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report.R
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report.R
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library('tidyverse')
df_input <- read_csv(
here::here("output", "input.csv"),
col_types = cols(patient_id = col_integer(),age = col_double())
)
head(df_input)
## Convert age into categorical variable using cut-off 80 years
df_input$age_c <- ifelse(df_input$age<80,1,0)
data <- df_input[df_input$age_c==1,]
data80 <- df_input[df_input$age_c==0,]
summary(df_input$age_c)
class(df_input$age_c)
#### calculate outcomes for under 80
summary(data$last_systolic_bp_measure)
summary(data$last_ambulatory_systolic_bp_measure)
summary(data$last_ambulatory_systolic_bp_measure_narrow)
summary(data$last_ambulatory_systolic_bp_measure)
# calculate SBP under 140 using different measurements
data$bp140 <- ifelse(data$last_ambulatory_systolic_bp_measure<140,1,0)
data$ambp140.narrow <- ifelse(data$last_ambulatory_systolic_bp_measure_narrow<140,1,0)
data$ambp140.broad <- ifelse(data$last_ambulatory_systolic_bp_measure<140,1,0)
# calculate SBP under 135 using different AMBP/HBPM
data$ambp135.narrow <- ifelse(data$last_ambulatory_systolic_bp_measure_narrow<135,1,0)
data$ambp135.broad <- ifelse(data$last_ambulatory_systolic_bp_measure<135,1,0)
summary(as.factor(data$ambp140.narrow))
summary(as.factor(data$ambp140.broad))
summary(as.factor(data$ambp135.narrow))
summary(as.factor(data$ambp135.broad))
summary(as.factor(data$bp140))
## Create table with SBP between 140 and 135
all.bp.narrow <- table(data$ambp140.narrow, data$ambp135.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
all.bp.narrow <- data.frame(all.bp.narrow)
write.csv(all.bp.narrow, file="all.bp.narrow.csv")
all.bp.broad <- table(data$ambp140.broad, data$ambp135.broad,
useNA = "ifany",
dnn = c("under140","under135"))
all.bp.broad <- data.frame(all.bp.broad)
write.csv(all.bp.broad, file="all.bp.broad.csv")
## stratified analysis by CVD, CKD and DM
## SBP 140 overall
ckd <- table(data$bp140, data$CKD_code,useNA = "ifany", dnn = c("SBP140","CKD"))
ckd <- data.frame(ckd)
cvd <- table(data$bp140, data$CVD_code,useNA = "ifany", dnn = c("SBP140","CVD"))
cvd <- data.frame(cvd)
t1d <- table(data$bp140, data$T1D_code,useNA = "ifany", dnn = c("SBP140","T1D"))
t1d <- data.frame(t1d)
t2d <- table(data$bp140, data$T2D_code,useNA = "ifany", dnn = c("SBP140","T2D"))
t2d <- data.frame(t2d)
bp.subgroups <- data.frame(ckd, cvd, t2d, t2d)
write.csv(bp.subgroups, file="bp.subgroups.csv")
## SBP between 140 and 135
data.ckd <- data[data$CKD_code==1,]
ckd.bp.narrow <- table(data.ckd$ambp140.narrow, data.ckd$ambp135.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
ckd.bp.narrow <- data.frame(ckd.bp.narrow)
write.csv(ckd.bp.narrow, file="ckd.bp.narrow.csv")
data.cvd <- data[data$CVD_code==1,]
cvd.bp.narrow <- table(data.cvd$ambp140.narrow, data.cvd$ambp135.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
cvd.bp.narrow <- data.frame(cvd.bp.narrow)
write.csv(cvd.bp.narrow, file="cvd.bp.narrow.csv")
data.t1d <- data[data$T1D_code==1,]
t1d.bp.narrow <- table(data.t1d$ambp140.narrow, data.t1d$ambp135.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
t1d.bp.narrow <- data.frame(t1d.bp.narrow)
write.csv(t1d.bp.narrow, file="t1d.bp.narrow.csv")
data.t2d <- data[data$T2D_code==1,]
t2d.bp.narrow <- table(data.t2d$ambp140.narrow, data.t2d$ambp135.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
t2d.bp.narrow <- data.frame(t2d.bp.narrow)
write.csv(t2d.bp.narrow, file="t2d.bp.narrow.csv")
#### calculate outcomes for over 80
summary(data80$last_systolic_bp_measure)
summary(data80$last_ambulatory_systolic_bp_measure)
summary(data80$last_ambulatory_systolic_bp_measure_narrow)
# calculate SBP under 150 using different measurements
data80$bp150 <- ifelse(data80$last_ambulatory_systolic_bp_measure<150,1,0)
data80$ambp150.narrow <- ifelse(data80$last_ambulatory_systolic_bp_measure_narrow<150,1,0)
data80$ambp150.broad <- ifelse(data80$last_ambulatory_systolic_bp_measure<150,1,0)
# calculate SBP under 145 using different AMBP/HBPM
data80$ambp145.narrow <- ifelse(data80$last_ambulatory_systolic_bp_measure_narrow<145,1,0)
data80$ambp145.broad <- ifelse(data80$last_ambulatory_systolic_bp_measure<145,1,0)
summary(as.factor(data80$ambp150.narrow))
summary(as.factor(data80$ambp150.broad))
summary(as.factor(data80$ambp145.narrow))
summary(as.factor(data80$ambp145.broad))
summary(as.factor(data80$bp150))
## Create table with SBP between 150 and 145
all.bp.narrow80 <- table(data80$ambp150.narrow, data80$ambp145.narrow,
useNA = "ifany",
dnn = c("under150","under145"))
all.bp.narrow80 <- data.frame(all.bp.narrow80)
write.csv(all.bp.narrow80, file="all.bp.narrow80.csv")
all.bp.broad80 <- table(data80$ambp150.broad, data80$ambp145.broad,
useNA = "ifany",
dnn = c("under150","under145"))
all.bp.broad80 <- data.frame(all.bp.broad80)
write.csv(all.bp.broad80, file="all.bp.broad80.csv")
## stratified analysis by CVD, CKD and DM
## SBP 140 overall
ckd80 <- table(data80$bp150, data80$CKD_code,useNA = "ifany", dnn = c("SBP150","CKD"))
ckd80 <- data.frame(ckd80)
cvd80 <- table(data80$bp150, data80$CVD_code,useNA = "ifany", dnn = c("SBP150","CVD"))
cvd80 <- data.frame(cvd80)
t1d80 <- table(data80$bp150, data80$T1D_code,useNA = "ifany", dnn = c("SBP150","T1D"))
t1d80 <- data.frame(t1d80)
t2d80 <- table(data80$bp150, data80$T2D_code,useNA = "ifany", dnn = c("SBP150","T2D"))
t2d80 <- data.frame(t2d80)
bp.subgroups80 <- data.frame(ckd80, cvd80, t2d80, t2d80)
write.csv(bp.subgroups80, file="bp.subgroups80.csv")
## SBP between 150 and 145
data.ckd80 <- data80[data80$CKD_code==1,]
ckd.bp.narrow80 <- table(data.ckd80$ambp150.narrow, data.ckd80$ambp145.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
ckd.bp.narrow80 <- data.frame(ckd.bp.narrow80)
write.csv(ckd.bp.narrow80, file="ckd.bp.narrow80.csv")
data.cvd80 <- data80[data80$CVD_code==1,]
cvd.bp.narrow80 <- table(data.cvd80$ambp150.narrow, data.cvd80$ambp145.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
cvd.bp.narrow80 <- data.frame(cvd.bp.narrow80)
write.csv(cvd.bp.narrow80, file="cvd.bp.narrow80.csv")
data.t1d80 <- data80[data80$T1D_code==1,]
t1d.bp.narrow80 <- table(data.t1d80$ambp150.narrow, data.t1d80$ambp145.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
t1d.bp.narrow80 <- data.frame(t1d.bp.narrow80)
write.csv(t1d.bp.narrow80, file="t1d.bp.narrow80.csv")
data.t2d80 <- data80[data80$T2D_code==1,]
t2d.bp.narrow80 <- table(data.t2d80$ambp150.narrow, data.t2d80$ambp145.narrow,
useNA = "ifany",
dnn = c("under140","under135"))
t2d.bp.narrow80 <- data.frame(t2d.bp.narrow80)
write.csv(t2d.bp.narrow80, file="t2d.bp.narrow80.csv")