R/icd10.R
In adamleejohnson/R-ukbiobank: UK Biobank Utilities
Defines functions
icd10_lookup
Documented in
icd10_lookup
#' @title ICD10 lookups
#' @description Perform ICD10 lookups using coding 19, as specified in \url{https://biobank.ndph.ox.ac.uk/ukb/coding.cgi?id=19}. For disease-specific `icd10_*()` functions, an internal `icd10_text_to_codes()` function is used to convert the text version of ICD10 names into their respective UKB codings.
#' @inheritParams ukbiobank
#' @inheritSection ukbiobank Instancing
#' @inheritSection ukbiobank Column names
#' @param codes ICD10 codes to look up.
#' @export
icd10_lookup <- function(data,
codes,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10,
icd10_date_col = f.41280.0.0.Date_of_first_in_patient_diagnosis_ICD10,
date_of_instance_col = f.53.0.0.Date_of_attending_assessment_centre) {
# convert icd10 codes to ukb codings
icd10_lookups <-
tibble(icd10 = codes) %>%
left_join(coding_icd10, by = "icd10") %>%
pull("coding")
# remove any columns with only NAs
data %<>% remove_na_columns()
codes %<>% unique()
# generate lists of column names
date_of_instance_colnames <- expand_instances(data, {{ date_of_instance_col }})
icd10_colnames <- expand_array(data, {{ icd10_col }})
icd10_date_colnames <- expand_array(data, {{ icd10_date_col }})
stopifnot(length(icd10_colnames) == length(icd10_date_colnames))
# define function that will return whether the patient has icd10 codes
# and were diagnosed on or before the date of the instance/assessment
icd10_by_instance <- function(inst) {
# Check if icd10 codes match the provided search codes
icd_match <-
data %>%
select(!!!icd10_colnames) %>%
mutate(across(everything(), ~ .x %in% icd10_lookups)) %>%
as.matrix()
# compare dates from the icd columns to dates of the instance,
# and create a filter based on whether the date is allowed
inst_dates <-
data %>%
pull(!!date_of_instance_colnames[[inst + 1]]) %>%
as.Date() %>%
as.integer() %>%
matrix(., length(.), length(icd10_date_colnames))
icd_dates <-
data %>%
select(!!!icd10_date_colnames) %>%
mutate(across(everything(), ~ as.integer(as.Date(.x)))) %>%
as.matrix()
keep_icd <- icd_dates <= inst_dates
keep_icd <- ifelse(is.na(keep_icd), F, keep_icd)
# Apply the filter based on whether the date of the icd diagnosis is allowed
icd_match <- icd_match & keep_icd
icd_match %>% any_by_row()
}
instance_combiner(
data,
lookup_by_instance_fn = icd10_by_instance,
after_instance = {{ after_instance }},
up_to_instance = {{ up_to_instance }}
)
}
#' @noRd
icd10_text_to_codes <- function(text) {
codes <-
text %>%
stringr::str_trim(.) %>%
stringr::str_split(., "\n", simplify = T) %>%
stringr::str_trim(.) %>%
stringr::str_split(., "\\s", 2, simplify = T)
codes <- codes[, 1]
codes <- codes[which(codes != "")]
codes %<>% unique()
}
#' @rdname icd10_lookup
#' @export
icd10_htn <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I10 Essential (primary) hypertension
I11 Hypertensive heart disease
I11.0 Hypertensive heart disease with (congestive) heart failure
I11.9 Hypertensive heart disease without (congestive) heart failure
I12 Hypertensive renal disease
I12.0 Hypertensive renal disease with renal failure
I12.9 Hypertensive renal disease without renal failure
I13 Hypertensive heart and renal disease
I13.0 Hypertensive heart and renal disease with (congestive) heart failure
I13.1 Hypertensive heart and renal disease with renal failure
I13.2 Hypertensive heart and renal disease with both (congestive) heart failure and renal failure
I13.9 Hypertensive heart and renal disease, unspecified
I15 Secondary hypertension
I15.0 Renovascular hypertension
I15.1 Hypertension secondary to other renal disorders
I15.2 Hypertension secondary to endocrine disorders
I15.8 Other secondary hypertension
I15.9 Seconday hypertension, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_hld <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
E78.0 Pure hypercholesterolaemia
E78.1 Pure hyperglyceridaemia
E78.2 Mixed hyperlipidaemia
E78.4 Other hyperlipidaemia
E78.5 Hyperlipidaemia, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_heart_failure <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I50 Heart failure
I50.0 Congestive heart failure
I50.1 Left ventricular failure
I50.9 Heart failure, unspecified
I11.0 Hypertensive heart disease with (congestive) heart failure
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_htn <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I27.0 Primary pulmonary hypertension
I27.2 Other secondary pulmonary hypertension
I27.8 Other specified pulmonary heart diseases
I27.9 Pulmonary heart disease, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_embolism <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I26 Pulmonary embolism
I26.0 Pulmonary embolism with mention of acute cor pulmonale
I26.9 Pulmonary embolism without mention of acute cor pulmonale
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_misc <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I28 Other diseases of pulmonary vessels
I28.0 Arteriovenous fistula of pulmonary vessels
I28.1 Aneurysm of pulmonary artery
I28.8 Other specified diseases of pulmonary vessels
I28.9 Disease of pulmonary vessels, unspecified
I37 Pulmonary valve disorders
I37.0 Pulmonary valve stenosis
I37.1 Pulmonary valve insufficiency
I37.2 Pulmonary valve stenosis with insufficiency
I37.8 Other pulmonary valve disorders
I37.9 Pulmonary valve disorder, unspecified
I39.3 Pulmonary valve disorders in diseases classified elsewhere
Q21.4 Aortopulmonary septal defect
Q22 Congenital malformations of pulmonary and tricuspid valves
Q22.0 Pulmonary valve atresia
Q22.1 Congenital pulmonary valve stenosis
Q22.2 Congenital pulmonary valve insufficiency
Q22.3 Other congenital malformations of pulmonary valve
Q24.3 Pulmonary infundibular stenosis
Q25.5 Atresia of pulmonary artery
Q25.6 Stenosis of pulmonary artery
Q25.7 Other congenital malformations of pulmonary artery
Q26.2 Total anomalous pulmonary venous connexion
Q26.3 Partial anomalous pulmonary venous connexion
Q26.4 Anomalous pulmonary venous connexion, unspecified
S25.4 Injury of pulmonary blood vessels
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_ILD <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
J70.2 Acute drug-induced interstitial lung disorders
J70.3 Chronic drug-induced interstitial lung disorders
J70.4 Drug-induced interstitial lung disorder, unspecified
J84 Other interstitial pulmonary diseases
J84.1 Other interstitial pulmonary diseases with fibrosis
J84.8 Other specified interstitial pulmonary diseases
J84.9 Interstitial pulmonary disease, unspecified
E84.0 Cystic fibrosis with pulmonary manifestations
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_copd <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
J43 Emphysema
J43.1 Panlobular emphysema
J43.2 Centrilobular emphysema
J43.8 Other emphysema
J43.9 Emphysema, unspecified
J44 Other chronic obstructive pulmonary disease
J44.0 Chronic obstructive pulmonary disease with acute lower respiratory infection
J44.1 Chronic obstructive pulmonary disease with acute exacerbation, unspecified
J44.8 Other specified chronic obstructive pulmonary disease
J44.9 Chronic obstructive pulmonary disease, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_heart_pulm_transplant <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
T86.2 Heart transplant failure and rejection
T86.3 Heart-lung transplant failure and rejection
Z94.2 Lung transplant status
Z94.3 Heart and lungs transplant status
Z99.4 Dependence on artificial heart
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_diabetes <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
E10 Insulin-dependent diabetes mellitus
E10.0 With coma
E10.1 With ketoacidosis
E10.2 With renal complications
E10.3 With ophthalmic complications
E10.4 With neurological complications
E10.5 With peripheral circulatory complications
E10.6 With other specified complications
E10.7 With multiple complications
E10.8 With unspecified complications
E10.9 Without complications
E11 Non-insulin-dependent diabetes mellitus
E11.0 With coma
E11.1 With ketoacidosis
E11.2 With renal complications
E11.3 With ophthalmic complications
E11.4 With neurological complications
E11.5 With peripheral circulatory complications
E11.6 With other specified complications
E11.7 With multiple complications
E11.8 With unspecified complications
E11.9 Without complications
E12 Malnutrition-related diabetes mellitus
E12.0 With coma
E12.1 With ketoacidosis
E12.2 With renal complications
E12.3 With ophthalmic complications
E12.4 With neurological complications
E12.5 With peripheral circulatory complications
E12.6 With other specified complications
E12.7 With multiple complications
E12.8 With unspecified complications
E12.9 Without complications
E13 Other specified diabetes mellitus
E13.0 With coma
E13.1 With ketoacidosis
E13.2 With renal complications
E13.3 With ophthalmic complications
E13.4 With neurological complications
E13.5 With peripheral circulatory complications
E13.6 With other specified complications
E13.7 With multiple complications
E13.8 With unspecified complications
E13.9 Without complications
E14 Unspecified diabetes mellitus
E14.0 With coma
E14.1 With ketoacidosis
E14.2 Withrenal complications
E14.3 With ophthalmic complications
E14.4 With neurological complications
E14.5 With peripheral circulatory complications
E14.6 With other specified complications
E14.7 With multiple complications
E14.8 With unspecified complications
E14.9 Without complications
N08.3 Glomerular disorders in diabetes mellitus
O24.0 Pre-existing diabetes mellitus, insulin-dependent
O24.1 Pre-existing diabetes mellitus, noninsulin-dependent
O24.2 Pre-existing malnutrition-related diabetes mellitus
O24.3 Pre-existing diabetes mellitus, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
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Defines functions icd10_lookup
Documented in icd10_lookup
#' @title ICD10 lookups
#' @description Perform ICD10 lookups using coding 19, as specified in \url{https://biobank.ndph.ox.ac.uk/ukb/coding.cgi?id=19}. For disease-specific `icd10_*()` functions, an internal `icd10_text_to_codes()` function is used to convert the text version of ICD10 names into their respective UKB codings.
#' @inheritParams ukbiobank
#' @inheritSection ukbiobank Instancing
#' @inheritSection ukbiobank Column names
#' @param codes ICD10 codes to look up.
#' @export
icd10_lookup <- function(data,
codes,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10,
icd10_date_col = f.41280.0.0.Date_of_first_in_patient_diagnosis_ICD10,
date_of_instance_col = f.53.0.0.Date_of_attending_assessment_centre) {
# convert icd10 codes to ukb codings
icd10_lookups <-
tibble(icd10 = codes) %>%
left_join(coding_icd10, by = "icd10") %>%
pull("coding")
# remove any columns with only NAs
data %<>% remove_na_columns()
codes %<>% unique()
# generate lists of column names
date_of_instance_colnames <- expand_instances(data, {{ date_of_instance_col }})
icd10_colnames <- expand_array(data, {{ icd10_col }})
icd10_date_colnames <- expand_array(data, {{ icd10_date_col }})
stopifnot(length(icd10_colnames) == length(icd10_date_colnames))
# define function that will return whether the patient has icd10 codes
# and were diagnosed on or before the date of the instance/assessment
icd10_by_instance <- function(inst) {
# Check if icd10 codes match the provided search codes
icd_match <-
data %>%
select(!!!icd10_colnames) %>%
mutate(across(everything(), ~ .x %in% icd10_lookups)) %>%
as.matrix()
# compare dates from the icd columns to dates of the instance,
# and create a filter based on whether the date is allowed
inst_dates <-
data %>%
pull(!!date_of_instance_colnames[[inst + 1]]) %>%
as.Date() %>%
as.integer() %>%
matrix(., length(.), length(icd10_date_colnames))
icd_dates <-
data %>%
select(!!!icd10_date_colnames) %>%
mutate(across(everything(), ~ as.integer(as.Date(.x)))) %>%
as.matrix()
keep_icd <- icd_dates <= inst_dates
keep_icd <- ifelse(is.na(keep_icd), F, keep_icd)
# Apply the filter based on whether the date of the icd diagnosis is allowed
icd_match <- icd_match & keep_icd
icd_match %>% any_by_row()
}
instance_combiner(
data,
lookup_by_instance_fn = icd10_by_instance,
after_instance = {{ after_instance }},
up_to_instance = {{ up_to_instance }}
)
}
#' @noRd
icd10_text_to_codes <- function(text) {
codes <-
text %>%
stringr::str_trim(.) %>%
stringr::str_split(., "\n", simplify = T) %>%
stringr::str_trim(.) %>%
stringr::str_split(., "\\s", 2, simplify = T)
codes <- codes[, 1]
codes <- codes[which(codes != "")]
codes %<>% unique()
}
#' @rdname icd10_lookup
#' @export
icd10_htn <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I10 Essential (primary) hypertension
I11 Hypertensive heart disease
I11.0 Hypertensive heart disease with (congestive) heart failure
I11.9 Hypertensive heart disease without (congestive) heart failure
I12 Hypertensive renal disease
I12.0 Hypertensive renal disease with renal failure
I12.9 Hypertensive renal disease without renal failure
I13 Hypertensive heart and renal disease
I13.0 Hypertensive heart and renal disease with (congestive) heart failure
I13.1 Hypertensive heart and renal disease with renal failure
I13.2 Hypertensive heart and renal disease with both (congestive) heart failure and renal failure
I13.9 Hypertensive heart and renal disease, unspecified
I15 Secondary hypertension
I15.0 Renovascular hypertension
I15.1 Hypertension secondary to other renal disorders
I15.2 Hypertension secondary to endocrine disorders
I15.8 Other secondary hypertension
I15.9 Seconday hypertension, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_hld <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
E78.0 Pure hypercholesterolaemia
E78.1 Pure hyperglyceridaemia
E78.2 Mixed hyperlipidaemia
E78.4 Other hyperlipidaemia
E78.5 Hyperlipidaemia, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_heart_failure <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I50 Heart failure
I50.0 Congestive heart failure
I50.1 Left ventricular failure
I50.9 Heart failure, unspecified
I11.0 Hypertensive heart disease with (congestive) heart failure
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_htn <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I27.0 Primary pulmonary hypertension
I27.2 Other secondary pulmonary hypertension
I27.8 Other specified pulmonary heart diseases
I27.9 Pulmonary heart disease, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_embolism <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I26 Pulmonary embolism
I26.0 Pulmonary embolism with mention of acute cor pulmonale
I26.9 Pulmonary embolism without mention of acute cor pulmonale
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_misc <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
I28 Other diseases of pulmonary vessels
I28.0 Arteriovenous fistula of pulmonary vessels
I28.1 Aneurysm of pulmonary artery
I28.8 Other specified diseases of pulmonary vessels
I28.9 Disease of pulmonary vessels, unspecified
I37 Pulmonary valve disorders
I37.0 Pulmonary valve stenosis
I37.1 Pulmonary valve insufficiency
I37.2 Pulmonary valve stenosis with insufficiency
I37.8 Other pulmonary valve disorders
I37.9 Pulmonary valve disorder, unspecified
I39.3 Pulmonary valve disorders in diseases classified elsewhere
Q21.4 Aortopulmonary septal defect
Q22 Congenital malformations of pulmonary and tricuspid valves
Q22.0 Pulmonary valve atresia
Q22.1 Congenital pulmonary valve stenosis
Q22.2 Congenital pulmonary valve insufficiency
Q22.3 Other congenital malformations of pulmonary valve
Q24.3 Pulmonary infundibular stenosis
Q25.5 Atresia of pulmonary artery
Q25.6 Stenosis of pulmonary artery
Q25.7 Other congenital malformations of pulmonary artery
Q26.2 Total anomalous pulmonary venous connexion
Q26.3 Partial anomalous pulmonary venous connexion
Q26.4 Anomalous pulmonary venous connexion, unspecified
S25.4 Injury of pulmonary blood vessels
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_pulm_ILD <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
J70.2 Acute drug-induced interstitial lung disorders
J70.3 Chronic drug-induced interstitial lung disorders
J70.4 Drug-induced interstitial lung disorder, unspecified
J84 Other interstitial pulmonary diseases
J84.1 Other interstitial pulmonary diseases with fibrosis
J84.8 Other specified interstitial pulmonary diseases
J84.9 Interstitial pulmonary disease, unspecified
E84.0 Cystic fibrosis with pulmonary manifestations
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_copd <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
J43 Emphysema
J43.1 Panlobular emphysema
J43.2 Centrilobular emphysema
J43.8 Other emphysema
J43.9 Emphysema, unspecified
J44 Other chronic obstructive pulmonary disease
J44.0 Chronic obstructive pulmonary disease with acute lower respiratory infection
J44.1 Chronic obstructive pulmonary disease with acute exacerbation, unspecified
J44.8 Other specified chronic obstructive pulmonary disease
J44.9 Chronic obstructive pulmonary disease, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_heart_pulm_transplant <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
T86.2 Heart transplant failure and rejection
T86.3 Heart-lung transplant failure and rejection
Z94.2 Lung transplant status
Z94.3 Heart and lungs transplant status
Z99.4 Dependence on artificial heart
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
#' @rdname icd10_lookup
#' @export
icd10_diabetes <- function(data,
after_instance = default_after_inst(),
up_to_instance = default_up_to_inst(),
icd10_col = f.41270.0.0.Diagnoses_ICD10) {
codings <- icd10_text_to_codes("
E10 Insulin-dependent diabetes mellitus
E10.0 With coma
E10.1 With ketoacidosis
E10.2 With renal complications
E10.3 With ophthalmic complications
E10.4 With neurological complications
E10.5 With peripheral circulatory complications
E10.6 With other specified complications
E10.7 With multiple complications
E10.8 With unspecified complications
E10.9 Without complications
E11 Non-insulin-dependent diabetes mellitus
E11.0 With coma
E11.1 With ketoacidosis
E11.2 With renal complications
E11.3 With ophthalmic complications
E11.4 With neurological complications
E11.5 With peripheral circulatory complications
E11.6 With other specified complications
E11.7 With multiple complications
E11.8 With unspecified complications
E11.9 Without complications
E12 Malnutrition-related diabetes mellitus
E12.0 With coma
E12.1 With ketoacidosis
E12.2 With renal complications
E12.3 With ophthalmic complications
E12.4 With neurological complications
E12.5 With peripheral circulatory complications
E12.6 With other specified complications
E12.7 With multiple complications
E12.8 With unspecified complications
E12.9 Without complications
E13 Other specified diabetes mellitus
E13.0 With coma
E13.1 With ketoacidosis
E13.2 With renal complications
E13.3 With ophthalmic complications
E13.4 With neurological complications
E13.5 With peripheral circulatory complications
E13.6 With other specified complications
E13.7 With multiple complications
E13.8 With unspecified complications
E13.9 Without complications
E14 Unspecified diabetes mellitus
E14.0 With coma
E14.1 With ketoacidosis
E14.2 Withrenal complications
E14.3 With ophthalmic complications
E14.4 With neurological complications
E14.5 With peripheral circulatory complications
E14.6 With other specified complications
E14.7 With multiple complications
E14.8 With unspecified complications
E14.9 Without complications
N08.3 Glomerular disorders in diabetes mellitus
O24.0 Pre-existing diabetes mellitus, insulin-dependent
O24.1 Pre-existing diabetes mellitus, noninsulin-dependent
O24.2 Pre-existing malnutrition-related diabetes mellitus
O24.3 Pre-existing diabetes mellitus, unspecified
")
icd10_lookup(data, codings, icd10_col = {{ icd10_col }}, after_instance = {{ after_instance }}, up_to_instance = {{ up_to_instance }})
}
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