_MARKET_DIAL + MARKET_DIAL;
cumulative_Sum_Market_Fatality + Market_Fatality;
CUMADMITLAGGED=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_HOSP),1) ;
CUMICULAGGED=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_ICU),1) ;
CUMVENTLAGGED=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_VENT),1) ;
CUMECMOLAGGED=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_ECMO),1) ;
CUMDIALLAGGED=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_DIAL),1) ;
CUMMARKETADMITLAG=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_MARKET_HOSP));
CUMMARKETICULAG=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_MARKET_ICU));
CUMMARKETVENTLAG=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_MARKET_VENT));
CUMMARKETECMOLAG=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_MARKET_ECMO));
CUMMARKETDIALLAG=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_MARKET_DIAL));
ARRAY FIXINGDOT _NUMERIC_;
DO OVER FIXINGDOT;
IF FIXINGDOT=. THEN FIXINGDOT=0;
END;
HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_HOSP-CUMADMITLAGGED,1);
ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_ICU-CUMICULAGGED,1);
VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_VENT-CUMVENTLAGGED,1);
ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_ECMO-CUMECMOLAGGED,1);
DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_DIAL-CUMDIALLAGGED,1);
Deceased_Today = Fatality;
Total_Deaths = Cumulative_sum_fatality;
MedSurgOccupancy=Hospital_Occupancy-ICU_Occupancy;
MARKET_HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_HOSP-CUMMARKETADMITLAG,1);
MARKET_ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_ICU-CUMMARKETICULAG,1);
MARKET_VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_VENT-CUMMARKETVENTLAG,1);
MARKET_ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_ECMO-CUMMARKETECMOLAG,1);
MARKET_DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_DIAL-CUMMARKETDIALLAG,1);
Market_Deceased_Today = Market_Fatality;
Market_Total_Deaths = cumulative_Sum_Market_Fatality;
Market_MEdSurg_Occupancy=Market_Hospital_Occupancy-MArket_ICU_Occupancy;
DATE = &DAY_ZERO. + round(DAY,1);
ADMIT_DATE = SUM(DATE, &IncubationPeriod.);
FORMAT ISOChangeEvent $30.;
%IF %sysevalf(%superq(ISOChangeDate)=,boolean)=0 %THEN %DO;
%DO j = 1 %TO %SYSFUNC(countw(&ISOChangeDate.,:));
IF DATE = &&ISOChangeDate&j THEN DO;
ISOChangeEvent = "&&ISOChangeEvent&j";
/* the values in EventY_Multiplier will get multiplied by Peak values later in the code */
EventY_Multiplier = 1.1+MOD(&j,2)/10;
END;
%END;
%END;
%ELSE %DO;
ISOChangeEvent = '';
EventY_Multiplier = .;
%END;
/* END: Common Post-Processing Across each Model Type and Approach */
DROP LAG: CUM: SIGMAINV SIGMAfraction RECOVERYDAYS RECOVERYDAYSfraction SOCIALD SOCIALDfraction BETA GAMMA R_T:;
RUN;
/* round time to integers - precision */
proc sql;
create table TMODEL_SEIR_SIM as
select sum(S_N,E_N) as SE, SIGMAfraction, RECOVERYDAYSfraction, SOCIALDfraction, round(Time,1) as Time
from TMODEL_SEIR_SIM
order by SIGMAfraction, RECOVERYDAYSfraction, SOCIALDfraction, Time
;
quit;
/* use a skeleton from the normal post-processing to processes every scenario.
by statement used for separating scenarios - order by in sql above prepares this
note that lag function used in conditional logic can be very tricky.
The code below has logic to override the lag at the start of each by group.
*/
DATA TMODEL_SEIR_SIM;
FORMAT ModelType $30. DATE date9.;
ModelType="SEIR with PROC (T)MODEL";
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
RETAIN counter CUMULATIVE_SUM_HOSP CUMULATIVE_SUM_ICU CUMULATIVE_SUM_VENT CUMULATIVE_SUM_ECMO CUMULATIVE_SUM_DIAL;
SET TMODEL_SEIR_SIM(RENAME=(TIME=DAY));
by SIGMAfraction RECOVERYDAYSfraction SOCIALDfraction;
if first.SOCIALD then do;
counter = 1;
CUMULATIVE_SUM_HOSP=0;
CUMULATIVE_SUM_ICU=0;
CUMULATIVE_SUM_VENT=0;
CUMULATIVE_SUM_ECMO=0;
CUMULATIVE_SUM_DIAL=0;
end;
else do;
counter+1;
end;
/* START: Common Post-Processing Across each Model Type and Approach */
NEWINFECTED=LAG&IncubationPeriod(SUM(LAG(SE),-1*SE));
if counter<&IncubationPeriod then NEWINFECTED=.; /* reset the lag for by group */
IF NEWINFECTED < 0 THEN NEWINFECTED=0;
HOSP = NEWINFECTED * &HOSP_RATE. * &MarketSharePercent.;
ICU = NEWINFECTED * &ICU_RATE. * &MarketSharePercent. * &HOSP_RATE.;
VENT = NEWINFECTED * &VENT_RATE. * &MarketSharePercent. * &HOSP_RATE.;
ECMO = NEWINFECTED * &ECMO_RATE. * &MarketSharePercent. * &HOSP_RATE.;
DIAL = NEWINFECTED * &DIAL_RATE. * &MarketSharePercent. * &HOSP_RATE.;
CUMULATIVE_SUM_HOSP + HOSP;
CUMULATIVE_SUM_ICU + ICU;
CUMULATIVE_SUM_VENT + VENT;
CUMULATIVE_SUM_ECMO + ECMO;
CUMULATIVE_SUM_DIAL + DIAL;
CUMADMITLAGGED=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_HOSP),1) ;
if counter<=&HOSP_LOS then CUMADMITLAGGED=.; /* reset the lag for by group */
CUMICULAGGED=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_ICU),1) ;
if counter<=&ICU_LOS then CUMICULAGGED=.; /* reset the lag for by group */
CUMVENTLAGGED=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_VENT),1) ;
if counter<=&VENT_LOS then CUMVENTLAGGED=.; /* reset the lag for by group */
CUMECMOLAGGED=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_ECMO),1) ;
if counter<=&ECMO_LOS then CUMECMOLAGGED=.; /* reset the lag for by group */
CUMDIALLAGGED=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_DIAL),1) ;
if counter<=&DIAL_LOS then CUMDIALLAGGED=.; /* reset the lag for by group */
ARRAY FIXINGDOT _NUMERIC_;
DO OVER FIXINGDOT;
IF FIXINGDOT=. THEN FIXINGDOT=0;
END;
HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_HOSP-CUMADMITLAGGED,1);
ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_ICU-CUMICULAGGED,1);
VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_VENT-CUMVENTLAGGED,1);
ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_ECMO-CUMECMOLAGGED,1);
DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_DIAL-CUMDIALLAGGED,1);
DATE = &DAY_ZERO. + DAY;
/* END: Common Post-Processing Across each Model Type and Approach */
KEEP ModelType ScenarioIndex DATE HOSPITAL_OCCUPANCY ICU_OCCUPANCY VENT_OCCUPANCY ECMO_OCCUPANCY DIAL_OCCUPANCY Sigma RECOVERYDAYS SOCIALD;
RUN;
PROC SQL noprint;
create table TMODEL_SEIR as
select * from
(select * from work.TMODEL_SEIR) B
left join
(select min(HOSPITAL_OCCUPANCY) as LOWER_HOSPITAL_OCCUPANCY,
min(ICU_OCCUPANCY) as LOWER_ICU_OCCUPANCY,
min(VENT_OCCUPANCY) as LOWER_VENT_OCCUPANCY,
min(ECMO_OCCUPANCY) as LOWER_ECMO_OCCUPANCY,
min(DIAL_OCCUPANCY) as LOWER_DIAL_OCCUPANCY,
max(HOSPITAL_OCCUPANCY) as UPPER_HOSPITAL_OCCUPANCY,
max(ICU_OCCUPANCY) as UPPER_ICU_OCCUPANCY,
max(VENT_OCCUPANCY) as UPPER_VENT_OCCUPANCY,
max(ECMO_OCCUPANCY) as UPPER_ECMO_OCCUPANCY,
max(DIAL_OCCUPANCY) as UPPER_DIAL_OCCUPANCY,
Date, ModelType, ScenarioIndex
from TMODEL_SEIR_SIM
group by Date, ModelType, ScenarioIndex
) U
on B.ModelType=U.ModelType and B.ScenarioIndex=U.ScenarioIndex and B.DATE=U.DATE
order by ScenarioIndex, ModelType, Date
;
drop table TMODEL_SEIR_SIM;
QUIT;
PROC APPEND base=work.MODEL_FINAL data=TMODEL_SEIR; run;
PROC SQL; drop table TMODEL_SEIR; drop table DINIT; QUIT;
%END;
%IF &PLOTS. = YES AND &HAVE_SASETS = YES %THEN %DO;
PROC SGPLOT DATA=work.MODEL_FINAL;
where ModelType='SEIR with PROC (T)MODEL' and ScenarioIndex=&ScenarioIndex.;
TITLE "Daily Occupancy - PROC TMODEL SEIR Approach";
TITLE2 "Scenario: &Scenario., Initial R0: %SYSFUNC(round(&R_T.,.01)) with Initial Social Distancing of %SYSEVALF(&SocialDistancing.*100)%";
TITLE3 "&sdchangetitle.";
SERIES X=DATE Y=HOSPITAL_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=ICU_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=VENT_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=ECMO_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=DIAL_OCCUPANCY / LINEATTRS=(THICKNESS=2);
XAXIS LABEL="Date";
YAXIS LABEL="Daily Occupancy";
RUN;
TITLE; TITLE2; TITLE3;
PROC SGPLOT DATA=work.MODEL_FINAL;
where ModelType='SEIR with PROC (T)MODEL' and ScenarioIndex=&ScenarioIndex.;
TITLE "Daily Occupancy - PROC TMODEL SEIR Approach With Uncertainty Bounds";
TITLE2 "Scenario: &Scenario., Initial R0: %SYSFUNC(round(&R_T.,.01)) with Initial Social Distancing of %SYSEVALF(&SocialDistancing.*100)%";
TITLE3 "&sdchangetitle.";
BAND x=DATE lower=LOWER_HOSPITAL_OCCUPANCY upper=UPPER_HOSPITAL_OCCUPANCY / fillattrs=(color=blue transparency=.8) name="b1";
BAND x=DATE lower=LOWER_ICU_OCCUPANCY upper=UPPER_ICU_OCCUPANCY / fillattrs=(color=red transparency=.8) name="b2";
BAND x=DATE lower=LOWER_VENT_OCCUPANCY upper=UPPER_VENT_OCCUPANCY / fillattrs=(color=green transparency=.8) name="b3";
BAND x=DATE lower=LOWER_ECMO_OCCUPANCY upper=UPPER_ECMO_OCCUPANCY / fillattrs=(color=brown transparency=.8) name="b4";
BAND x=DATE lower=LOWER_DIAL_OCCUPANCY upper=UPPER_DIAL_OCCUPANCY / fillattrs=(color=purple transparency=.8) name="b5";
SERIES X=DATE Y=HOSPITAL_OCCUPANCY / LINEATTRS=(color=blue THICKNESS=2) name="l1";
SERIES X=DATE Y=ICU_OCCUPANCY / LINEATTRS=(color=red THICKNESS=2) name="l2";
SERIES X=DATE Y=VENT_OCCUPANCY / LINEATTRS=(color=green THICKNESS=2) name="l3";
SERIES X=DATE Y=ECMO_OCCUPANCY / LINEATTRS=(color=brown THICKNESS=2) name="l4";
SERIES X=DATE Y=DIAL_OCCUPANCY / LINEATTRS=(color=purple THICKNESS=2) name="l5";
keylegend "l1" "l2" "l3" "l4" "l5";
XAXIS LABEL="Date";
YAXIS LABEL="Daily Occupancy";
RUN;
TITLE; TITLE2; TITLE3;
%END;
/*PROC TMODEL SIR APPROACH*/
/* these are the calculations for variables used from above:
* calculated parameters used in model post-processing;
%LET HOSP_RATE = %SYSEVALF(&Admission_Rate. * &DiagnosedRate.);
%LET ICU_RATE = %SYSEVALF(&ICUPercent. * &DiagnosedRate.);
%LET VENT_RATE = %SYSEVALF(&VentPErcent. * &DiagnosedRate.);
* calculated parameters used in models;
%LET I = %SYSEVALF(&KnownAdmits. /
&MarketSharePercent. /
(&Admission_Rate. * &DiagnosedRate.));
%LET GAMMA = %SYSEVALF(1 / &RecoveryDays.);
%IF &SIGMA. <= 0 %THEN %LET SIGMA = 0.00000001;
%LET SIGMAINV = %SYSEVALF(1 / &SIGMA.);
%LET BETA = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &SocialDistancing.));
%LET R_T = %SYSEVALF(&BETA. / &GAMMA. * &Population.);
%IF %sysevalf(%superq(SocialDistancingChange)=,boolean)=0 %THEN %DO;
%LET sdchangetitle=Adjust R0 (Date / Event / R0 / Social Distancing):;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
%LET SocialDistancingChange&j = %scan(&SocialDistancingChange.,&j,:);
%LET BETAChange&j = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &&SocialDistancingChange&j));
%LET R_T_Change&j = %SYSEVALF(&&BETAChange&j / &GAMMA. * &Population.);
%LET ISOChangeDate&j = %scan(&ISOChangeDate.,&j,:);
%LET ISOChangeEvent&j = %scan(&ISOChangeEvent.,&j,:);
%LET sdchangetitle = &sdchangetitle. (%sysfunc(INPUTN(&&ISOChangeDate&j., date10.), date9.) / &&ISOChangeEvent&j / %SYSFUNC(round(&&R_T_Change&j,.01)) / %SYSEVALF(&&SocialDistancingChange&j.*100)%);
%END;
%END;
%ELSE %DO;
%LET sdchangetitle=No Adjustment to R0 over time;
%END;
*/
/* If this is a new scenario then run it */
%IF &ScenarioExist = 0 AND &HAVE_SASETS = YES %THEN %DO;
/*DATA FOR PROC TMODEL APPROACHES*/
DATA DINIT(Label="Initial Conditions of Simulation");
S_N = &Population. - (&I. / &DiagnosedRate.) - &InitRecovered.;
E_N = &E.;
I_N = &I. / &DiagnosedRate.;
R_N = &InitRecovered.;
*R0 = &R_T.;
/* prevent range below zero on each loop */
DO RECOVERYDAYSfraction = 0.8 TO 1.2 BY 0.1;
RECOVERYDAYS = RECOVERYDAYSfraction*&RecoveryDays;
RECOVERYDAYSfraction = round(RECOVERYDAYSfraction,.00001);
DO SOCIALDfraction = -.2 TO .2 BY 0.1;
SOCIALD = SOCIALDfraction + &SocialDistancing;
SOCIALDfraction = round(SOCIALDfraction,.00001);
IF SOCIALD >=0 and SOCIALD<=1 THEN DO;
GAMMA = 1 / RECOVERYDAYS;
BETA = ((2 ** (1 / &doublingtime.) - 1) + GAMMA) /
&Population. * (1 - SOCIALD);
R_T = BETA / GAMMA * &Population.;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
BETAChange&j = ((2 ** (1 / &doublingtime.) - 1) + GAMMA) /
&Population. * (1 - &&SocialDistancingChange&j);
R_T_Change&j = BETAChange&j / GAMMA * &Population.;
%END;
DO TIME = 0 TO &N_DAYS. by 1;
OUTPUT;
END;
END;
END;
END;
RUN;
%IF &HAVE_V151 = YES %THEN %DO; PROC TMODEL DATA = DINIT NOPRINT; performance nthreads=4 bypriority=1 partpriority=1; %END;
%ELSE %DO; PROC MODEL DATA = DINIT NOPRINT; %END;
/* PARAMETER SETTINGS */
PARMS N &Population.;
BOUNDS 1 <= R_T <= 13;
%LET jmax = %SYSFUNC(countw(&SocialDistancingChange.,:));
RESTRICT R_T > 0 %DO j = 1 %TO &jmax; , R_T_Change&j > 0 %END;;
%IF &jmax = 0 %THEN %DO; BETA = BETA; %END;
%ELSE %DO;
%DO j = 1 %TO &jmax;
%LET j2 = %eval(&j + 1);
%IF &j = 1 %THEN %DO;
change_0 = (TIME < (&&ISOChangeDate&j - &DAY_ZERO));
%END;
%IF &j = &jmax %THEN %DO;
change_&j = (TIME >= (&&ISOChangeDate&j - &DAY_ZERO));
%END;
%ELSE %DO;
change_&j = ((TIME >= (&&ISOChangeDate&j - &DAY_ZERO.)) & (TIME < (&&ISOChangeDate&j2 - &DAY_ZERO.)));
%END;
%END;
BETA = change_0*R_T*GAMMA/N %DO j = 1 %TO &jmax; + change_&j*R_T_Change&j*GAMMA/N %END;;
%END;
/* DIFFERENTIAL EQUATIONS */
/* a. Decrease in healthy susceptible persons through infections: number of encounters of (S,I)*TransmissionProb*/
DERT.S_N = -BETA*S_N*I_N;
/* c. inflow from b. - outflow through recovery or death during illness*/
DERT.I_N = BETA*S_N*I_N - GAMMA*I_N;
/* d. Recovered and death humans through "promotion" inflow from c.*/
DERT.R_N = GAMMA*I_N;
/* SOLVE THE EQUATIONS */
SOLVE S_N I_N R_N / TIME=TIME OUT = TMODEL_SIR_SIM;
by RECOVERYDAYSfraction SOCIALDfraction;
RUN;
QUIT;
/* use the center point of the ranges for the requested scenario inputs */
DATA TMODEL_SIR;
FORMAT ModelType $30. DATE ADMIT_DATE DATE9.;
ModelType="SIR with PROC (T)MODEL";
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
RETAIN LAG_S LAG_I LAG_R LAG_N CUMULATIVE_SUM_HOSP CUMULATIVE_SUM_ICU CUMULATIVE_SUM_VENT CUMULATIVE_SUM_ECMO CUMULATIVE_SUM_DIAL Cumulative_sum_fatality
CUMULATIVE_SUM_MARKET_HOSP CUMULATIVE_SUM_MARKET_ICU CUMULATIVE_SUM_MARKET_VENT CUMULATIVE_SUM_MARKET_ECMO CUMULATIVE_SUM_MARKET_DIAL cumulative_Sum_Market_Fatality;
LAG_S = S_N;
E_N = &E.; LAG_E = E_N; /* placeholder for post-processing of SIR model */
LAG_I = I_N;
LAG_R = R_N;
LAG_N = N;
SET TMODEL_SIR_SIM(RENAME=(TIME=DAY) DROP=_ERRORS_ _MODE_ _TYPE_);
WHERE RECOVERYDAYSfraction=1 and SOCIALDfraction=0;
N = SUM(S_N, E_N, I_N, R_N);
SCALE = LAG_N / N;
/* START: Common Post-Processing Across each Model Type and Approach */
NEWINFECTED=LAG&IncubationPeriod(SUM(LAG(SUM(S_N,E_N)),-1*SUM(S_N,E_N)));
IF NEWINFECTED < 0 THEN NEWINFECTED=0;
HOSP = NEWINFECTED * &HOSP_RATE. * &MarketSharePercent.;
ICU = NEWINFECTED * &ICU_RATE. * &MarketSharePercent. * &HOSP_RATE.;
VENT = NEWINFECTED * &VENT_RATE. * &MarketSharePercent. * &HOSP_RATE.;
ECMO = NEWINFECTED * &ECMO_RATE. * &MarketSharePercent. * &HOSP_RATE.;
DIAL = NEWINFECTED * &DIAL_RATE. * &MarketSharePercent. * &HOSP_RATE.;
Fatality = NEWINFECTED * &FatalityRate * &MarketSharePercent. * &HOSP_RATE.;
MARKET_HOSP = NEWINFECTED * &HOSP_RATE.;
MARKET_ICU = NEWINFECTED * &ICU_RATE. * &HOSP_RATE.;
MARKET_VENT = NEWINFECTED * &VENT_RATE. * &HOSP_RATE.;
MARKET_ECMO = NEWINFECTED * &ECMO_RATE. * &HOSP_RATE.;
MARKET_DIAL = NEWINFECTED * &DIAL_RATE. * &HOSP_RATE.;
Market_Fatality = NEWINFECTED * &FatalityRate. * &HOSP_RATE.;
CUMULATIVE_SUM_HOSP + HOSP;
CUMULATIVE_SUM_ICU + ICU;
CUMULATIVE_SUM_VENT + VENT;
CUMULATIVE_SUM_ECMO + ECMO;
CUMULATIVE_SUM_DIAL + DIAL;
Cumulative_sum_fatality + Fatality;
CUMULATIVE_SUM_MARKET_HOSP + MARKET_HOSP;
CUMULATIVE_SUM_MARKET_ICU + MARKET_ICU;
CUMULATIVE_SUM_MARKET_VENT + MARKET_VENT;
CUMULATIVE_SUM_MARKET_ECMO + MARKET_ECMO;
CUMULATIVE_SUM_MARKET_DIAL + MARKET_DIAL;
cumulative_Sum_Market_Fatality + Market_Fatality;
CUMADMITLAGGED=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_HOSP),1) ;
CUMICULAGGED=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_ICU),1) ;
CUMVENTLAGGED=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_VENT),1) ;
CUMECMOLAGGED=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_ECMO),1) ;
CUMDIALLAGGED=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_DIAL),1) ;
CUMMARKETADMITLAG=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_MARKET_HOSP));
CUMMARKETICULAG=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_MARKET_ICU));
CUMMARKETVENTLAG=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_MARKET_VENT));
CUMMARKETECMOLAG=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_MARKET_ECMO));
CUMMARKETDIALLAG=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_MARKET_DIAL));
ARRAY FIXINGDOT _NUMERIC_;
DO OVER FIXINGDOT;
IF FIXINGDOT=. THEN FIXINGDOT=0;
END;
HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_HOSP-CUMADMITLAGGED,1);
ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_ICU-CUMICULAGGED,1);
VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_VENT-CUMVENTLAGGED,1);
ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_ECMO-CUMECMOLAGGED,1);
DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_DIAL-CUMDIALLAGGED,1);
Deceased_Today = Fatality;
Total_Deaths = Cumulative_sum_fatality;
MedSurgOccupancy=Hospital_Occupancy-ICU_Occupancy;
MARKET_HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_HOSP-CUMMARKETADMITLAG,1);
MARKET_ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_ICU-CUMMARKETICULAG,1);
MARKET_VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_VENT-CUMMARKETVENTLAG,1);
MARKET_ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_ECMO-CUMMARKETECMOLAG,1);
MARKET_DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_MARKET_DIAL-CUMMARKETDIALLAG,1);
Market_Deceased_Today = Market_Fatality;
Market_Total_Deaths = cumulative_Sum_Market_Fatality;
Market_MEdSurg_Occupancy=Market_Hospital_Occupancy-MArket_ICU_Occupancy;
DATE = &DAY_ZERO. + round(DAY,1);
ADMIT_DATE = SUM(DATE, &IncubationPeriod.);
FORMAT ISOChangeEvent $30.;
%IF %sysevalf(%superq(ISOChangeDate)=,boolean)=0 %THEN %DO;
%DO j = 1 %TO %SYSFUNC(countw(&ISOChangeDate.,:));
IF DATE = &&ISOChangeDate&j THEN DO;
ISOChangeEvent = "&&ISOChangeEvent&j";
/* the values in EventY_Multiplier will get multiplied by Peak values later in the code */
EventY_Multiplier = 1.1+MOD(&j,2)/10;
END;
%END;
%END;
%ELSE %DO;
ISOChangeEvent = '';
EventY_Multiplier = .;
%END;
/* END: Common Post-Processing Across each Model Type and Approach */
DROP LAG: CUM: RECOVERYDAYSfraction RECOVERYDAYS SOCIALDfraction SOCIALD BETA GAMMA R_T:;
RUN;
/* round time to integers - precision */
proc sql;
create table TMODEL_SIR_SIM as
select S_N as SE, RECOVERYDAYSfraction, SOCIALDfraction, round(Time,1) as Time
from TMODEL_SIR_SIM
order by RECOVERYDAYSfraction, SOCIALDfraction, Time
;
quit;
/* use a skeleton from the normal post-processing to processes every scenario.
by statement used for separating scenarios - order by in sql above prepares this
note that lag function used in conditional logic can be very tricky.
The code below has logic to override the lag at the start of each by group.
*/
DATA TMODEL_SIR_SIM;
FORMAT ModelType $30. DATE date9.;
ModelType="SIR with PROC (T)MODEL";
FORMAT ScenarioName $50. ScenarioNameUnique $100. ScenarioSource $10. ScenarioUser $25.;
ScenarioName="&Scenario.";
ScenarioIndex=&ScenarioIndex.;
ScenarioUser="&SYSUSERID.";
ScenarioSource="&ScenarioSource.";
ScenarioNameUnique=cats("&Scenario.",' (',ScenarioIndex,'-',"&SYSUSERID.",'-',"&ScenarioSource.",')');
RETAIN counter CUMULATIVE_SUM_HOSP CUMULATIVE_SUM_ICU CUMULATIVE_SUM_VENT CUMULATIVE_SUM_ECMO CUMULATIVE_SUM_DIAL;
SET TMODEL_SIR_SIM(RENAME=(TIME=DAY));
by RECOVERYDAYSfraction SOCIALDfraction;
if first.SOCIALD then do;
counter = 1;
CUMULATIVE_SUM_HOSP=0;
CUMULATIVE_SUM_ICU=0;
CUMULATIVE_SUM_VENT=0;
CUMULATIVE_SUM_ECMO=0;
CUMULATIVE_SUM_DIAL=0;
end;
else do;
counter+1;
end;
/* START: Common Post-Processing Across each Model Type and Approach */
NEWINFECTED=LAG&IncubationPeriod(SUM(LAG(SE),-1*SE));
if counter<&IncubationPeriod then NEWINFECTED=.; /* reset the lag for by group */
IF NEWINFECTED < 0 THEN NEWINFECTED=0;
HOSP = NEWINFECTED * &HOSP_RATE. * &MarketSharePercent.;
ICU = NEWINFECTED * &ICU_RATE. * &MarketSharePercent. * &HOSP_RATE.;
VENT = NEWINFECTED * &VENT_RATE. * &MarketSharePercent. * &HOSP_RATE.;
ECMO = NEWINFECTED * &ECMO_RATE. * &MarketSharePercent. * &HOSP_RATE.;
DIAL = NEWINFECTED * &DIAL_RATE. * &MarketSharePercent. * &HOSP_RATE.;
CUMULATIVE_SUM_HOSP + HOSP;
CUMULATIVE_SUM_ICU + ICU;
CUMULATIVE_SUM_VENT + VENT;
CUMULATIVE_SUM_ECMO + ECMO;
CUMULATIVE_SUM_DIAL + DIAL;
CUMADMITLAGGED=ROUND(LAG&HOSP_LOS.(CUMULATIVE_SUM_HOSP),1) ;
if counter<=&HOSP_LOS then CUMADMITLAGGED=.; /* reset the lag for by group */
CUMICULAGGED=ROUND(LAG&ICU_LOS.(CUMULATIVE_SUM_ICU),1) ;
if counter<=&ICU_LOS then CUMICULAGGED=.; /* reset the lag for by group */
CUMVENTLAGGED=ROUND(LAG&VENT_LOS.(CUMULATIVE_SUM_VENT),1) ;
if counter<=&VENT_LOS then CUMVENTLAGGED=.; /* reset the lag for by group */
CUMECMOLAGGED=ROUND(LAG&ECMO_LOS.(CUMULATIVE_SUM_ECMO),1) ;
if counter<=&ECMO_LOS then CUMECMOLAGGED=.; /* reset the lag for by group */
CUMDIALLAGGED=ROUND(LAG&DIAL_LOS.(CUMULATIVE_SUM_DIAL),1) ;
if counter<=&DIAL_LOS then CUMDIALLAGGED=.; /* reset the lag for by group */
ARRAY FIXINGDOT _NUMERIC_;
DO OVER FIXINGDOT;
IF FIXINGDOT=. THEN FIXINGDOT=0;
END;
HOSPITAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_HOSP-CUMADMITLAGGED,1);
ICU_OCCUPANCY= ROUND(CUMULATIVE_SUM_ICU-CUMICULAGGED,1);
VENT_OCCUPANCY= ROUND(CUMULATIVE_SUM_VENT-CUMVENTLAGGED,1);
ECMO_OCCUPANCY= ROUND(CUMULATIVE_SUM_ECMO-CUMECMOLAGGED,1);
DIAL_OCCUPANCY= ROUND(CUMULATIVE_SUM_DIAL-CUMDIALLAGGED,1);
DATE = &DAY_ZERO. + DAY;
/* END: Common Post-Processing Across each Model Type and Approach */
KEEP ModelType ScenarioIndex DATE HOSPITAL_OCCUPANCY ICU_OCCUPANCY VENT_OCCUPANCY ECMO_OCCUPANCY DIAL_OCCUPANCY RECOVERYDAYS SOCIALD;
RUN;
PROC SQL noprint;
create table TMODEL_SIR as
select * from
(select * from work.TMODEL_SIR) B
left join
(select min(HOSPITAL_OCCUPANCY) as LOWER_HOSPITAL_OCCUPANCY,
min(ICU_OCCUPANCY) as LOWER_ICU_OCCUPANCY,
min(VENT_OCCUPANCY) as LOWER_VENT_OCCUPANCY,
min(ECMO_OCCUPANCY) as LOWER_ECMO_OCCUPANCY,
min(DIAL_OCCUPANCY) as LOWER_DIAL_OCCUPANCY,
max(HOSPITAL_OCCUPANCY) as UPPER_HOSPITAL_OCCUPANCY,
max(ICU_OCCUPANCY) as UPPER_ICU_OCCUPANCY,
max(VENT_OCCUPANCY) as UPPER_VENT_OCCUPANCY,
max(ECMO_OCCUPANCY) as UPPER_ECMO_OCCUPANCY,
max(DIAL_OCCUPANCY) as UPPER_DIAL_OCCUPANCY,
Date, ModelType, ScenarioIndex
from TMODEL_SIR_SIM
group by Date, ModelType, ScenarioIndex
) U
on B.ModelType=U.ModelType and B.ScenarioIndex=U.ScenarioIndex and B.DATE=U.DATE
order by ScenarioIndex, ModelType, Date
;
drop table TMODEL_SIR_SIM;
QUIT;
PROC APPEND base=work.MODEL_FINAL data=TMODEL_SIR NOWARN FORCE; run;
PROC SQL; drop table TMODEL_SIR; drop table DINIT; QUIT;
%END;
%IF &PLOTS. = YES AND &HAVE_SASETS = YES %THEN %DO;
PROC SGPLOT DATA=work.MODEL_FINAL;
where ModelType='SIR with PROC (T)MODEL' and ScenarioIndex=&ScenarioIndex.;
TITLE "Daily Occupancy - PROC TMODEL SIR Approach";
TITLE2 "Scenario: &Scenario., Initial R0: %SYSFUNC(round(&R_T.,.01)) with Initial Social Distancing of %SYSEVALF(&SocialDistancing.*100)%";
TITLE3 "&sdchangetitle.";
SERIES X=DATE Y=HOSPITAL_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=ICU_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=VENT_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=ECMO_OCCUPANCY / LINEATTRS=(THICKNESS=2);
SERIES X=DATE Y=DIAL_OCCUPANCY / LINEATTRS=(THICKNESS=2);
XAXIS LABEL="Date";
YAXIS LABEL="Daily Occupancy";
RUN;
TITLE; TITLE2; TITLE3;
PROC SGPLOT DATA=work.MODEL_FINAL;
where ModelType='SIR with PROC (T)MODEL' and ScenarioIndex=&ScenarioIndex.;
TITLE "Daily Occupancy - PROC TMODEL SIR Approach With Uncertainty Bounds";
TITLE2 "Scenario: &Scenario., Initial R0: %SYSFUNC(round(&R_T.,.01)) with Initial Social Distancing of %SYSEVALF(&SocialDistancing.*100)%";
TITLE3 "&sdchangetitle.";
BAND x=DATE lower=LOWER_HOSPITAL_OCCUPANCY upper=UPPER_HOSPITAL_OCCUPANCY / fillattrs=(color=blue transparency=.8) name="b1";
BAND x=DATE lower=LOWER_ICU_OCCUPANCY upper=UPPER_ICU_OCCUPANCY / fillattrs=(color=red transparency=.8) name="b2";
BAND x=DATE lower=LOWER_VENT_OCCUPANCY upper=UPPER_VENT_OCCUPANCY / fillattrs=(color=green transparency=.8) name="b3";
BAND x=DATE lower=LOWER_ECMO_OCCUPANCY upper=UPPER_ECMO_OCCUPANCY / fillattrs=(color=brown transparency=.8) name="b4";
BAND x=DATE lower=LOWER_DIAL_OCCUPANCY upper=UPPER_DIAL_OCCUPANCY / fillattrs=(color=purple transparency=.8) name="b5";
SERIES X=DATE Y=HOSPITAL_OCCUPANCY / LINEATTRS=(color=blue THICKNESS=2) name="l1";
SERIES X=DATE Y=ICU_OCCUPANCY / LINEATTRS=(color=red THICKNESS=2) name="l2";
SERIES X=DATE Y=VENT_OCCUPANCY / LINEATTRS=(color=green THICKNESS=2) name="l3";
SERIES X=DATE Y=ECMO_OCCUPANCY / LINEATTRS=(color=brown THICKNESS=2) name="l4";
SERIES X=DATE Y=DIAL_OCCUPANCY / LINEATTRS=(color=purple THICKNESS=2) name="l5";
keylegend "l1" "l2" "l3" "l4" "l5";
XAXIS LABEL="Date";
YAXIS LABEL="Daily Occupancy";
RUN;
TITLE; TITLE2; TITLE3;
%END;
/* DATA STEP APPROACH FOR SEIR */
/* these are the calculations for variables used from above:
* calculated parameters used in model post-processing;
%LET HOSP_RATE = %SYSEVALF(&Admission_Rate. * &DiagnosedRate.);
%LET ICU_RATE = %SYSEVALF(&ICUPercent. * &DiagnosedRate.);
%LET VENT_RATE = %SYSEVALF(&VentPErcent. * &DiagnosedRate.);
* calculated parameters used in models;
%LET I = %SYSEVALF(&KnownAdmits. /
&MarketSharePercent. /
(&Admission_Rate. * &DiagnosedRate.));
%LET GAMMA = %SYSEVALF(1 / &RecoveryDays.);
%IF &SIGMA. <= 0 %THEN %LET SIGMA = 0.00000001;
%LET SIGMAINV = %SYSEVALF(1 / &SIGMA.);
%LET BETA = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /
&Population. * (1 - &SocialDistancing.));
%LET R_T = %SYSEVALF(&BETA. / &GAMMA. * &Population.);
%IF %sysevalf(%superq(SocialDistancingChange)=,boolean)=0 %THEN %DO;
%LET sdchangetitle=Adjust R0 (Date / Event / R0 / Social Distancing):;
%DO j = 1 %TO %SYSFUNC(countw(&SocialDistancingChange.,:));
%LET SocialDistancingChange&j = %scan(&SocialDistancingChange.,&j,:);
%LET BETAChange&j = %SYSEVALF(((2 ** (1 / &doublingtime.) - 1) + &GAMMA.) /