#--------------- #Read in data #--------------- covid_p<-read.csv('covid_p.csv',header=T) str(covid_p) dim(covid_p) #make factor covid_p$time<-factor(covid_p$time) #make 'before' the baseline covid_p$time<-relevel(covid_p$time,"before") #adjustment of visits for blood and swabs #these sample types were collected during these visits as per the protocol covid_p$Adjusted.Actual.Visits<-covid_p$Actual.Visits-covid_p$b2adjustment #--------------- #Attendance rate #--------------- m1<-glm( Actual.Visits~offset(log(Theoretical.Visits))+time,data=covid_p,family="poisson") summary(m1) #There is no significant difference in attendance rate before and after covid p = pchisq(m1$null.deviance-m1$deviance, m1$df.null-m1$df.residual, lower.tail=FALSE);p #attendance rate pre covid exp(summary(m1)$'coefficients'[1,c(1)])*100 #attendance rate post covid exp(summary(m1)$'coefficients'[1,c(1)]+summary(m1)$'coefficients'[2,c(1)])*100 #--------------------- #Stool collection rate #--------------------- m3<-glm( stool~offset(log(Actual.Visits))+time,data=covid_p,family="poisson") summary(m3) #There is no significant difference in stool collection rate before and after covid p = pchisq(m3$null.deviance-m3$deviance, m3$df.null-m3$df.residual, lower.tail=FALSE);p #collection rate of stools was exp(summary(m3)$'coefficients'[1,c(1)])*100 #--------------------- #Blood collection rate #--------------------- m5<-glm( blood~offset(log(Adjusted.Actual.Visits))+time,data=covid_p,family="poisson") summary(m5) #there is a significant different in blood collection rate before and after covid p = pchisq(m5$null.deviance-m5$deviance, 1, lower.tail=FALSE);p #coefficient exp(summary(m5)$'coefficients'[2,c(1)]) #confidence interval ci<-confint(m5)[2,] exp(ci) #--------------------- #Swab collection rate #--------------------- m7<-glm( swab~offset(log(Adjusted.Actual.Visits))+time,data=covid_p,family="poisson") summary(m7) p = pchisq(m7$null.deviance-m7$deviance, 1, lower.tail=FALSE);p #coefficient exp(summary(m7)$'coefficients'[2,c(1)]) ci<-confint(m7)[2,] #confidence interval exp(ci)