#' Glomerular Filtration Rate (GFR)
#'
#' This function extracts glomerular filtration rate 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
#' 19747 \tab \tab 451F.00 \tab \tab Glomerular filtration rate\cr
#' }
#'
#' @param cohort A dataframe containing at least one column called patid
#' @return A dataframe containing all glomerular filtration rate records
#' @export
gfr <- function(cohort) {
# Draw out the cohort patids.
cohort_patid <-
cohort %>%
pull(patid)
# Retrieve medical table entries for the relevant readcodes.
gfr_gold <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("medical"))) %>%
filter(readcode %in% c("451F.00")) %>%
collect()
# Draw out the medcodes.
gfr_gold_medcode <-
gfr_gold %>%
pull(medcode)
# Identify relevant enttypes and units of measurement (on separate script).
# Retrieve all test table entries for the cohort.
gfr_cohort <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("test"))) %>%
filter(patid %in% cohort_patid,
medcode %in% gfr_gold_medcode,
enttype %in% c("288", "315", "466", "480"),
data3 %in% c("0", "21", "90", "208", "249", "251", "288", "298")) %>%
collect()
# Retrieve entity table records for use below.
gfr_entity <-
tbl(con,
in_schema(schema = sql("cprd0121.dbo"),
table = sql("entity"))) %>%
filter(enttype %in% c("288", "315", "466", "480")) %>%
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.
gfr_cohort_1 <-
gfr_cohort %>%
mutate(data1_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data1_lkup),
data2_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data2_lkup),
data3_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data3_lkup),
data4_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data4_lkup),
data5_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data5_lkup),
data6_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data6_lkup),
data7_lkup = VLOOKUP(gfr_cohort$enttype,
gfr_entity,
enttype,
data7_lkup),
operator_data1 = VLOOKUP(paste0(data1_lkup, data1),
lookup,
together,
text),
value_data2 = "Value",
unit_of_measure_data3 = VLOOKUP(paste0(data3_lkup, data3),
lookup,
together,
text),
qualifier_data4 = VLOOKUP(paste0(data4_lkup, data4),
lookup,
together,
text),
normal_range_from_data5 = "Normal range from",
normal_range_to_data6 = "Normal range to",
normal_range_basis_data7 = VLOOKUP(paste0(data7_lkup, data7),
lookup,
together,
text),
consultation_type = VLOOKUP(paste0("SED", constype),
lookup,
together,
text),
medical_type = VLOOKUP(medcode,
gfr_gold,
medcode,
desc),
entity_type = VLOOKUP(enttype,
gfr_entity,
enttype,
description)) %>%
select(patid, eventdate, sysdate, constype, consultation_type, consid, staffid,
medcode, medical_type, enttype, entity_type, data1, operator_data1, data2, value_data2,
data3, unit_of_measure_data3, data4, qualifier_data4, data5, normal_range_from_data5,
data6, normal_range_to_data6)
return(gfr_cohort_1)
}
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