## Codes for histo
# Description:
desc <- "Histoplasmosis"
# Diagnosis codes:
tmp <- read_csv("~/Documents/GitHub/delay_dx/params/ssd_codes/histo/ssd_codes.csv")
# tmp2 <- tmp %>%
# filter(icd_version == 9) %>%
# distinct(code = icd_codes) %>%
# left_join(mutate(icd::icd9cm_hierarchy,code=as.character(code))) %>%
# distinct(code,desc=short_desc)
#
# cat(paste0("'",tmp2$code,"',", " #",tmp2$desc),sep="\n")
#
# tmp2 <- tmp %>%
# filter(icd_version == 10) %>%
# distinct(code = icd_codes) %>%
# left_join(mutate(icd::icd10cm2019,code=as.character(code))) %>%
# distinct(code,desc=short_desc)
#
# cat(paste0("'",tmp2$code,"',", " #",tmp2$desc),sep="\n")
icd9_codes <- ((('7806', #Fever and other physiologic disturbances of temperature regulation
'78060', #Fever NOS
'78079', #Malaise and fatigue NEC
'78321', #Abnormal loss of weight
'7808', #Generalizd hyperhidrosis
'7840', #Headache
'78605', #Shortness of breath
'78607', #Wheezing
'7862', #Cough
'7863', #Hemoptysis
'78630', #Hemoptysis NOS
'78650', #Chest pain NOS
'78652', #Painful respiration
'78659', #Chest pain NEC
'78702', #Nausea alone
'78791', #Diarrhea
'78900', #Abdmnal pain unspcf site
'78901', #Abdmnal pain rt upr quad
'78906', #Abdmnal pain epigastric
'78907', #Abdmnal pain generalized
'010', #Primary tuberculous infection
'011', #Pulmonary tuberculosis
'012', #Other respiratory tuberculosis
'013', #Tuberculosis of meninges and central nervous system
'014', #Tuberculosis of intestines, peritoneum, and mesenteric glands
'015', #Tuberculosis of bones and joints
'016', #Tuberculosis of genitourinary system
'017', #Tuberculosis of other organs
'018', #Miliary tuberculosis
'07999', #Viral infection NOS
'4619', #Acute sinusitis NOS
'462', #Acute pharyngitis
'4658', #Acute uri mult sites NEC
'4659', #Acute uri NOS
'4660', #Acute bronchitis
'4739', #Chronic sinusitis NOS
'4829', #Bacterial pneumonia NOS
'486', #Pneumonia, organism NOS
'490', #Bronchitis NOS
'4919', #Chronic bronchitis NOS
'5130', #Abscess of lung
'5990', #Urin tract infection NOS
'7908', #Viremia NOS
'135', #Sarcoidosis
'1623', #Mal neo upper lobe lung
'1625', #Mal neo lower lobe lung
'1629', #Mal neo bronch/lung NOS
'2123', #Benign neo bronchus/lung
'2357', #Unc behav neo lung
'2391', #Respiratory neoplasm NOS
'4239', #Pericardial disease NOS
'4280', #CHF NOS
'49120', #Obst chr bronc w/o exac
'49121', #Obs chr bronc w(ac) exac
'4920', #Emphysematous bleb
'4928', #Emphysema NEC
'49320', #Chronic obst asthma NOS
'49322', #Ch obst asth w (ac) exac
'49390', #Asthma NOS
'496', #Chr airway obstruct NEC
'5110', #Pleurisy w/o effus or TB
'5111', #Bact pleur/effus not TB
'51189', #Effusion NEC exc tb
'514', #Pulm congest/hypostasis
'515', #Postinflam pulm fibrosis
'5169', #Alveol pneumonopathy NOS
'51851', #Ac resp flr fol trma/srg
'51853', #Ac/chr rsp flr fol tr/sg
'51881', #Acute respiratry failure
'51884', #Acute & chronc resp fail
'51889', #Other lung disease NEC
'78609', #Respiratory abnorm NEC
'53081', #Esophageal reflux
'5609', #Intestinal obstruct NOS
'2761', #Hyposmolality
'28419', #Other pancytopenia
'2859', #Anemia NOS
'2875', #Thrombocytopenia NOS
'28860', #Leukocytosis NOS
'2893', #Lymphadenitis NOS
'4293', #Cardiomegaly
'5119', #Pleural effusion NOS
'5128', #Other pneumothorax and air leak
'51289', #Other pneumothorax
'5180', #Pulmonary collapse
'5183', #Pulmonary eosinophilia
'5559', #Regional enteritis NOS
'57420', #Cholelithiasis NOS
'72981', #Swelling of limb
'7822', #Local suprficial swellng
'7842', #Swelling in head & neck
'7856', #Enlargement lymph nodes
'7866', #Chest swelling/mass/lump
'7892', #Splenomegaly
'7904', #Elev transaminase/ldh
'7931', #Lung field
'79311', #Solitary pulmonry nodule
'79319', #Ot nonsp ab fnd lung fld
'79902', #Hypoxemia
'V741' #Screening-pulmonary TB
)))
icd10_codes <- ((('R042', #Hemoptysis
'R05', #Cough
'R0600', #Dyspnea, unspecified
'R0602', #Shortness of breath
'R0609', #Other forms of dyspnea
'R062', #Wheezing
'R063', #Periodic breathing
'R0683', #Snoring
'R0689', #Other abnormalities of breathing
'R071', #Chest pain on breathing
'R0781', #Pleurodynia
'R0782', #Intercostal pain
'R0789', #Other chest pain
'R079', #Chest pain, unspecified
'R1011', #Right upper quadrant pain
'R1013', #Epigastric pain
'R1084', #Generalized abdominal pain
'R109', #Unspecified abdominal pain
'R110', #Nausea
'R197', #Diarrhea, unspecified
'R509', #Fever, unspecified
'R51', #Headache
'R531', #Weakness
'R5381', #Other malaise
'R5383', #Other fatigue
'R61', #Generalized hyperhidrosis
'R634', #Abnormal weight loss
'A15', #Respiratory tuberculosis
'A17', #Tuberculosis of nervous system
'A18', #Tuberculosis of other organs
'A19', #Miliary tuberculosis
'B349', #Viral infection, unspecified
'B9789', #Oth viral agents as the cause of diseases classd elswhr
'G933', #Postviral fatigue syndrome
'J0190', #Acute sinusitis, unspecified
'J029', #Acute pharyngitis, unspecified
'J069', #Acute upper respiratory infection, unspecified
'J159', #Unspecified bacterial pneumonia
'J182', #Hypostatic pneumonia, unspecified organism
'J189', #Pneumonia, unspecified organism
'J209', #Acute bronchitis, unspecified
'J329', #Chronic sinusitis, unspecified
'J40', #Bronchitis, not specified as acute or chronic
'J851', #Abscess of lung with pneumonia
'J852', #Abscess of lung without pneumonia
'N390', #Urinary tract infection, site not specified
'R502', #Drug induced fever
'C3410', #Malignant neoplasm of upper lobe, unsp bronchus or lung
'C3411', #Malignant neoplasm of upper lobe, right bronchus or lung
'C3430', #Malignant neoplasm of lower lobe, unsp bronchus or lung
'C3490', #Malignant neoplasm of unsp part of unsp bronchus or lung
'D1430', #Benign neoplasm of unspecified bronchus and lung
'D381', #Neoplasm of uncertain behavior of trachea, bronchus and lung
'D491', #Neoplasm of unspecified behavior of respiratory system
'D649', #Anemia, unspecified
'D860', #Sarcoidosis of lung
'D869', #Sarcoidosis, unspecified
'I319', #Disease of pericardium, unspecified
'I509', #Heart failure, unspecified
'I889', #Nonspecific lymphadenitis, unspecified
'J42', #Unspecified chronic bronchitis
'J439', #Emphysema, unspecified
'J441', #Chronic obstructive pulmonary disease w (acute) exacerbation
'J449', #Chronic obstructive pulmonary disease, unspecified
'J45909', #Unspecified asthma, uncomplicated
'J45998', #Other asthma
'J811', #Chronic pulmonary edema
'J82', #Pulmonary eosinophilia, not elsewhere classified
'J8410', #Pulmonary fibrosis, unspecified
'J8489', #Other specified interstitial pulmonary diseases
'J849', #Interstitial pulmonary disease, unspecified
'J850', #Gangrene and necrosis of lung
'J869', #Pyothorax without fistula
'J918', #Pleural effusion in other conditions classified elsewhere
'J9383', #Other pneumothorax
'J941', #Fibrothorax
'J948', #Other specified pleural conditions
'J949', #Pleural condition, unspecified
'J9600', #Acute respiratory failure, unsp w hypoxia or hypercapnia
'J9601', #Acute respiratory failure with hypoxia
'J9621', #Acute and chronic respiratory failure with hypoxia
'J9690', #Respiratory failure, unsp, unsp w hypoxia or hypercapnia
'J9819', #Other pulmonary collapse
'J984', #Other disorders of lung
'R049', #Hemorrhage from respiratory passages, unspecified
'R091', #Pleurisy
'K219', #Gastro-esophageal reflux disease without esophagitis
'K5090', #Crohn's disease, unspecified, without complications
'K5660', #Unspecified intestinal obstruction
'K8020', #Calculus of gallbladder w/o cholecystitis w/o obstruction
'D61818', #Other pancytopenia
'D696', #Thrombocytopenia, unspecified
'D72829', #Elevated white blood cell count, unspecified
'E871', #Hypo-osmolality and hyponatremia
'I517', #Cardiomegaly
'J90', #Pleural effusion, not elsewhere classified
'J939', #Pneumothorax, unspecified
'J9811', #Atelectasis
'R0902', #Hypoxemia
'R161', #Splenomegaly, not elsewhere classified
'R220', #Localized swelling, mass and lump, head
'R221', #Localized swelling, mass and lump, neck
'R222', #Localized swelling, mass and lump, trunk
'R590', #Localized enlarged lymph nodes
'R591', #Generalized enlarged lymph nodes
'R599', #Enlarged lymph nodes, unspecified
'R740', #Nonspec elev of levels of transamns & lactic acid dehydrgnse
'R911', #Solitary pulmonary nodule
'R918', #Other nonspecific abnormal finding of lung field
'Z111' #Encounter for screening for respiratory tuberculosis
)))
# Procedure codes:
pr_codes_icd9 <- ()
pr_codes_icd10 <- ()
pr_codes_cpt <- ()
# Medication codes
rx_codes <- ()
