R/caliber.R
default_overlapping_disease_categories_csv.RdReturns the file path to csv included with this package for resolving
overlapping disease categories in mapped CALIBER codes. To be used with
reformat_caliber_for_ukb().
default_overlapping_disease_categories_csv()A file path.
Other CALIBER:
download_caliber_repo(),
get_caliber_categories_mapping(),
read_caliber_raw(),
reformat_caliber_for_ukb()
# return file path
default_overlapping_disease_categories_csv()
#> [1] "/home/runner/work/codemapper/codemapper/renv/library/R-4.2/x86_64-pc-linux-gnu/codemapper/extdata/caliber_mapped_overlapping_disease_categories.csv"
# read file into R
read.csv(default_overlapping_disease_categories_csv())
#> disease
#> 1 Diabetes
#> 2 Diabetes
#> 3 Diabetic neurological complications
#> 4 Diabetic neurological complications
#> 5 Diabetic neurological complications
#> 6 Diabetic neurological complications
#> 7 End stage renal disease
#> 8 End stage renal disease
#> 9 Erectile dysfunction
#> 10 Erectile dysfunction
#> 11 Primary Malignancy_Other Organs
#> 12 Primary Malignancy_Other Organs
#> 13 Primary Malignancy_Other Organs
#> 14 Primary Malignancy_Other Organs
#> 15 Primary Malignancy_Other Organs
#> 16 Primary Malignancy_Other Organs
#> 17 Primary Malignancy_Other Organs
#> 18 Primary Malignancy_Other Organs
#> 19 Primary Malignancy_Other Organs
#> 20 Primary Malignancy_Other Organs
#> 21 Primary Malignancy_Other Organs
#> 22 Primary Malignancy_Other Organs
#> 23 Primary Malignancy_Other Organs
#> 24 Primary Malignancy_Other Organs
#> 25 Primary Malignancy_Other Organs
#> 26 Primary Malignancy_Other Organs
#> 27 Primary Malignancy_Other Organs
#> 28 Primary Malignancy_Other Organs
#> 29 Tuberculosis
#> 30 Tuberculosis
#> 31 Unstable Angina
#> 32 Unstable Angina
#> description
#> 1 DIABETES MELLITUS
#> 2 DIABETES MELLITUS
#> 3 Diabetic (femoral mononeuropathy) & (Diabetic amyotrophy)
#> 4 Diabetic (femoral mononeuropathy) & (Diabetic amyotrophy)
#> 5 Diabetic amyotrophy
#> 6 Diabetic amyotrophy
#> 7 End stage renal failure
#> 8 End stage renal failure
#> 9 Erectile dysfunction
#> 10 Erectile dysfunction
#> 11 HEAD, FACE AND NECK
#> 12 HEAD, FACE AND NECK
#> 13 UPPER LIMB, INCLUDING SHOULDER
#> 14 UPPER LIMB, INCLUDING SHOULDER
#> 15 LOWER LIMB, INCLUDING HIP
#> 16 LOWER LIMB, INCLUDING HIP
#> 17 THORAX
#> 18 THORAX
#> 19 ABDOMEN
#> 20 ABDOMEN
#> 21 PELVIS
#> 22 PELVIS
#> 23 TRUNK, UNSPECIFIED
#> 24 TRUNK, UNSPECIFIED
#> 25 OTHER
#> 26 OTHER
#> 27 OTHER
#> 28 OTHER
#> 29 Late effects of tuberculosis of bones and joints
#> 30 Late effects of tuberculosis of bones and joints
#> 31 Worsening angina
#> 32 Worsening angina
#> category code_type code
#> 1 Diabetes not otherwise specified (6) icd9 6480
#> 2 Secondary diabetes (5) icd9 6480
#> 3 Diagnosis of diabetic neurological complications read3 Xa0lK
#> 4 History of diabetic neurological complications read3 Xa0lK
#> 5 Diagnosis of diabetic neurological complications read3 XaPmX
#> 6 History of diabetic neurological complications read3 XaPmX
#> 7 Diagnosis of End stage renal disease read3 X30J0
#> 8 Procedure for End stage renal disease read3 X30J0
#> 9 Diagnosis of erectile dysfunction read3 E2273
#> 10 Possible diagnosis of erectile dysfunction read3 E2273
#> 11 Diagnosis of Primary Malignancy_Other Organs icd9 1710
#> 12 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1710
#> 13 Diagnosis of Primary Malignancy_Other Organs icd9 1712
#> 14 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1712
#> 15 Diagnosis of Primary Malignancy_Other Organs icd9 1713
#> 16 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1713
#> 17 Diagnosis of Primary Malignancy_Other Organs icd9 1714
#> 18 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1714
#> 19 Diagnosis of Primary Malignancy_Other Organs icd9 1715
#> 20 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1715
#> 21 Diagnosis of Primary Malignancy_Other Organs icd9 1716
#> 22 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1716
#> 23 Diagnosis of Primary Malignancy_Other Organs icd9 1717
#> 24 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1717
#> 25 Diagnosis of Primary Malignancy_Other Organs icd9 1718
#> 26 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1718
#> 27 Diagnosis of Primary Malignancy_Other Organs icd9 1878
#> 28 Possible Diagnosis of Primary Malignancy_Other Organs icd9 1878
#> 29 Diagnosis of tuberculosis read3 AE03.
#> 30 History of tuberculosis read3 AE03.
#> 31 Unstable angina (3) read3 XE0Ui
#> 32 Worsening angina (2) read3 XE0Ui
#> author keep
#> 1 caliber Y
#> 2 caliber
#> 3 caliber Y
#> 4 caliber
#> 5 caliber Y
#> 6 caliber
#> 7 caliber Y
#> 8 caliber
#> 9 caliber Y
#> 10 caliber
#> 11 caliber Y
#> 12 caliber
#> 13 caliber Y
#> 14 caliber
#> 15 caliber Y
#> 16 caliber
#> 17 caliber Y
#> 18 caliber
#> 19 caliber Y
#> 20 caliber
#> 21 caliber Y
#> 22 caliber
#> 23 caliber Y
#> 24 caliber
#> 25 caliber Y
#> 26 caliber
#> 27 caliber Y
#> 28 caliber
#> 29 caliber Y
#> 30 caliber
#> 31 caliber
#> 32 caliber Y