aminadibi
commented
7 years ago In order to make the change, 8 regression formulas in input.R must be updated:
- COPD: Prevalence and Incidence, for males and females
- FEV1 Progression: Prevalence and Incidence, for males and females
This is the corresponding piece of code:
##COPD
input$COPD$logit_p_COPD_betas_by_sex<-cbind(
male=c(intercept=-6,age=log(1.96)/10,age2=0,pack_years=log(1.20)/10,current_smoking=0,year=0,asthma=0),
female=c(intercept=-6.2,age=log(1.94)/10,age2=0,pack_years=log(1.20)/10,current_smoking=0,year=0,asthma=0))
input_help$COPD$logit_p_COPD_betas_by_sex<-"Logit of the probability of having COPD (FEV1/FVC<0.7) at time of creation (separately by sex)"
input$COPD$ln_h_COPD_betas_by_sex<-cbind(
male =c(Intercept =-6.65,age = 0.046 ,age2 = 0,pack_years = 0.016, smoking_status = 0,year = 0,asthma = 0)
,female =c(Intercept =-6.92 ,age = 0.05, age2 =0,pack_years = 0.016, smoking_status = 0 ,year = 0,asthma = 0))
input_help$COPD$ln_h_COPD_betas_by_sex<-"Log-hazard of developing COPD (FEV1/FVC<0.7) for those who did not have COPD at creation time (separately by sex)"
##Lung function
input$lung_function$fev1_0_prev_betas_by_sex<-cbind(
male=c(intercept=-1.969651,age=-0.027212,height=3.786599,pack_years=-0.005458,current_smoker=0,sgrq=0),
female=c(intercept=-0.8339577 ,age=-0.0252077 ,height=2.7785297,pack_years=-0.0063040,current_smoker=0,sgrq=0))
input_help$lung_function$fev1_0_prev_betas_by_sex<-"Regression (OLS) coefficients for mean of FEV1 at time of creation for those with COPD (separately by sex)"
input$lung_function$fev1_0_prev_sd_by_sex<-c(male=0.6148,female=0.4242)
input_help$lung_function$fev1_0_prev_sd_by_sex<-"SD of FEV1 at time of creation for those with COPD (separately by sex)"
input$lung_function$fev1_0_inc_betas_by_sex<-cbind(
male=c(intercept=-5.9429280+3.2719928*0.7,age=-0.0253224,height=4.7959326,pack_years=-0.0033031,current_smoker=0,sgrq=0),
female=c(intercept=-3.1143794+2.1388758*0.7,age=-0.0234219,height=3.2741914,pack_years=-0.0032205,current_smoker=0,sgrq=0))
input_help$lung_function$fev1_0_inc_betas_by_sex<-"Regression (OLS) coefficients for mean of FEV1 at time of development of COPD(separately by sex)"
input$lung_function$fev1_0_inc_sd_by_sex<-c(male=0.54,female=0.36)
input_help$lung_function$fev1_0_inc_sd_by_sex<-"SD of FEV1 at time of development of COPD (separately by sex)"The definition of COPD is already embedded in how the coefficients in these equations are calculated, the 0.7 threshold is never explicitly mentioned in the code.
These equations come at play under the EVENT_COPD heading in model.WIP.cpp:
void event_COPD_process(agent *ag)
{
(*ag).fev1=input.lung_function.fev1_0_inc_betas_by_sex[0][(*ag).sex]
+input.lung_function.fev1_0_inc_betas_by_sex[1][(*ag).sex]*((*ag).age_at_creation+(*ag).local_time)
+input.lung_function.fev1_0_inc_betas_by_sex[2][(*ag).sex]*(*ag).height
+input.lung_function.fev1_0_inc_betas_by_sex[3][(*ag).sex]*(*ag).pack_years
+rand_norm()*input.lung_function.fev1_0_inc_sd_by_sex[(*ag).sex];
double pred_fev1=CALC_PRED_FEV1(ag);
(*ag)._pred_fev1=pred_fev1;
if ((*ag).fev1/pred_fev1<0.3) (*ag).gold=4;
else
if ((*ag).fev1/pred_fev1<0.5) (*ag).gold=3;
else
if ((*ag).fev1/pred_fev1<0.8) (*ag).gold=2;
else (*ag).gold=1;
double temp[2];
rbvnorm(input.lung_function.dfev1_re_rho,temp);
(*ag).fev1_slope=input.lung_function.dfev1_betas[0]
+temp[0]*input.lung_function.dfev1_re_sds[0]
+input.lung_function.dfev1_betas[1]*(*ag).sex
+input.lung_function.dfev1_betas[2]*((*ag).age_at_creation+(*ag).local_time)
+input.lung_function.dfev1_betas[3]*(*ag).fev1
+input.lung_function.dfev1_betas[4]*(*ag).smoking_status;
(*ag).fev1_slope_t=input.lung_function.dfev1_betas[5]+temp[1]*input.lung_function.dfev1_re_sds[1];
(*ag).lung_function_LPT=(*ag).local_time;
#if OUTPUT_EX>1
output_ex.cumul_non_COPD_time+=(*ag).local_time;
#endif
#if (OUTPUT_EX & OUTPUT_EX_COPD) > 0
output_ex.n_inc_COPD_by_ctime_age[(int)floor((*ag).time_at_creation+(*ag).local_time)][(int)floor((*ag).age_at_creation+(*ag).local_time)]+=1;
#endif
}
shahzadg
The definition of COPD should be upgraded to LLN, instead of the fixed 0.7 ratio threshold for FEV1/FVC, as per Hankinson JL, Odencrantz JR, Fedan KB. Spirometric reference values from a sample of the general US population. American journal of respiratory and critical care medicine. 1999 Jan 1;159(1):179-87.
The change has already taken place in POHEM model.