R/bp.R
In Puddlepp/goldfunctions: Extracts Data From CPRD GOLD
Defines functions
bp
Documented in
bp
#' Blood Pressure
#'
#' This function extracts systolic and diastolic test results from CPRD GOLD.
#' It assumes that your cohort contains a column named patid.
#'
#' Codes:
#'
#' \tabular{lllll}{
#' Medcode \tab \tab Readcode \tab \tab Description\cr
#' 1 \tab \tab 246..00 \tab \tab O/E - blood pressure reading\cr
#' 57 \tab \tab 246..11 \tab \tab O/E - BP reading\cr
#' 100 \tab \tab 246..12 \tab \tab O/E - blood pressure\cr
#' 101 \tab \tab 2461 \tab \tab O/E - BP reading very low\cr
#' 102 \tab \tab 662L.00 \tab \tab 24 hr blood pressure monitoring\cr
#' 103 \tab \tab 246V.00 \tab \tab Average 24 hour diastolic blood pressure\cr
#' 351 \tab \tab G20..11 \tab \tab High blood pressure\cr
#' 676 \tab \tab R1y2.00 \tab \tab \[D\]Raised blood pressure reading\cr
#' 803 \tab \tab 68B1.00 \tab \tab Hypertension screen\cr
#' 859 \tab \tab 2464 \tab \tab O/E - BP reading normal\cr
#' 1956 \tab \tab 9OD..11 \tab \tab BP screen administration\cr
#' 3481 \tab \tab 2465 \tab \tab O/E - BP borderline raised\cr
#' 5020 \tab \tab 2466 \tab \tab O/E - BP reading raised\cr
#' 5341 \tab \tab 2462 \tab \tab O/E - BP reading low\cr
#' 5760 \tab \tab ZV70B00 \tab \tab \[V\]Examination of blood pressure\cr
#' 6598 \tab \tab R1y3.00 \tab \tab \[D\]Low blood pressure reading\cr
#' 8574 \tab \tab 662Q.00 \tab \tab Borderline blood pressure\cr
#' 8732 \tab \tab G2...11 \tab \tab BP - hypertensive disease\cr
#' 10055 \tab \tab R1y4.00 \tab \tab \[D\]BP reading labile\cr
#' 14448 \tab \tab 315B.00 \tab \tab Ambulatory blood pressure recording\cr
#' 14452 \tab \tab 2468 \tab \tab O/E - BP reading:postural drop\cr
#' 14640 \tab \tab 246C.00 \tab \tab Lying blood pressure reading\cr
#' 14641 \tab \tab 246D.00 \tab \tab Standing blood pressure reading\cr
#' 14642 \tab \tab 246E.00 \tab \tab Sitting blood pressure reading\cr
#' 14643 \tab \tab 2467 \tab \tab O/E - BP reading very high\cr
#' 15126 \tab \tab 6623 \tab \tab Pre-treatment BP reading\cr
#' 16288 \tab \tab 9OD7.00 \tab \tab BP screen - 3rd recall\cr
#' 16478 \tab \tab 9OD2.00 \tab \tab BP screen - 2nd call\cr
#' 16541 \tab \tab 9OD..12 \tab \tab Blood pressure screen admin\cr
#' 18418 \tab \tab 246Q.00 \tab \tab Sitting systolic blood pressure\cr
#' 19905 \tab \tab 246J.00 \tab \tab O/E - BP reading: no postural drop\cr
#' 20049 \tab \tab 662V.00 \tab \tab Blood pressure monitoring\cr
#' 22476 \tab \tab 662j.00 \tab \tab Blood pressure recorded by patient at home\cr
#' 22595 \tab \tab 246A.00 \tab \tab O/E - Diastolic BP reading\cr
#' 23312 \tab \tab 2469 \tab \tab O/E - Systolic BP reading\cr
#' 25553 \tab \tab 246G.00 \tab \tab O/E - BP labile\cr
#' 27271 \tab \tab 246B.00 \tab \tab O/E - BP stable\cr
#' 27272 \tab \tab 246Z.00 \tab \tab O/E-blood pressure reading NOS\cr
#' 27273 \tab \tab 246F.00 \tab \tab O/E - blood pressure decreased\cr
#' 27274 \tab \tab 2463 \tab \tab O/E - BP borderline low\cr
#' 27534 \tab \tab 662C.00 \tab \tab O/E - check high BP\cr
#' 29261 \tab \tab 246d.00 \tab \tab Average home systolic blood pressure\cr
#' 29390 \tab \tab 662B.00 \tab \tab O/E - initial high BP\cr
#' 31305 \tab \tab 246c.00 \tab \tab Average home diastolic blood pressure\cr
#' 33330 \tab \tab 246K.00 \tab \tab Target systolic blood pressure\cr
#' 34186 \tab \tab 9OD5.00 \tab \tab BP screen - 1st recall\cr
#' 34187 \tab \tab 9OD6.00 \tab \tab BP screen - 2nd recall\cr
#' 34231 \tab \tab 9OD1.00 \tab \tab BP screen - 1st call\cr
#' 34244 \tab \tab 9OD3.00 \tab \tab BP screen - 3rd call\cr
#' 34618 \tab \tab 246Y.00 \tab \tab Average day interval systolic blood pressure\cr
#' 37242 \tab \tab 246N.00 \tab \tab Standing systolic blood pressure\cr
#' 37243 \tab \tab 246P.00 \tab \tab Standing diastolic blood pressure\cr
#' 37312 \tab \tab 2460 \tab \tab O/E - BP unrecordable\cr
#' 38277 \tab \tab 246W.00 \tab \tab Average 24 hour systolic blood pressure\cr
#' 38278 \tab \tab 246b.00 \tab \tab Average night interval systolic blood pressure\cr
#' 41052 \tab \tab 246e.00 \tab \tab Ambulatory systolic blood pressure\cr
#' 41445 \tab \tab 246X.00 \tab \tab Average day interval diastolic blood pressure\cr
#' 42280 \tab \tab 246R.00 \tab \tab Sitting diastolic blood pressure\cr
#' 43282 \tab \tab 246S.00 \tab \tab Lying systolic blood pressure\cr
#' 43547 \tab \tab 246a.00 \tab \tab Average night interval diastolic blood pressure\cr
#' 43719 \tab \tab 9OD9.00 \tab \tab BP ABNORMAL - 1st recall\cr
#' 47932 \tab \tab 9ODA.00 \tab \tab BP ABNORMAL - 2nd recall\cr
#' 48008 \tab \tab 246f.00 \tab \tab Ambulatory diastolic blood pressure\cr
#' 51357 \tab \tab 246L.00 \tab \tab Target diastolic blood pressure\cr
#' 55411 \tab \tab 9ODB.00 \tab \tab BP ABNORMAL - 3rd recall\cr
#' 65990 \tab \tab 246T.00 \tab \tab Lying diastolic blood pressure\cr
#' 94807 \tab \tab 246g.00 \tab \tab Self measured blood pressure reading\cr
#' }
#'
#' @param cohort A dataframe containing at least one column called patid
#' @return A dataframe containing all systolic and diastolic blood pressure records
#' @export
bp <- function(cohort) {
# Draw out the cohort patids.
cohort_patid <-
cohort %>%
pull(patid)
# Retrieve medical table entries for the relevant readcodes.
bp_gold <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("medical"))) %>%
filter(readcode %in% c( "246..00", "246..11", "246..12", "2461.00", "662L.00",
"246V.00", "G20..11", "R1y2.00", "68B1.00", "2464.00",
"9OD..11", "2465.00", "2466.00", "2462.00", "ZV70B00",
"R1y3.00", "662Q.00", "G2...11", "R1y4.00", "315B.00",
"2468.00", "246C.00", "246D.00", "246E.00", "2467.00",
"6623.00", "9OD7.00", "9OD2.00", "9OD..12", "246Q.00",
"246J.00", "662V.00", "662j.00", "246A.00", "2469.00",
"246G.00", "246B.00", "246Z.00", "246F.00", "2463.00",
"662C.00", "246d.00", "662B.00", "246c.00", "246K.00",
"9OD5.00", "9OD6.00", "9OD1.00", "9OD3.00", "246Y.00",
"246N.00", "246P.00", "2460.00", "246W.00", "246b.00",
"246e.00", "246X.00", "246R.00", "246S.00", "246a.00",
"9OD9.00", "9ODA.00", "246f.00", "246L.00", "9ODB.00",
"246T.00", "246g.00")) %>%
collect()
# Draw out the medcodes.
bp_gold_medcode <-
bp_gold %>%
pull(medcode)
# Identify relevant enttypes and units of measurement (on separate script).
# Retrieve all clinical table entries for the cohort.
bp_cohort <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("clinical"))) %>%
filter(patid %in% cohort_patid,
medcode %in% bp_gold_medcode,
enttype %in% c("1")) %>%
collect()
# Draw out the adids.
bp_cohort_adid <-
bp_cohort %>%
pull(adid)
# Retrieve all additional table entries for the cohort.
bp_additional <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("additional"))) %>%
filter(adid %in% bp_cohort_adid) %>%
collect()
# Combine the clinical and additional tables
bp_cohort_1 <-
full_join(x = bp_cohort,
y = bp_additional,
by = c("patid",
"eventdate",
"sysdate",
"enttype",
"adid"))
# Retrieve entity table records for use below.
bp_entity <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("entity"))) %>%
filter(enttype %in% c("1")) %>%
collect()
# Retrieve lookup_xxx table entries and prepare them for lookups below.
lookup <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("lookup_xxx"))) %>%
collect() %>%
mutate(together = paste0(reference, code))
# Complete all lookups for our cohort table.
bp_cohort_2 <-
bp_cohort_1 %>%
mutate(data5_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data5_lkup),
data6_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data6_lkup),
data7_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data7_lkup),
diastolic_data1 = "Diastolic",
systolic_data2 = "Systolic",
korotkoff_data3 = "Korotkoff",
event_time_data4 = "Event time",
laterality_data5 = VLOOKUP(paste0(data5_lkup, data5),
lookup,
together,
text),
posture_data6 = VLOOKUP(paste0(data6_lkup, data6),
lookup,
together,
text),
cuff_data7 = VLOOKUP(paste0(data7_lkup, data7),
lookup,
together,
text),
consultation_type = VLOOKUP(paste0("SED", constype),
lookup,
together,
text),
medical_type = VLOOKUP(medcode,
bp_gold,
medcode,
desc),
entity_type = VLOOKUP(enttype,
bp_entity,
enttype,
description)) %>%
select(patid, eventdate, sysdate, constype, consultation_type, consid, staffid,
medcode, medical_type, enttype, entity_type, data1, diastolic_data1,
data2, systolic_data2, data3, korotkoff_data3, data4, event_time_data4,
data5, laterality_data5, data6, posture_data6, data7, cuff_data7)
return(bp_cohort_2)
}
Puddlepp/goldfunctions documentation built on Dec. 18, 2021, 8:41 a.m.
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Defines functions bp
Documented in bp
#' Blood Pressure
#'
#' This function extracts systolic and diastolic test results from CPRD GOLD.
#' It assumes that your cohort contains a column named patid.
#'
#' Codes:
#'
#' \tabular{lllll}{
#' Medcode \tab \tab Readcode \tab \tab Description\cr
#' 1 \tab \tab 246..00 \tab \tab O/E - blood pressure reading\cr
#' 57 \tab \tab 246..11 \tab \tab O/E - BP reading\cr
#' 100 \tab \tab 246..12 \tab \tab O/E - blood pressure\cr
#' 101 \tab \tab 2461 \tab \tab O/E - BP reading very low\cr
#' 102 \tab \tab 662L.00 \tab \tab 24 hr blood pressure monitoring\cr
#' 103 \tab \tab 246V.00 \tab \tab Average 24 hour diastolic blood pressure\cr
#' 351 \tab \tab G20..11 \tab \tab High blood pressure\cr
#' 676 \tab \tab R1y2.00 \tab \tab \[D\]Raised blood pressure reading\cr
#' 803 \tab \tab 68B1.00 \tab \tab Hypertension screen\cr
#' 859 \tab \tab 2464 \tab \tab O/E - BP reading normal\cr
#' 1956 \tab \tab 9OD..11 \tab \tab BP screen administration\cr
#' 3481 \tab \tab 2465 \tab \tab O/E - BP borderline raised\cr
#' 5020 \tab \tab 2466 \tab \tab O/E - BP reading raised\cr
#' 5341 \tab \tab 2462 \tab \tab O/E - BP reading low\cr
#' 5760 \tab \tab ZV70B00 \tab \tab \[V\]Examination of blood pressure\cr
#' 6598 \tab \tab R1y3.00 \tab \tab \[D\]Low blood pressure reading\cr
#' 8574 \tab \tab 662Q.00 \tab \tab Borderline blood pressure\cr
#' 8732 \tab \tab G2...11 \tab \tab BP - hypertensive disease\cr
#' 10055 \tab \tab R1y4.00 \tab \tab \[D\]BP reading labile\cr
#' 14448 \tab \tab 315B.00 \tab \tab Ambulatory blood pressure recording\cr
#' 14452 \tab \tab 2468 \tab \tab O/E - BP reading:postural drop\cr
#' 14640 \tab \tab 246C.00 \tab \tab Lying blood pressure reading\cr
#' 14641 \tab \tab 246D.00 \tab \tab Standing blood pressure reading\cr
#' 14642 \tab \tab 246E.00 \tab \tab Sitting blood pressure reading\cr
#' 14643 \tab \tab 2467 \tab \tab O/E - BP reading very high\cr
#' 15126 \tab \tab 6623 \tab \tab Pre-treatment BP reading\cr
#' 16288 \tab \tab 9OD7.00 \tab \tab BP screen - 3rd recall\cr
#' 16478 \tab \tab 9OD2.00 \tab \tab BP screen - 2nd call\cr
#' 16541 \tab \tab 9OD..12 \tab \tab Blood pressure screen admin\cr
#' 18418 \tab \tab 246Q.00 \tab \tab Sitting systolic blood pressure\cr
#' 19905 \tab \tab 246J.00 \tab \tab O/E - BP reading: no postural drop\cr
#' 20049 \tab \tab 662V.00 \tab \tab Blood pressure monitoring\cr
#' 22476 \tab \tab 662j.00 \tab \tab Blood pressure recorded by patient at home\cr
#' 22595 \tab \tab 246A.00 \tab \tab O/E - Diastolic BP reading\cr
#' 23312 \tab \tab 2469 \tab \tab O/E - Systolic BP reading\cr
#' 25553 \tab \tab 246G.00 \tab \tab O/E - BP labile\cr
#' 27271 \tab \tab 246B.00 \tab \tab O/E - BP stable\cr
#' 27272 \tab \tab 246Z.00 \tab \tab O/E-blood pressure reading NOS\cr
#' 27273 \tab \tab 246F.00 \tab \tab O/E - blood pressure decreased\cr
#' 27274 \tab \tab 2463 \tab \tab O/E - BP borderline low\cr
#' 27534 \tab \tab 662C.00 \tab \tab O/E - check high BP\cr
#' 29261 \tab \tab 246d.00 \tab \tab Average home systolic blood pressure\cr
#' 29390 \tab \tab 662B.00 \tab \tab O/E - initial high BP\cr
#' 31305 \tab \tab 246c.00 \tab \tab Average home diastolic blood pressure\cr
#' 33330 \tab \tab 246K.00 \tab \tab Target systolic blood pressure\cr
#' 34186 \tab \tab 9OD5.00 \tab \tab BP screen - 1st recall\cr
#' 34187 \tab \tab 9OD6.00 \tab \tab BP screen - 2nd recall\cr
#' 34231 \tab \tab 9OD1.00 \tab \tab BP screen - 1st call\cr
#' 34244 \tab \tab 9OD3.00 \tab \tab BP screen - 3rd call\cr
#' 34618 \tab \tab 246Y.00 \tab \tab Average day interval systolic blood pressure\cr
#' 37242 \tab \tab 246N.00 \tab \tab Standing systolic blood pressure\cr
#' 37243 \tab \tab 246P.00 \tab \tab Standing diastolic blood pressure\cr
#' 37312 \tab \tab 2460 \tab \tab O/E - BP unrecordable\cr
#' 38277 \tab \tab 246W.00 \tab \tab Average 24 hour systolic blood pressure\cr
#' 38278 \tab \tab 246b.00 \tab \tab Average night interval systolic blood pressure\cr
#' 41052 \tab \tab 246e.00 \tab \tab Ambulatory systolic blood pressure\cr
#' 41445 \tab \tab 246X.00 \tab \tab Average day interval diastolic blood pressure\cr
#' 42280 \tab \tab 246R.00 \tab \tab Sitting diastolic blood pressure\cr
#' 43282 \tab \tab 246S.00 \tab \tab Lying systolic blood pressure\cr
#' 43547 \tab \tab 246a.00 \tab \tab Average night interval diastolic blood pressure\cr
#' 43719 \tab \tab 9OD9.00 \tab \tab BP ABNORMAL - 1st recall\cr
#' 47932 \tab \tab 9ODA.00 \tab \tab BP ABNORMAL - 2nd recall\cr
#' 48008 \tab \tab 246f.00 \tab \tab Ambulatory diastolic blood pressure\cr
#' 51357 \tab \tab 246L.00 \tab \tab Target diastolic blood pressure\cr
#' 55411 \tab \tab 9ODB.00 \tab \tab BP ABNORMAL - 3rd recall\cr
#' 65990 \tab \tab 246T.00 \tab \tab Lying diastolic blood pressure\cr
#' 94807 \tab \tab 246g.00 \tab \tab Self measured blood pressure reading\cr
#' }
#'
#' @param cohort A dataframe containing at least one column called patid
#' @return A dataframe containing all systolic and diastolic blood pressure records
#' @export
bp <- function(cohort) {
# Draw out the cohort patids.
cohort_patid <-
cohort %>%
pull(patid)
# Retrieve medical table entries for the relevant readcodes.
bp_gold <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("medical"))) %>%
filter(readcode %in% c( "246..00", "246..11", "246..12", "2461.00", "662L.00",
"246V.00", "G20..11", "R1y2.00", "68B1.00", "2464.00",
"9OD..11", "2465.00", "2466.00", "2462.00", "ZV70B00",
"R1y3.00", "662Q.00", "G2...11", "R1y4.00", "315B.00",
"2468.00", "246C.00", "246D.00", "246E.00", "2467.00",
"6623.00", "9OD7.00", "9OD2.00", "9OD..12", "246Q.00",
"246J.00", "662V.00", "662j.00", "246A.00", "2469.00",
"246G.00", "246B.00", "246Z.00", "246F.00", "2463.00",
"662C.00", "246d.00", "662B.00", "246c.00", "246K.00",
"9OD5.00", "9OD6.00", "9OD1.00", "9OD3.00", "246Y.00",
"246N.00", "246P.00", "2460.00", "246W.00", "246b.00",
"246e.00", "246X.00", "246R.00", "246S.00", "246a.00",
"9OD9.00", "9ODA.00", "246f.00", "246L.00", "9ODB.00",
"246T.00", "246g.00")) %>%
collect()
# Draw out the medcodes.
bp_gold_medcode <-
bp_gold %>%
pull(medcode)
# Identify relevant enttypes and units of measurement (on separate script).
# Retrieve all clinical table entries for the cohort.
bp_cohort <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("clinical"))) %>%
filter(patid %in% cohort_patid,
medcode %in% bp_gold_medcode,
enttype %in% c("1")) %>%
collect()
# Draw out the adids.
bp_cohort_adid <-
bp_cohort %>%
pull(adid)
# Retrieve all additional table entries for the cohort.
bp_additional <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("additional"))) %>%
filter(adid %in% bp_cohort_adid) %>%
collect()
# Combine the clinical and additional tables
bp_cohort_1 <-
full_join(x = bp_cohort,
y = bp_additional,
by = c("patid",
"eventdate",
"sysdate",
"enttype",
"adid"))
# Retrieve entity table records for use below.
bp_entity <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("entity"))) %>%
filter(enttype %in% c("1")) %>%
collect()
# Retrieve lookup_xxx table entries and prepare them for lookups below.
lookup <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("lookup_xxx"))) %>%
collect() %>%
mutate(together = paste0(reference, code))
# Complete all lookups for our cohort table.
bp_cohort_2 <-
bp_cohort_1 %>%
mutate(data5_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data5_lkup),
data6_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data6_lkup),
data7_lkup = VLOOKUP(bp_cohort_1$enttype,
bp_entity,
enttype,
data7_lkup),
diastolic_data1 = "Diastolic",
systolic_data2 = "Systolic",
korotkoff_data3 = "Korotkoff",
event_time_data4 = "Event time",
laterality_data5 = VLOOKUP(paste0(data5_lkup, data5),
lookup,
together,
text),
posture_data6 = VLOOKUP(paste0(data6_lkup, data6),
lookup,
together,
text),
cuff_data7 = VLOOKUP(paste0(data7_lkup, data7),
lookup,
together,
text),
consultation_type = VLOOKUP(paste0("SED", constype),
lookup,
together,
text),
medical_type = VLOOKUP(medcode,
bp_gold,
medcode,
desc),
entity_type = VLOOKUP(enttype,
bp_entity,
enttype,
description)) %>%
select(patid, eventdate, sysdate, constype, consultation_type, consid, staffid,
medcode, medical_type, enttype, entity_type, data1, diastolic_data1,
data2, systolic_data2, data3, korotkoff_data3, data4, event_time_data4,
data5, laterality_data5, data6, posture_data6, data7, cuff_data7)
return(bp_cohort_2)
}
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