R/ssd_codes/tb.R
In aarmiller/codeBuildr: This package provides functions for loading project codes
## Codes for tb
# Description:
desc <- "Tuberculosis"
# Diagnosis codes:
# library(tidyverse)
# tmp <- read_csv("~/Documents/GitHub/delay_dx/params/ssd_codes/tb/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")
#
# icd::icd10cm2019
# 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 <- as.character(c('7806', #Fever and other physiologic disturbances of temperature regulation
'78060', #Fever NOS
'78061', #Fever in other diseases
'78079', #Malaise and fatigue NEC
'7808', #Generalizd hyperhidrosis
'78321', #Abnormal loss of weight
'7841', #Throat pain
'78441', #Aphonia
'78442', #Dysphonia
'7849', #Other symptoms involving head and neck
'78491', #Postnasal drip
'78499', #Head & neck symptoms NEC
'78602', #Orthopnea
'78605', #Shortness of breath
'78607', #Wheezing
'7862', #Cough
'7863', #Hemoptysis
'78630', #Hemoptysis NOS
'7864', #Abnormal sputum
'78650', #Chest pain NOS
'78651', #Precordial pain
'78652', #Painful respiration
'78659', #Chest pain NEC
'0389', #Septicemia NOS
'07999', #Viral infection NOS
'1124', #Candidiasis of lung
'1140', #Primary coccidioidomycos
'1144', #Ch pl coccidioidomycosis
'11505', #Histoplasm caps pneumon
'11515', #Histoplasm dub pneumonia
'11595', #Histoplasmosis pneumonia
'1304', #Toxoplasma pneumonitis
'1363', #Pneumocystosis
'310', #Specific nonpsychotic mental disorders due to brain damage
'340', #Multiple sclerosis
'391', #Rheumatic fever with heart involvement
'460', #Acute nasopharyngitis
'4610', #Ac maxillary sinusitis
'4611', #Ac frontal sinusitis
'4612', #Ac ethmoidal sinusitis
'4613', #Ac sphenoidal sinusitis
'4619', #Acute sinusitis NOS
'462', #Acute pharyngitis
'463', #Acute tonsillitis
'4640', #Acute laryngitis
'46400', #Ac laryngitis w/o obst
'46401', #Ac laryngitis w obstruct
'46411', #Ac tracheitis w obstruct
'46420', #Ac laryngotrach no obstr
'46421', #Ac laryngotrach w obstr
'46430', #Ac epiglottitis no obstr
'46431', #Ac epiglottitis w obstr
'4644', #Croup
'46450', #Supraglottis w/o obs NOS
'46451', #Supraglottis w obstr NOS
'4650', #Acute laryngopharyngitis
'4658', #Acute uri mult sites NEC
'4659', #Acute uri NOS
'4660', #Acute bronchitis
'4661', #Acute bronchiolitis
'46611', #Acu broncholitis d/t RSV
'46619', #Acu brnchlts d/t oth org
'4722', #Chronic nasopharyngitis
'4730', #Chr maxillary sinusitis
'4731', #Chr frontal sinusitis
'4732', #Chr ethmoidal sinusitis
'4733', #Chr sphenoidal sinusitis
'4738', #Chronic sinusitis NEC
'4739', #Chronic sinusitis NOS
'4740', #Chronic tonsillitis and adenoiditis
'47400', #Chronic tonsillitis
'47401', #Chronic adenoiditis
'47402', #Chronic tonsils&adenoids
'47410', #Hypertrophy T and A
'47411', #Hypertrophy tonsils
'475', #Peritonsillar abscess
'4760', #Chronic laryngitis
'4761', #Chr laryngotracheitis
'47821', #Cellulitis of pharynx
'47822', #Parapharyngeal abscess
'47824', #Retropharyngeal abscess
'47871', #Laryngeal cellulitis
'4789', #Upper resp dis NEC/NOS
'4800', #Adenoviral pneumonia
'4801', #Resp syncyt viral pneum
'4802', #Parinfluenza viral pneum
'4808', #Viral pneumonia NEC
'4809', #Viral pneumonia NOS
'481', #Pneumococcal pneumonia
'4820', #K. pneumoniae pneumonia
'4821', #Pseudomonal pneumonia
'4822', #H.influenzae pneumonia
'4823', #Pneumonia due to Streptococcus
'48230', #Streptococcal pneumn NOS
'48231', #Pneumonia strptococcus a
'48232', #Pneumonia strptococcus b
'48239', #Pneumonia oth strep
'4824', #Pneumonia due to Staphylococcus
'48240', #Staphylococcal pneu NOS
'48241', #Meth sus pneum d/t Staph
'48242', #Meth res pneu d/t Staph
'48249', #Staph pneumonia NEC
'4828', #Pneumonia due to other specified bacteria
'48281', #Pneumonia anaerobes
'48283', #Pneumo oth grm-neg bact
'48284', #Legionnaires' disease
'48289', #Pneumonia oth spcf bact
'4829', #Bacterial pneumonia NOS
'483', #Pneumonia due to other specified organism
'4830', #Pneu mycplsm pneumoniae
'4831', #Pneumonia d/t chlamydia
'4838', #Pneumon oth spec orgnsm
'4841', #Pneum w cytomeg incl dis
'4843', #Pneumonia in whoop cough
'4846', #Pneum in aspergillosis
'4847', #Pneum in oth sys mycoses
'4848', #Pneum in infect dis NEC
'485', #Bronchopneumonia org NOS
'486', #Pneumonia, organism NOS
'4870', #Influenza with pneumonia
'4871', #Flu w resp manifest NEC
'4878', #Flu w manifestation NEC
'488', #Influenza due to certain identified influenza viruses
'4881', #Influenza due to identified 2009 H1N1 influenza virus
'48811', #Flu dt 2009 H1N1 w pneu
'48812', #Flu-2009 H1N1 w oth resp
'48819', #Flu-2009 H1N1 w oth man
'48881', #Flu dt nvl A vrs w pneu
'48882', #Flu dt nvl A w oth resp
'48889', #Flu dt novel A w oth man
'490', #Bronchitis NOS
'4910', #Simple chr bronchitis
'4911', #Mucopurul chr bronchitis
'4918', #Chronic bronchitis NEC
'4919', #Chronic bronchitis NOS
'5100', #Empyema with fistula
'5130', #Abscess of lung
'5131', #Abscess of mediastinum
'5192', #Mediastinitis
'5990', #Urin tract infection NOS
'830', #Dislocation of jaw
'99591', #Sepsis
'135', #Sarcoidosis
'1622', #Malig neo main bronchus
'1623', #Mal neo upper lobe lung
'1624', #Mal neo middle lobe lung
'1625', #Mal neo lower lobe lung
'1628', #Mal neo bronch/lung NEC
'1629', #Mal neo bronch/lung NOS
'1630', #Mal neo parietal pleura
'1631', #Mal neo visceral pleura
'1638', #Malig neopl pleura NEC
'1639', #Malig neopl pleura NOS
'1650', #Mal neo upper resp NOS
'1658', #Mal neo thorax/resp NEC
'1659', #Mal neo resp system NOS
'1970', #Secondary malig neo lung
'20921', #Mal carcinoid bronc/lung
'2123', #Benign neo bronchus/lung
'2311', #Ca in situ trachea
'2318', #Ca in situ resp sys NEC
'2319', #Ca in situ resp sys NOS
'2357', #Unc behav neo lung
'2391', #Respiratory neoplasm NOS
'2891', #Chronic lymphadenitis
'4168', #Chr pulmon heart dis NEC
'4239', #Pericardial disease NOS
'4280', #CHF NOS
'4464', #Wegener's granulomatosis
'46410', #Ac tracheitis no obstruc
'4720', #Chronic rhinitis
'47412', #Hypertrophy adenoids
'4742', #Adenoid vegetations
'4748', #Chr T & A dis NEC
'4749', #Chr T & A dis NOS
'4770', #Rhinitis due to pollen
'4772', #Allerg rhinitis-cat/dog
'4778', #Allergic rhinitis NEC
'4779', #Allergic rhinitis NOS
'4781', #Other diseases of nasal cavity and sinuses
'47819', #Nasal & sinus dis NEC
'47820', #Disease of pharynx NOS
'47829', #Disease of pharynx NEC
'47830', #Vocal cord paralysis NOS
'47831', #Vocal paral unilat part
'47832', #Vocal paral unilat total
'47833', #Vocal paral bilat part
'47834', #Vocal paral bilat total
'4784', #Vocal cord/larynx polyp
'4785', #Vocal cord disease NEC
'47870', #Disease of larynx NOS
'47874', #Stenosis of larynx
'47875', #Laryngeal spasm
'47879', #Disease of larynx NEC
'4788', #Urt hypersens react NOS
'4912', #Obstructive chronic bronchitis
'49120', #Obst chr bronc w/o exac
'49121', #Obs chr bronc w(ac) exac
'49122', #Obs chr bronc w ac bronc
'4920', #Emphysematous bleb
'4928', #Emphysema NEC
'49300', #Extrinsic asthma NOS
'49301', #Ext asthma w status asth
'49302', #Ext asthma w(acute) exac
'49310', #Intrinsic asthma NOS
'49311', #Int asthma w status asth
'49312', #Int asthma w (ac) exac
'49320', #Chronic obst asthma NOS
'49321', #Ch ob asthma w stat asth
'49322', #Ch obst asth w (ac) exac
'49381', #Exercse ind bronchospasm
'49382', #Cough variant asthma
'49390', #Asthma NOS
'49392', #Asthma NOS w (ac) exac
'494', #Bronchiectasis
'4940', #Bronchiectas w/o ac exac
'4941', #Bronchiectasis w ac exac
'4950', #Farmers' lung
'4951', #Bagassosis
'4952', #Bird-fanciers' lung
'4953', #Suberosis
'4954', #Malt workers' lung
'4955', #Mushroom workers' lung
'4956', #Mapl bark-stripprs' lung
'4957', #"ventilation" pneumonit
'4958', #Allerg alveol/pneum NEC
'4959', #Allerg alveol/pneum NOS
'496', #Chr airway obstruct NEC
'500', #Coal workers' pneumocon
'501', #Asbestosis
'502', #Silica pneumocon NEC
'503', #Inorg dust pneumocon NEC
'504', #Dust pneumonopathy NEC
'505', #Pneumoconiosis NOS
'5060', #Fum/vapor bronc/pneumon
'5061', #Fum/vapor ac pulm edema
'5062', #Fum/vapor up resp inflam
'5063', #Fum/vap ac resp cond NEC
'5064', #Fum/vapor chr resp cond
'5069', #Fum/vapor resp cond NOS
'5070', #Food/vomit pneumonitis
'5071', #Oil/essence pneumonitis
'5078', #Solid/liq pneumonit NEC
'5080', #Ac pul manif d/t radiat
'5081', #Chr pul manif d/t radiat
'5082', #Resp cond dt smoke inhal
'5088', #Resp cond: ext agent NEC
'5089', #Resp cond: ext agent NOS
'5110', #Pleurisy w/o effus or TB
'5111', #Bact pleur/effus not TB
'5118', #Other specified forms of effusion, except tuberculous
'51189', #Effusion NEC exc tb
'5120', #Spont tens pneumothorax
'5128', #Other pneumothorax and air leak
'51281', #Prim spont pneumothorax
'51282', #Sec spont pneumothorax
'51283', #Chronic pneumothorax
'51284', #Other air leak
'51289', #Other pneumothorax
'514', #Pulm congest/hypostasis
'515', #Postinflam pulm fibrosis
'5160', #Pul alveolar proteinosis
'5161', #Idio pulm hemosiderosis
'5162', #Pulm alveolar microlith
'5163', #Idiopathic interstitial pneumonia
'51630', #Idiopath inters pneu NOS
'51631', #Idiopath pulmon fibrosis
'51632', #Idio non-spec inter pneu
'51633', #Acute interstitial pneum
'51634', #Resp brncio interst lung
'51635', #Idiopth lym interst pneu
'51636', #Cryptogenic organiz pneu
'51637', #Desquamatv interst pneu
'5164', #Lymphangioleiomyomatosis
'5165', #Adlt pul Langs cell hist
'5168', #Alveol pneumonopathy NEC
'5169', #Alveol pneumonopathy NOS
'5171', #Rheumatic pneumonia
'5172', #Syst sclerosis lung dis
'5173', #Acute chest syndrome
'5178', #Lung involv in oth dis
'5181', #Interstitial emphysema
'5182', #Compensatory emphysema
'5183', #Pulmonary eosinophilia
'5184', #Acute lung edema NOS
'51881', #Acute respiratry failure
'51882', #Other pulmonary insuff
'51883', #Chronic respiratory fail
'51884', #Acute & chronc resp fail
'51889', #Other lung disease NEC
'5191', #Other diseases of trachea and bronchus, not elsewhere classified
'51911', #Acute bronchospasm
'51919', #Trachea & bronch dis NEC
'5193', #Mediastinum disease NEC
'5194', #Disorders of diaphragm
'5198', #Resp system disease NEC
'5199', #Resp system disease NOS
'78440', #Voice/resonance dis NOS
'78449', #Voice/resonance dis NEC
'7847', #Epistaxis
'7848', #Hemorrhage from throat
'78600', #Respiratory abnorm NOS
'78609', #Respiratory abnorm NEC
'78639', #Hemoptysis NEC
'7869', #Resp sys/chest symp NEC
'79311', #Solitary pulmonry nodule
'7942', #Abn pulmonary func study
'7991', #Respiratory arrest
'2639', #Protein-cal malnutr NOS
'2761', #Hyposmolality
'28529', #Anemia-other chronic dis
'2859', #Anemia NOS
'28860', #Leukocytosis NOS
'2893', #Lymphadenitis NOS
'4293', #Cardiomegaly
'5119', #Pleural effusion NOS
'5180', #Pulmonary collapse
'7822', #Local suprficial swellng
'7842', #Swelling in head & neck
'7850', #Tachycardia NOS
'7856', #Enlargement lymph nodes
'7866', #Chest swelling/mass/lump
'7867', #Abnormal chest sounds
'7931', #Lung field
'79319', #Ot nonsp ab fnd lung fld
'79902', #Hypoxemia
'7994' #Cachexia
))
icd10_codes <- as.character(c('R042', #Hemoptysis
'R05', #Cough
'R0600', #Dyspnea, unspecified
'R0601', #Orthopnea
'R0602', #Shortness of breath
'R0603', #Acute respiratory distress
'R0609', #Other forms of dyspnea
'R062', #Wheezing
'R0689', #Other abnormalities of breathing
'R069', #Unspecified abnormalities of breathing
'R071', #Chest pain on breathing
'R072', #Precordial pain
'R0781', #Pleurodynia
'R0782', #Intercostal pain
'R0789', #Other chest pain
'R079', #Chest pain, unspecified
'R093', #Abnormal sputum
'R490', #Dysphonia
'R498', #Other voice and resonance disorders
'R499', #Unspecified voice and resonance disorder
'R50', #Fever of other and unknown origin
'R5081', #Fever presenting with conditions classified elsewhere
'R509', #Fever, unspecified
'R531', #Weakness
'R5381', #Other malaise
'R5383', #Other fatigue
'R61', #Generalized hyperhidrosis
'R634', #Abnormal weight loss
'A310', #Pulmonary mycobacterial infection
'A3701', #Whooping cough due to Bordetella pertussis with pneumonia
'A3711', #Whooping cough due to Bordetella parapertussis w pneumonia
'A419', #Sepsis, unspecified organism
'A430', #Pulmonary nocardiosis
'A481', #Legionnaires' disease
'B250', #Cytomegaloviral pneumonitis
'B349', #Viral infection, unspecified
'B371', #Pulmonary candidiasis
'B380', #Acute pulmonary coccidioidomycosis
'B381', #Chronic pulmonary coccidioidomycosis
'B382', #Pulmonary coccidioidomycosis, unspecified
'B390', #Acute pulmonary histoplasmosis capsulati
'B391', #Chronic pulmonary histoplasmosis capsulati
'B392', #Pulmonary histoplasmosis capsulati, unspecified
'B583', #Pulmonary toxoplasmosis
'B59', #Pneumocystosis
'B7781', #Ascariasis pneumonia
'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
'D860', #Sarcoidosis of lung
'D869', #Sarcoidosis, unspecified
'J00', #Acute nasopharyngitis [common cold]
'J0100', #Acute maxillary sinusitis, unspecified
'J0101', #Acute recurrent maxillary sinusitis
'J0110', #Acute frontal sinusitis, unspecified
'J0111', #Acute recurrent frontal sinusitis
'J0120', #Acute ethmoidal sinusitis, unspecified
'J0121', #Acute recurrent ethmoidal sinusitis
'J0130', #Acute sphenoidal sinusitis, unspecified
'J0131', #Acute recurrent sphenoidal sinusitis
'J0140', #Acute pansinusitis, unspecified
'J0141', #Acute recurrent pansinusitis
'J0180', #Other acute sinusitis
'J0181', #Other acute recurrent sinusitis
'J0190', #Acute sinusitis, unspecified
'J0191', #Acute recurrent sinusitis, unspecified
'J020', #Streptococcal pharyngitis
'J028', #Acute pharyngitis due to other specified organisms
'J029', #Acute pharyngitis, unspecified
'J0300', #Acute streptococcal tonsillitis, unspecified
'J0301', #Acute recurrent streptococcal tonsillitis
'J0380', #Acute tonsillitis due to other specified organisms
'J0381', #Acute recurrent tonsillitis due to other specified organisms
'J0390', #Acute tonsillitis, unspecified
'J0391', #Acute recurrent tonsillitis, unspecified
'J040', #Acute laryngitis
'J0410', #Acute tracheitis without obstruction
'J0411', #Acute tracheitis with obstruction
'J042', #Acute laryngotracheitis
'J0430', #Supraglottitis, unspecified, without obstruction
'J0431', #Supraglottitis, unspecified, with obstruction
'J050', #Acute obstructive laryngitis [croup]
'J0510', #Acute epiglottitis without obstruction
'J0511', #Acute epiglottitis with obstruction
'J060', #Acute laryngopharyngitis
'J069', #Acute upper respiratory infection, unspecified
'J09X1', #Influenza due to ident novel influenza A virus w pneumonia
'J09X2', #Flu due to ident novel influenza A virus w oth resp manifest
'J09X3', #Influenza due to ident novel influenza A virus w GI manifest
'J09X9', #Flu due to ident novel influenza A virus w oth manifest
'J1000', #Flu due to oth ident flu virus w unsp type of pneumonia
'J1001', #Flu due to oth ident flu virus w same oth ident flu virus pn
'J1008', #Influenza due to oth ident influenza virus w oth pneumonia
'J101', #Flu due to oth ident influenza virus w oth resp manifest
'J102', #Influenza due to oth ident influenza virus w GI manifest
'J1089', #Influenza due to oth ident influenza virus w oth manifest
'J1100', #Flu due to unidentified flu virus w unsp type of pneumonia
'J1108', #Flu due to unidentified flu virus w specified pneumonia
'J111', #Flu due to unidentified influenza virus w oth resp manifest
'J112', #Influenza due to unidentified influenza virus w GI manifest
'J1181', #Flu due to unidentified influenza virus w encephalopathy
'J1182', #Influenza due to unidentified influenza virus w myocarditis
'J1183', #Influenza due to unidentified influenza virus w otitis media
'J1189', #Influenza due to unidentified influenza virus w oth manifest
'J120', #Adenoviral pneumonia
'J121', #Respiratory syncytial virus pneumonia
'J122', #Parainfluenza virus pneumonia
'J123', #Human metapneumovirus pneumonia
'J1289', #Other viral pneumonia
'J129', #Viral pneumonia, unspecified
'J13', #Pneumonia due to Streptococcus pneumoniae
'J14', #Pneumonia due to Hemophilus influenzae
'J150', #Pneumonia due to Klebsiella pneumoniae
'J151', #Pneumonia due to Pseudomonas
'J1520', #Pneumonia due to staphylococcus, unspecified
'J15211', #Pneumonia due to methicillin suscep staph
'J15212', #Pneumonia due to Methicillin resistant Staphylococcus aureus
'J1529', #Pneumonia due to other staphylococcus
'J153', #Pneumonia due to streptococcus, group B
'J154', #Pneumonia due to other streptococci
'J155', #Pneumonia due to Escherichia coli
'J156', #Pneumonia due to other Gram-negative bacteria
'J157', #Pneumonia due to Mycoplasma pneumoniae
'J158', #Pneumonia due to other specified bacteria
'J159', #Unspecified bacterial pneumonia
'J160', #Chlamydial pneumonia
'J168', #Pneumonia due to other specified infectious organisms
'J17', #Pneumonia in diseases classified elsewhere
'J180', #Bronchopneumonia, unspecified organism
'J181', #Lobar pneumonia, unspecified organism
'J182', #Hypostatic pneumonia, unspecified organism
'J188', #Other pneumonia, unspecified organism
'J189', #Pneumonia, unspecified organism
'J200', #Acute bronchitis due to Mycoplasma pneumoniae
'J201', #Acute bronchitis due to Hemophilus influenzae
'J202', #Acute bronchitis due to streptococcus
'J203', #Acute bronchitis due to coxsackievirus
'J204', #Acute bronchitis due to parainfluenza virus
'J205', #Acute bronchitis due to respiratory syncytial virus
'J206', #Acute bronchitis due to rhinovirus
'J207', #Acute bronchitis due to echovirus
'J208', #Acute bronchitis due to other specified organisms
'J209', #Acute bronchitis, unspecified
'J210', #Acute bronchiolitis due to respiratory syncytial virus
'J211', #Acute bronchiolitis due to human metapneumovirus
'J218', #Acute bronchiolitis due to other specified organisms
'J219', #Acute bronchiolitis, unspecified
'J22', #Unspecified acute lower respiratory infection
'J311', #Chronic nasopharyngitis
'J312', #Chronic pharyngitis
'J320', #Chronic maxillary sinusitis
'J321', #Chronic frontal sinusitis
'J322', #Chronic ethmoidal sinusitis
'J323', #Chronic sphenoidal sinusitis
'J324', #Chronic pansinusitis
'J328', #Other chronic sinusitis
'J329', #Chronic sinusitis, unspecified
'J3501', #Chronic tonsillitis
'J3502', #Chronic adenoiditis
'J3503', #Chronic tonsillitis and adenoiditis
'J352', #Hypertrophy of adenoids
'J353', #Hypertrophy of tonsils with hypertrophy of adenoids
'J358', #Other chronic diseases of tonsils and adenoids
'J359', #Chronic disease of tonsils and adenoids, unspecified
'J36', #Peritonsillar abscess
'J390', #Retropharyngeal and parapharyngeal abscess
'J391', #Other abscess of pharynx
'J40', #Bronchitis, not specified as acute or chronic
'J410', #Simple chronic bronchitis
'J411', #Mucopurulent chronic bronchitis
'J42', #Unspecified chronic bronchitis
'J440', #Chronic obstructive pulmon disease w acute lower resp infct
'J470', #Bronchiectasis with acute lower respiratory infection
'J851', #Abscess of lung with pneumonia
'J852', #Abscess of lung without pneumonia
'J853', #Abscess of mediastinum
'J860', #Pyothorax with fistula
'J9311', #Primary spontaneous pneumothorax
'J9611', #Chronic respiratory failure with hypoxia
'J9691', #Respiratory failure, unspecified with hypoxia
'J9809', #Other diseases of bronchus, not elsewhere classified
'J985', #Diseases of mediastinum, not elsewhere classified
'J9859', #Other diseases of mediastinum, not elsewhere classified
'J989', #Respiratory disorder, unspecified
'R066', #Hiccough
'R0682', #Tachypnea, not elsewhere classified
'R070', #Pain in throat
'R0901', #Asphyxia
'R0982', #Postnasal drip
'C33', #Malignant neoplasm of trachea
'C3400', #Malignant neoplasm of unspecified main bronchus
'C3401', #Malignant neoplasm of right main bronchus
'C3402', #Malignant neoplasm of left main bronchus
'C3410', #Malignant neoplasm of upper lobe, unsp bronchus or lung
'C3411', #Malignant neoplasm of upper lobe, right bronchus or lung
'C3412', #Malignant neoplasm of upper lobe, left bronchus or lung
'C342', #Malignant neoplasm of middle lobe, bronchus or lung
'C3430', #Malignant neoplasm of lower lobe, unsp bronchus or lung
'C3431', #Malignant neoplasm of lower lobe, right bronchus or lung
'C3432', #Malignant neoplasm of lower lobe, left bronchus or lung
'C3480', #Malignant neoplasm of ovrlp sites of unsp bronchus and lung
'C3481', #Malignant neoplasm of ovrlp sites of right bronchus and lung
'C3482', #Malignant neoplasm of ovrlp sites of left bronchus and lung
'C3490', #Malignant neoplasm of unsp part of unsp bronchus or lung
'C3491', #Malignant neoplasm of unsp part of right bronchus or lung
'C3492', #Malignant neoplasm of unsp part of left bronchus or lung
'C384', #Malignant neoplasm of pleura
'C390', #Malignant neoplasm of upper respiratory tract, part unsp
'C399', #Malignant neoplasm of lower respiratory tract, part unsp
'C450', #Mesothelioma of pleura
'C7A090', #Malignant carcinoid tumor of the bronchus and lung
'D021', #Carcinoma in situ of trachea
'D0220', #Carcinoma in situ of unspecified bronchus and lung
'D0221', #Carcinoma in situ of right bronchus and lung
'D0222', #Carcinoma in situ of left bronchus and lung
'D023', #Carcinoma in situ of other parts of respiratory system
'D024', #Carcinoma in situ of respiratory system, unspecified
'I509', #Heart failure, unspecified
'J300', #Vasomotor rhinitis
'J301', #Allergic rhinitis due to pollen
'J302', #Other seasonal allergic rhinitis
'J3081', #Allergic rhinitis due to animal (cat) (dog) hair and dander
'J3089', #Other allergic rhinitis
'J309', #Allergic rhinitis, unspecified
'J310', #Chronic rhinitis
'J342', #Deviated nasal septum
'J3489', #Other specified disorders of nose and nasal sinuses
'J351', #Hypertrophy of tonsils
'J370', #Chronic laryngitis
'J371', #Chronic laryngotracheitis
'J3800', #Paralysis of vocal cords and larynx, unspecified
'J3801', #Paralysis of vocal cords and larynx, unilateral
'J3802', #Paralysis of vocal cords and larynx, bilateral
'J381', #Polyp of vocal cord and larynx
'J382', #Nodules of vocal cords
'J383', #Other diseases of vocal cords
'J384', #Edema of larynx
'J385', #Laryngeal spasm
'J386', #Stenosis of larynx
'J387', #Other diseases of larynx
'J392', #Other diseases of pharynx
'J393', #Upper respiratory tract hypersensitivity reaction, site unsp
'J398', #Other specified diseases of upper respiratory tract
'J399', #Disease of upper respiratory tract, unspecified
'J418', #Mixed simple and mucopurulent chronic bronchitis
'J430', #Unilateral pulmonary emphysema [MacLeod's syndrome]
'J431', #Panlobular emphysema
'J432', #Centrilobular emphysema
'J438', #Other emphysema
'J439', #Emphysema, unspecified
'J441', #Chronic obstructive pulmonary disease w (acute) exacerbation
'J449', #Chronic obstructive pulmonary disease, unspecified
'J4520', #Mild intermittent asthma, uncomplicated
'J4521', #Mild intermittent asthma with (acute) exacerbation
'J4522', #Mild intermittent asthma with status asthmaticus
'J4530', #Mild persistent asthma, uncomplicated
'J4531', #Mild persistent asthma with (acute) exacerbation
'J4532', #Mild persistent asthma with status asthmaticus
'J4540', #Moderate persistent asthma, uncomplicated
'J4541', #Moderate persistent asthma with (acute) exacerbation
'J4542', #Moderate persistent asthma with status asthmaticus
'J4550', #Severe persistent asthma, uncomplicated
'J4551', #Severe persistent asthma with (acute) exacerbation
'J4552', #Severe persistent asthma with status asthmaticus
'J45901', #Unspecified asthma with (acute) exacerbation
'J45902', #Unspecified asthma with status asthmaticus
'J45909', #Unspecified asthma, uncomplicated
'J45990', #Exercise induced bronchospasm
'J45991', #Cough variant asthma
'J45998', #Other asthma
'J471', #Bronchiectasis with (acute) exacerbation
'J479', #Bronchiectasis, uncomplicated
'J60', #Coalworker's pneumoconiosis
'J61', #Pneumoconiosis due to asbestos and other mineral fibers
'J620', #Pneumoconiosis due to talc dust
'J628', #Pneumoconiosis due to other dust containing silica
'J630', #Aluminosis (of lung)
'J631', #Bauxite fibrosis (of lung)
'J632', #Berylliosis
'J633', #Graphite fibrosis (of lung)
'J634', #Siderosis
'J635', #Stannosis
'J636', #Pneumoconiosis due to other specified inorganic dusts
'J64', #Unspecified pneumoconiosis
'J660', #Byssinosis
'J661', #Flax-dressers' disease
'J662', #Cannabinosis
'J668', #Airway disease due to other specific organic dusts
'J670', #Farmer's lung
'J671', #Bagassosis
'J672', #Bird fancier's lung
'J673', #Suberosis
'J674', #Maltworker's lung
'J675', #Mushroom-worker's lung
'J676', #Maple-bark-stripper's lung
'J677', #Air conditioner and humidifier lung
'J678', #Hypersensitivity pneumonitis due to other organic dusts
'J679', #Hypersensitivity pneumonitis due to unspecified organic dust
'J680', #Bronchitis & pneumonitis d/t chemicals, gas, fumes & vapors
'J681', #Pulmonary edema due to chemicals, gases, fumes and vapors
'J682', #Upper resp inflam d/t chemicals, gas, fumes and vapors, NEC
'J683', #Oth ac & subac resp cond d/t chemicals, gas, fumes & vapors
'J684', #Chronic resp cond due to chemicals, gases, fumes and vapors
'J688', #Oth resp cond due to chemicals, gases, fumes and vapors
'J689', #Unsp resp cond due to chemicals, gases, fumes and vapors
'J690', #Pneumonitis due to inhalation of food and vomit
'J691', #Pneumonitis due to inhalation of oils and essences
'J698', #Pneumonitis due to inhalation of other solids and liquids
'J700', #Acute pulmonary manifestations due to radiation
'J701', #Chronic and other pulmonary manifestations due to radiation
'J702', #Acute drug-induced interstitial lung disorders
'J703', #Chronic drug-induced interstitial lung disorders
'J704', #Drug-induced interstitial lung disorders, unspecified
'J705', #Respiratory conditions due to smoke inhalation
'J708', #Respiratory conditions due to oth external agents
'J709', #Respiratory conditions due to unspecified external agent
'J80', #Acute respiratory distress syndrome
'J810', #Acute pulmonary edema
'J811', #Chronic pulmonary edema
'J82', #Pulmonary eosinophilia, not elsewhere classified
'J8401', #Alveolar proteinosis
'J8402', #Pulmonary alveolar microlithiasis
'J8403', #Idiopathic pulmonary hemosiderosis
'J8409', #Other alveolar and parieto-alveolar conditions
'J8410', #Pulmonary fibrosis, unspecified
'J84111', #Idiopathic interstitial pneumonia, not otherwise specified
'J84112', #Idiopathic pulmonary fibrosis
'J84113', #Idiopathic non-specific interstitial pneumonitis
'J84114', #Acute interstitial pneumonitis
'J84115', #Respiratory bronchiolitis interstitial lung disease
'J84116', #Cryptogenic organizing pneumonia
'J84117', #Desquamative interstitial pneumonia
'J8417', #Oth interstit pulmon dis w fibrosis in dis classd elswhr
'J842', #Lymphoid interstitial pneumonia
'J8481', #Lymphangioleiomyomatosis
'J8482', #Adult pulmonary Langerhans cell histiocytosis
'J8489', #Other specified interstitial pulmonary diseases
'J849', #Interstitial pulmonary disease, unspecified
'J850', #Gangrene and necrosis of lung
'J869', #Pyothorax without fistula
'J920', #Pleural plaque with presence of asbestos
'J929', #Pleural plaque without asbestos
'J930', #Spontaneous tension pneumothorax
'J9312', #Secondary spontaneous pneumothorax
'J9381', #Chronic pneumothorax
'J9382', #Other air leak
'J9383', #Other pneumothorax
'J940', #Chylous effusion
'J941', #Fibrothorax
'J942', #Hemothorax
'J948', #Other specified pleural conditions
'J949', #Pleural condition, unspecified
'J9600', #Acute respiratory failure, unsp w hypoxia or hypercapnia
'J9601', #Acute respiratory failure with hypoxia
'J9602', #Acute respiratory failure with hypercapnia
'J9610', #Chronic respiratory failure, unsp w hypoxia or hypercapnia
'J9612', #Chronic respiratory failure with hypercapnia
'J9620', #Acute and chr resp failure, unsp w hypoxia or hypercapnia
'J9621', #Acute and chronic respiratory failure with hypoxia
'J9622', #Acute and chronic respiratory failure with hypercapnia
'J9690', #Respiratory failure, unsp, unsp w hypoxia or hypercapnia
'J9692', #Respiratory failure, unspecified with hypercapnia
'J9801', #Acute bronchospasm
'J9819', #Other pulmonary collapse
'J982', #Interstitial emphysema
'J983', #Compensatory emphysema
'J984', #Other disorders of lung
'J9851', #Mediastinitis
'J986', #Disorders of diaphragm
'J988', #Other specified respiratory disorders
'J99', #Respiratory disorders in diseases classified elsewhere
'N390', #Urinary tract infection, site not specified
'R040', #Epistaxis
'R041', #Hemorrhage from throat
'R048', #Hemorrhage from other sites in respiratory passages
'R0489', #Hemorrhage from other sites in respiratory passages
'R049', #Hemorrhage from respiratory passages, unspecified
'R091', #Pleurisy
'R0981', #Nasal congestion
'D649', #Anemia, unspecified
'D72829', #Elevated white blood cell count, unspecified
'E871', #Hypo-osmolality and hyponatremia
'I517', #Cardiomegaly
'J90', #Pleural effusion, not elsewhere classified
'J918', #Pleural effusion in other conditions classified elsewhere
'J939', #Pneumothorax, unspecified
'J9811', #Atelectasis
'R000', #Tachycardia, unspecified
'R0902', #Hypoxemia
'R220', #Localized swelling, mass and lump, head
'R221', #Localized swelling, mass and lump, neck
'R222', #Localized swelling, mass and lump, trunk
'R59', #Enlarged lymph nodes
'R590', #Localized enlarged lymph nodes
'R591', #Generalized enlarged lymph nodes
'R599', #Enlarged lymph nodes, unspecified
'R911', #Solitary pulmonary nodule
'R918' #Other nonspecific abnormal finding of lung field
))
# Procedure codes:
pr_codes_icd9 <- c()
pr_codes_icd10 <- c()
pr_codes_cpt <- c()
# Medication codes
rx_codes <- c()
aarmiller/codeBuildr documentation built on April 14, 2025, 1:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## Codes for tb
# Description:
desc <- "Tuberculosis"
# Diagnosis codes:
# library(tidyverse)
# tmp <- read_csv("~/Documents/GitHub/delay_dx/params/ssd_codes/tb/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")
#
# icd::icd10cm2019
# 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 <- as.character(c('7806', #Fever and other physiologic disturbances of temperature regulation
'78060', #Fever NOS
'78061', #Fever in other diseases
'78079', #Malaise and fatigue NEC
'7808', #Generalizd hyperhidrosis
'78321', #Abnormal loss of weight
'7841', #Throat pain
'78441', #Aphonia
'78442', #Dysphonia
'7849', #Other symptoms involving head and neck
'78491', #Postnasal drip
'78499', #Head & neck symptoms NEC
'78602', #Orthopnea
'78605', #Shortness of breath
'78607', #Wheezing
'7862', #Cough
'7863', #Hemoptysis
'78630', #Hemoptysis NOS
'7864', #Abnormal sputum
'78650', #Chest pain NOS
'78651', #Precordial pain
'78652', #Painful respiration
'78659', #Chest pain NEC
'0389', #Septicemia NOS
'07999', #Viral infection NOS
'1124', #Candidiasis of lung
'1140', #Primary coccidioidomycos
'1144', #Ch pl coccidioidomycosis
'11505', #Histoplasm caps pneumon
'11515', #Histoplasm dub pneumonia
'11595', #Histoplasmosis pneumonia
'1304', #Toxoplasma pneumonitis
'1363', #Pneumocystosis
'310', #Specific nonpsychotic mental disorders due to brain damage
'340', #Multiple sclerosis
'391', #Rheumatic fever with heart involvement
'460', #Acute nasopharyngitis
'4610', #Ac maxillary sinusitis
'4611', #Ac frontal sinusitis
'4612', #Ac ethmoidal sinusitis
'4613', #Ac sphenoidal sinusitis
'4619', #Acute sinusitis NOS
'462', #Acute pharyngitis
'463', #Acute tonsillitis
'4640', #Acute laryngitis
'46400', #Ac laryngitis w/o obst
'46401', #Ac laryngitis w obstruct
'46411', #Ac tracheitis w obstruct
'46420', #Ac laryngotrach no obstr
'46421', #Ac laryngotrach w obstr
'46430', #Ac epiglottitis no obstr
'46431', #Ac epiglottitis w obstr
'4644', #Croup
'46450', #Supraglottis w/o obs NOS
'46451', #Supraglottis w obstr NOS
'4650', #Acute laryngopharyngitis
'4658', #Acute uri mult sites NEC
'4659', #Acute uri NOS
'4660', #Acute bronchitis
'4661', #Acute bronchiolitis
'46611', #Acu broncholitis d/t RSV
'46619', #Acu brnchlts d/t oth org
'4722', #Chronic nasopharyngitis
'4730', #Chr maxillary sinusitis
'4731', #Chr frontal sinusitis
'4732', #Chr ethmoidal sinusitis
'4733', #Chr sphenoidal sinusitis
'4738', #Chronic sinusitis NEC
'4739', #Chronic sinusitis NOS
'4740', #Chronic tonsillitis and adenoiditis
'47400', #Chronic tonsillitis
'47401', #Chronic adenoiditis
'47402', #Chronic tonsils&adenoids
'47410', #Hypertrophy T and A
'47411', #Hypertrophy tonsils
'475', #Peritonsillar abscess
'4760', #Chronic laryngitis
'4761', #Chr laryngotracheitis
'47821', #Cellulitis of pharynx
'47822', #Parapharyngeal abscess
'47824', #Retropharyngeal abscess
'47871', #Laryngeal cellulitis
'4789', #Upper resp dis NEC/NOS
'4800', #Adenoviral pneumonia
'4801', #Resp syncyt viral pneum
'4802', #Parinfluenza viral pneum
'4808', #Viral pneumonia NEC
'4809', #Viral pneumonia NOS
'481', #Pneumococcal pneumonia
'4820', #K. pneumoniae pneumonia
'4821', #Pseudomonal pneumonia
'4822', #H.influenzae pneumonia
'4823', #Pneumonia due to Streptococcus
'48230', #Streptococcal pneumn NOS
'48231', #Pneumonia strptococcus a
'48232', #Pneumonia strptococcus b
'48239', #Pneumonia oth strep
'4824', #Pneumonia due to Staphylococcus
'48240', #Staphylococcal pneu NOS
'48241', #Meth sus pneum d/t Staph
'48242', #Meth res pneu d/t Staph
'48249', #Staph pneumonia NEC
'4828', #Pneumonia due to other specified bacteria
'48281', #Pneumonia anaerobes
'48283', #Pneumo oth grm-neg bact
'48284', #Legionnaires' disease
'48289', #Pneumonia oth spcf bact
'4829', #Bacterial pneumonia NOS
'483', #Pneumonia due to other specified organism
'4830', #Pneu mycplsm pneumoniae
'4831', #Pneumonia d/t chlamydia
'4838', #Pneumon oth spec orgnsm
'4841', #Pneum w cytomeg incl dis
'4843', #Pneumonia in whoop cough
'4846', #Pneum in aspergillosis
'4847', #Pneum in oth sys mycoses
'4848', #Pneum in infect dis NEC
'485', #Bronchopneumonia org NOS
'486', #Pneumonia, organism NOS
'4870', #Influenza with pneumonia
'4871', #Flu w resp manifest NEC
'4878', #Flu w manifestation NEC
'488', #Influenza due to certain identified influenza viruses
'4881', #Influenza due to identified 2009 H1N1 influenza virus
'48811', #Flu dt 2009 H1N1 w pneu
'48812', #Flu-2009 H1N1 w oth resp
'48819', #Flu-2009 H1N1 w oth man
'48881', #Flu dt nvl A vrs w pneu
'48882', #Flu dt nvl A w oth resp
'48889', #Flu dt novel A w oth man
'490', #Bronchitis NOS
'4910', #Simple chr bronchitis
'4911', #Mucopurul chr bronchitis
'4918', #Chronic bronchitis NEC
'4919', #Chronic bronchitis NOS
'5100', #Empyema with fistula
'5130', #Abscess of lung
'5131', #Abscess of mediastinum
'5192', #Mediastinitis
'5990', #Urin tract infection NOS
'830', #Dislocation of jaw
'99591', #Sepsis
'135', #Sarcoidosis
'1622', #Malig neo main bronchus
'1623', #Mal neo upper lobe lung
'1624', #Mal neo middle lobe lung
'1625', #Mal neo lower lobe lung
'1628', #Mal neo bronch/lung NEC
'1629', #Mal neo bronch/lung NOS
'1630', #Mal neo parietal pleura
'1631', #Mal neo visceral pleura
'1638', #Malig neopl pleura NEC
'1639', #Malig neopl pleura NOS
'1650', #Mal neo upper resp NOS
'1658', #Mal neo thorax/resp NEC
'1659', #Mal neo resp system NOS
'1970', #Secondary malig neo lung
'20921', #Mal carcinoid bronc/lung
'2123', #Benign neo bronchus/lung
'2311', #Ca in situ trachea
'2318', #Ca in situ resp sys NEC
'2319', #Ca in situ resp sys NOS
'2357', #Unc behav neo lung
'2391', #Respiratory neoplasm NOS
'2891', #Chronic lymphadenitis
'4168', #Chr pulmon heart dis NEC
'4239', #Pericardial disease NOS
'4280', #CHF NOS
'4464', #Wegener's granulomatosis
'46410', #Ac tracheitis no obstruc
'4720', #Chronic rhinitis
'47412', #Hypertrophy adenoids
'4742', #Adenoid vegetations
'4748', #Chr T & A dis NEC
'4749', #Chr T & A dis NOS
'4770', #Rhinitis due to pollen
'4772', #Allerg rhinitis-cat/dog
'4778', #Allergic rhinitis NEC
'4779', #Allergic rhinitis NOS
'4781', #Other diseases of nasal cavity and sinuses
'47819', #Nasal & sinus dis NEC
'47820', #Disease of pharynx NOS
'47829', #Disease of pharynx NEC
'47830', #Vocal cord paralysis NOS
'47831', #Vocal paral unilat part
'47832', #Vocal paral unilat total
'47833', #Vocal paral bilat part
'47834', #Vocal paral bilat total
'4784', #Vocal cord/larynx polyp
'4785', #Vocal cord disease NEC
'47870', #Disease of larynx NOS
'47874', #Stenosis of larynx
'47875', #Laryngeal spasm
'47879', #Disease of larynx NEC
'4788', #Urt hypersens react NOS
'4912', #Obstructive chronic bronchitis
'49120', #Obst chr bronc w/o exac
'49121', #Obs chr bronc w(ac) exac
'49122', #Obs chr bronc w ac bronc
'4920', #Emphysematous bleb
'4928', #Emphysema NEC
'49300', #Extrinsic asthma NOS
'49301', #Ext asthma w status asth
'49302', #Ext asthma w(acute) exac
'49310', #Intrinsic asthma NOS
'49311', #Int asthma w status asth
'49312', #Int asthma w (ac) exac
'49320', #Chronic obst asthma NOS
'49321', #Ch ob asthma w stat asth
'49322', #Ch obst asth w (ac) exac
'49381', #Exercse ind bronchospasm
'49382', #Cough variant asthma
'49390', #Asthma NOS
'49392', #Asthma NOS w (ac) exac
'494', #Bronchiectasis
'4940', #Bronchiectas w/o ac exac
'4941', #Bronchiectasis w ac exac
'4950', #Farmers' lung
'4951', #Bagassosis
'4952', #Bird-fanciers' lung
'4953', #Suberosis
'4954', #Malt workers' lung
'4955', #Mushroom workers' lung
'4956', #Mapl bark-stripprs' lung
'4957', #"ventilation" pneumonit
'4958', #Allerg alveol/pneum NEC
'4959', #Allerg alveol/pneum NOS
'496', #Chr airway obstruct NEC
'500', #Coal workers' pneumocon
'501', #Asbestosis
'502', #Silica pneumocon NEC
'503', #Inorg dust pneumocon NEC
'504', #Dust pneumonopathy NEC
'505', #Pneumoconiosis NOS
'5060', #Fum/vapor bronc/pneumon
'5061', #Fum/vapor ac pulm edema
'5062', #Fum/vapor up resp inflam
'5063', #Fum/vap ac resp cond NEC
'5064', #Fum/vapor chr resp cond
'5069', #Fum/vapor resp cond NOS
'5070', #Food/vomit pneumonitis
'5071', #Oil/essence pneumonitis
'5078', #Solid/liq pneumonit NEC
'5080', #Ac pul manif d/t radiat
'5081', #Chr pul manif d/t radiat
'5082', #Resp cond dt smoke inhal
'5088', #Resp cond: ext agent NEC
'5089', #Resp cond: ext agent NOS
'5110', #Pleurisy w/o effus or TB
'5111', #Bact pleur/effus not TB
'5118', #Other specified forms of effusion, except tuberculous
'51189', #Effusion NEC exc tb
'5120', #Spont tens pneumothorax
'5128', #Other pneumothorax and air leak
'51281', #Prim spont pneumothorax
'51282', #Sec spont pneumothorax
'51283', #Chronic pneumothorax
'51284', #Other air leak
'51289', #Other pneumothorax
'514', #Pulm congest/hypostasis
'515', #Postinflam pulm fibrosis
'5160', #Pul alveolar proteinosis
'5161', #Idio pulm hemosiderosis
'5162', #Pulm alveolar microlith
'5163', #Idiopathic interstitial pneumonia
'51630', #Idiopath inters pneu NOS
'51631', #Idiopath pulmon fibrosis
'51632', #Idio non-spec inter pneu
'51633', #Acute interstitial pneum
'51634', #Resp brncio interst lung
'51635', #Idiopth lym interst pneu
'51636', #Cryptogenic organiz pneu
'51637', #Desquamatv interst pneu
'5164', #Lymphangioleiomyomatosis
'5165', #Adlt pul Langs cell hist
'5168', #Alveol pneumonopathy NEC
'5169', #Alveol pneumonopathy NOS
'5171', #Rheumatic pneumonia
'5172', #Syst sclerosis lung dis
'5173', #Acute chest syndrome
'5178', #Lung involv in oth dis
'5181', #Interstitial emphysema
'5182', #Compensatory emphysema
'5183', #Pulmonary eosinophilia
'5184', #Acute lung edema NOS
'51881', #Acute respiratry failure
'51882', #Other pulmonary insuff
'51883', #Chronic respiratory fail
'51884', #Acute & chronc resp fail
'51889', #Other lung disease NEC
'5191', #Other diseases of trachea and bronchus, not elsewhere classified
'51911', #Acute bronchospasm
'51919', #Trachea & bronch dis NEC
'5193', #Mediastinum disease NEC
'5194', #Disorders of diaphragm
'5198', #Resp system disease NEC
'5199', #Resp system disease NOS
'78440', #Voice/resonance dis NOS
'78449', #Voice/resonance dis NEC
'7847', #Epistaxis
'7848', #Hemorrhage from throat
'78600', #Respiratory abnorm NOS
'78609', #Respiratory abnorm NEC
'78639', #Hemoptysis NEC
'7869', #Resp sys/chest symp NEC
'79311', #Solitary pulmonry nodule
'7942', #Abn pulmonary func study
'7991', #Respiratory arrest
'2639', #Protein-cal malnutr NOS
'2761', #Hyposmolality
'28529', #Anemia-other chronic dis
'2859', #Anemia NOS
'28860', #Leukocytosis NOS
'2893', #Lymphadenitis NOS
'4293', #Cardiomegaly
'5119', #Pleural effusion NOS
'5180', #Pulmonary collapse
'7822', #Local suprficial swellng
'7842', #Swelling in head & neck
'7850', #Tachycardia NOS
'7856', #Enlargement lymph nodes
'7866', #Chest swelling/mass/lump
'7867', #Abnormal chest sounds
'7931', #Lung field
'79319', #Ot nonsp ab fnd lung fld
'79902', #Hypoxemia
'7994' #Cachexia
))
icd10_codes <- as.character(c('R042', #Hemoptysis
'R05', #Cough
'R0600', #Dyspnea, unspecified
'R0601', #Orthopnea
'R0602', #Shortness of breath
'R0603', #Acute respiratory distress
'R0609', #Other forms of dyspnea
'R062', #Wheezing
'R0689', #Other abnormalities of breathing
'R069', #Unspecified abnormalities of breathing
'R071', #Chest pain on breathing
'R072', #Precordial pain
'R0781', #Pleurodynia
'R0782', #Intercostal pain
'R0789', #Other chest pain
'R079', #Chest pain, unspecified
'R093', #Abnormal sputum
'R490', #Dysphonia
'R498', #Other voice and resonance disorders
'R499', #Unspecified voice and resonance disorder
'R50', #Fever of other and unknown origin
'R5081', #Fever presenting with conditions classified elsewhere
'R509', #Fever, unspecified
'R531', #Weakness
'R5381', #Other malaise
'R5383', #Other fatigue
'R61', #Generalized hyperhidrosis
'R634', #Abnormal weight loss
'A310', #Pulmonary mycobacterial infection
'A3701', #Whooping cough due to Bordetella pertussis with pneumonia
'A3711', #Whooping cough due to Bordetella parapertussis w pneumonia
'A419', #Sepsis, unspecified organism
'A430', #Pulmonary nocardiosis
'A481', #Legionnaires' disease
'B250', #Cytomegaloviral pneumonitis
'B349', #Viral infection, unspecified
'B371', #Pulmonary candidiasis
'B380', #Acute pulmonary coccidioidomycosis
'B381', #Chronic pulmonary coccidioidomycosis
'B382', #Pulmonary coccidioidomycosis, unspecified
'B390', #Acute pulmonary histoplasmosis capsulati
'B391', #Chronic pulmonary histoplasmosis capsulati
'B392', #Pulmonary histoplasmosis capsulati, unspecified
'B583', #Pulmonary toxoplasmosis
'B59', #Pneumocystosis
'B7781', #Ascariasis pneumonia
'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
'D860', #Sarcoidosis of lung
'D869', #Sarcoidosis, unspecified
'J00', #Acute nasopharyngitis [common cold]
'J0100', #Acute maxillary sinusitis, unspecified
'J0101', #Acute recurrent maxillary sinusitis
'J0110', #Acute frontal sinusitis, unspecified
'J0111', #Acute recurrent frontal sinusitis
'J0120', #Acute ethmoidal sinusitis, unspecified
'J0121', #Acute recurrent ethmoidal sinusitis
'J0130', #Acute sphenoidal sinusitis, unspecified
'J0131', #Acute recurrent sphenoidal sinusitis
'J0140', #Acute pansinusitis, unspecified
'J0141', #Acute recurrent pansinusitis
'J0180', #Other acute sinusitis
'J0181', #Other acute recurrent sinusitis
'J0190', #Acute sinusitis, unspecified
'J0191', #Acute recurrent sinusitis, unspecified
'J020', #Streptococcal pharyngitis
'J028', #Acute pharyngitis due to other specified organisms
'J029', #Acute pharyngitis, unspecified
'J0300', #Acute streptococcal tonsillitis, unspecified
'J0301', #Acute recurrent streptococcal tonsillitis
'J0380', #Acute tonsillitis due to other specified organisms
'J0381', #Acute recurrent tonsillitis due to other specified organisms
'J0390', #Acute tonsillitis, unspecified
'J0391', #Acute recurrent tonsillitis, unspecified
'J040', #Acute laryngitis
'J0410', #Acute tracheitis without obstruction
'J0411', #Acute tracheitis with obstruction
'J042', #Acute laryngotracheitis
'J0430', #Supraglottitis, unspecified, without obstruction
'J0431', #Supraglottitis, unspecified, with obstruction
'J050', #Acute obstructive laryngitis [croup]
'J0510', #Acute epiglottitis without obstruction
'J0511', #Acute epiglottitis with obstruction
'J060', #Acute laryngopharyngitis
'J069', #Acute upper respiratory infection, unspecified
'J09X1', #Influenza due to ident novel influenza A virus w pneumonia
'J09X2', #Flu due to ident novel influenza A virus w oth resp manifest
'J09X3', #Influenza due to ident novel influenza A virus w GI manifest
'J09X9', #Flu due to ident novel influenza A virus w oth manifest
'J1000', #Flu due to oth ident flu virus w unsp type of pneumonia
'J1001', #Flu due to oth ident flu virus w same oth ident flu virus pn
'J1008', #Influenza due to oth ident influenza virus w oth pneumonia
'J101', #Flu due to oth ident influenza virus w oth resp manifest
'J102', #Influenza due to oth ident influenza virus w GI manifest
'J1089', #Influenza due to oth ident influenza virus w oth manifest
'J1100', #Flu due to unidentified flu virus w unsp type of pneumonia
'J1108', #Flu due to unidentified flu virus w specified pneumonia
'J111', #Flu due to unidentified influenza virus w oth resp manifest
'J112', #Influenza due to unidentified influenza virus w GI manifest
'J1181', #Flu due to unidentified influenza virus w encephalopathy
'J1182', #Influenza due to unidentified influenza virus w myocarditis
'J1183', #Influenza due to unidentified influenza virus w otitis media
'J1189', #Influenza due to unidentified influenza virus w oth manifest
'J120', #Adenoviral pneumonia
'J121', #Respiratory syncytial virus pneumonia
'J122', #Parainfluenza virus pneumonia
'J123', #Human metapneumovirus pneumonia
'J1289', #Other viral pneumonia
'J129', #Viral pneumonia, unspecified
'J13', #Pneumonia due to Streptococcus pneumoniae
'J14', #Pneumonia due to Hemophilus influenzae
'J150', #Pneumonia due to Klebsiella pneumoniae
'J151', #Pneumonia due to Pseudomonas
'J1520', #Pneumonia due to staphylococcus, unspecified
'J15211', #Pneumonia due to methicillin suscep staph
'J15212', #Pneumonia due to Methicillin resistant Staphylococcus aureus
'J1529', #Pneumonia due to other staphylococcus
'J153', #Pneumonia due to streptococcus, group B
'J154', #Pneumonia due to other streptococci
'J155', #Pneumonia due to Escherichia coli
'J156', #Pneumonia due to other Gram-negative bacteria
'J157', #Pneumonia due to Mycoplasma pneumoniae
'J158', #Pneumonia due to other specified bacteria
'J159', #Unspecified bacterial pneumonia
'J160', #Chlamydial pneumonia
'J168', #Pneumonia due to other specified infectious organisms
'J17', #Pneumonia in diseases classified elsewhere
'J180', #Bronchopneumonia, unspecified organism
'J181', #Lobar pneumonia, unspecified organism
'J182', #Hypostatic pneumonia, unspecified organism
'J188', #Other pneumonia, unspecified organism
'J189', #Pneumonia, unspecified organism
'J200', #Acute bronchitis due to Mycoplasma pneumoniae
'J201', #Acute bronchitis due to Hemophilus influenzae
'J202', #Acute bronchitis due to streptococcus
'J203', #Acute bronchitis due to coxsackievirus
'J204', #Acute bronchitis due to parainfluenza virus
'J205', #Acute bronchitis due to respiratory syncytial virus
'J206', #Acute bronchitis due to rhinovirus
'J207', #Acute bronchitis due to echovirus
'J208', #Acute bronchitis due to other specified organisms
'J209', #Acute bronchitis, unspecified
'J210', #Acute bronchiolitis due to respiratory syncytial virus
'J211', #Acute bronchiolitis due to human metapneumovirus
'J218', #Acute bronchiolitis due to other specified organisms
'J219', #Acute bronchiolitis, unspecified
'J22', #Unspecified acute lower respiratory infection
'J311', #Chronic nasopharyngitis
'J312', #Chronic pharyngitis
'J320', #Chronic maxillary sinusitis
'J321', #Chronic frontal sinusitis
'J322', #Chronic ethmoidal sinusitis
'J323', #Chronic sphenoidal sinusitis
'J324', #Chronic pansinusitis
'J328', #Other chronic sinusitis
'J329', #Chronic sinusitis, unspecified
'J3501', #Chronic tonsillitis
'J3502', #Chronic adenoiditis
'J3503', #Chronic tonsillitis and adenoiditis
'J352', #Hypertrophy of adenoids
'J353', #Hypertrophy of tonsils with hypertrophy of adenoids
'J358', #Other chronic diseases of tonsils and adenoids
'J359', #Chronic disease of tonsils and adenoids, unspecified
'J36', #Peritonsillar abscess
'J390', #Retropharyngeal and parapharyngeal abscess
'J391', #Other abscess of pharynx
'J40', #Bronchitis, not specified as acute or chronic
'J410', #Simple chronic bronchitis
'J411', #Mucopurulent chronic bronchitis
'J42', #Unspecified chronic bronchitis
'J440', #Chronic obstructive pulmon disease w acute lower resp infct
'J470', #Bronchiectasis with acute lower respiratory infection
'J851', #Abscess of lung with pneumonia
'J852', #Abscess of lung without pneumonia
'J853', #Abscess of mediastinum
'J860', #Pyothorax with fistula
'J9311', #Primary spontaneous pneumothorax
'J9611', #Chronic respiratory failure with hypoxia
'J9691', #Respiratory failure, unspecified with hypoxia
'J9809', #Other diseases of bronchus, not elsewhere classified
'J985', #Diseases of mediastinum, not elsewhere classified
'J9859', #Other diseases of mediastinum, not elsewhere classified
'J989', #Respiratory disorder, unspecified
'R066', #Hiccough
'R0682', #Tachypnea, not elsewhere classified
'R070', #Pain in throat
'R0901', #Asphyxia
'R0982', #Postnasal drip
'C33', #Malignant neoplasm of trachea
'C3400', #Malignant neoplasm of unspecified main bronchus
'C3401', #Malignant neoplasm of right main bronchus
'C3402', #Malignant neoplasm of left main bronchus
'C3410', #Malignant neoplasm of upper lobe, unsp bronchus or lung
'C3411', #Malignant neoplasm of upper lobe, right bronchus or lung
'C3412', #Malignant neoplasm of upper lobe, left bronchus or lung
'C342', #Malignant neoplasm of middle lobe, bronchus or lung
'C3430', #Malignant neoplasm of lower lobe, unsp bronchus or lung
'C3431', #Malignant neoplasm of lower lobe, right bronchus or lung
'C3432', #Malignant neoplasm of lower lobe, left bronchus or lung
'C3480', #Malignant neoplasm of ovrlp sites of unsp bronchus and lung
'C3481', #Malignant neoplasm of ovrlp sites of right bronchus and lung
'C3482', #Malignant neoplasm of ovrlp sites of left bronchus and lung
'C3490', #Malignant neoplasm of unsp part of unsp bronchus or lung
'C3491', #Malignant neoplasm of unsp part of right bronchus or lung
'C3492', #Malignant neoplasm of unsp part of left bronchus or lung
'C384', #Malignant neoplasm of pleura
'C390', #Malignant neoplasm of upper respiratory tract, part unsp
'C399', #Malignant neoplasm of lower respiratory tract, part unsp
'C450', #Mesothelioma of pleura
'C7A090', #Malignant carcinoid tumor of the bronchus and lung
'D021', #Carcinoma in situ of trachea
'D0220', #Carcinoma in situ of unspecified bronchus and lung
'D0221', #Carcinoma in situ of right bronchus and lung
'D0222', #Carcinoma in situ of left bronchus and lung
'D023', #Carcinoma in situ of other parts of respiratory system
'D024', #Carcinoma in situ of respiratory system, unspecified
'I509', #Heart failure, unspecified
'J300', #Vasomotor rhinitis
'J301', #Allergic rhinitis due to pollen
'J302', #Other seasonal allergic rhinitis
'J3081', #Allergic rhinitis due to animal (cat) (dog) hair and dander
'J3089', #Other allergic rhinitis
'J309', #Allergic rhinitis, unspecified
'J310', #Chronic rhinitis
'J342', #Deviated nasal septum
'J3489', #Other specified disorders of nose and nasal sinuses
'J351', #Hypertrophy of tonsils
'J370', #Chronic laryngitis
'J371', #Chronic laryngotracheitis
'J3800', #Paralysis of vocal cords and larynx, unspecified
'J3801', #Paralysis of vocal cords and larynx, unilateral
'J3802', #Paralysis of vocal cords and larynx, bilateral
'J381', #Polyp of vocal cord and larynx
'J382', #Nodules of vocal cords
'J383', #Other diseases of vocal cords
'J384', #Edema of larynx
'J385', #Laryngeal spasm
'J386', #Stenosis of larynx
'J387', #Other diseases of larynx
'J392', #Other diseases of pharynx
'J393', #Upper respiratory tract hypersensitivity reaction, site unsp
'J398', #Other specified diseases of upper respiratory tract
'J399', #Disease of upper respiratory tract, unspecified
'J418', #Mixed simple and mucopurulent chronic bronchitis
'J430', #Unilateral pulmonary emphysema [MacLeod's syndrome]
'J431', #Panlobular emphysema
'J432', #Centrilobular emphysema
'J438', #Other emphysema
'J439', #Emphysema, unspecified
'J441', #Chronic obstructive pulmonary disease w (acute) exacerbation
'J449', #Chronic obstructive pulmonary disease, unspecified
'J4520', #Mild intermittent asthma, uncomplicated
'J4521', #Mild intermittent asthma with (acute) exacerbation
'J4522', #Mild intermittent asthma with status asthmaticus
'J4530', #Mild persistent asthma, uncomplicated
'J4531', #Mild persistent asthma with (acute) exacerbation
'J4532', #Mild persistent asthma with status asthmaticus
'J4540', #Moderate persistent asthma, uncomplicated
'J4541', #Moderate persistent asthma with (acute) exacerbation
'J4542', #Moderate persistent asthma with status asthmaticus
'J4550', #Severe persistent asthma, uncomplicated
'J4551', #Severe persistent asthma with (acute) exacerbation
'J4552', #Severe persistent asthma with status asthmaticus
'J45901', #Unspecified asthma with (acute) exacerbation
'J45902', #Unspecified asthma with status asthmaticus
'J45909', #Unspecified asthma, uncomplicated
'J45990', #Exercise induced bronchospasm
'J45991', #Cough variant asthma
'J45998', #Other asthma
'J471', #Bronchiectasis with (acute) exacerbation
'J479', #Bronchiectasis, uncomplicated
'J60', #Coalworker's pneumoconiosis
'J61', #Pneumoconiosis due to asbestos and other mineral fibers
'J620', #Pneumoconiosis due to talc dust
'J628', #Pneumoconiosis due to other dust containing silica
'J630', #Aluminosis (of lung)
'J631', #Bauxite fibrosis (of lung)
'J632', #Berylliosis
'J633', #Graphite fibrosis (of lung)
'J634', #Siderosis
'J635', #Stannosis
'J636', #Pneumoconiosis due to other specified inorganic dusts
'J64', #Unspecified pneumoconiosis
'J660', #Byssinosis
'J661', #Flax-dressers' disease
'J662', #Cannabinosis
'J668', #Airway disease due to other specific organic dusts
'J670', #Farmer's lung
'J671', #Bagassosis
'J672', #Bird fancier's lung
'J673', #Suberosis
'J674', #Maltworker's lung
'J675', #Mushroom-worker's lung
'J676', #Maple-bark-stripper's lung
'J677', #Air conditioner and humidifier lung
'J678', #Hypersensitivity pneumonitis due to other organic dusts
'J679', #Hypersensitivity pneumonitis due to unspecified organic dust
'J680', #Bronchitis & pneumonitis d/t chemicals, gas, fumes & vapors
'J681', #Pulmonary edema due to chemicals, gases, fumes and vapors
'J682', #Upper resp inflam d/t chemicals, gas, fumes and vapors, NEC
'J683', #Oth ac & subac resp cond d/t chemicals, gas, fumes & vapors
'J684', #Chronic resp cond due to chemicals, gases, fumes and vapors
'J688', #Oth resp cond due to chemicals, gases, fumes and vapors
'J689', #Unsp resp cond due to chemicals, gases, fumes and vapors
'J690', #Pneumonitis due to inhalation of food and vomit
'J691', #Pneumonitis due to inhalation of oils and essences
'J698', #Pneumonitis due to inhalation of other solids and liquids
'J700', #Acute pulmonary manifestations due to radiation
'J701', #Chronic and other pulmonary manifestations due to radiation
'J702', #Acute drug-induced interstitial lung disorders
'J703', #Chronic drug-induced interstitial lung disorders
'J704', #Drug-induced interstitial lung disorders, unspecified
'J705', #Respiratory conditions due to smoke inhalation
'J708', #Respiratory conditions due to oth external agents
'J709', #Respiratory conditions due to unspecified external agent
'J80', #Acute respiratory distress syndrome
'J810', #Acute pulmonary edema
'J811', #Chronic pulmonary edema
'J82', #Pulmonary eosinophilia, not elsewhere classified
'J8401', #Alveolar proteinosis
'J8402', #Pulmonary alveolar microlithiasis
'J8403', #Idiopathic pulmonary hemosiderosis
'J8409', #Other alveolar and parieto-alveolar conditions
'J8410', #Pulmonary fibrosis, unspecified
'J84111', #Idiopathic interstitial pneumonia, not otherwise specified
'J84112', #Idiopathic pulmonary fibrosis
'J84113', #Idiopathic non-specific interstitial pneumonitis
'J84114', #Acute interstitial pneumonitis
'J84115', #Respiratory bronchiolitis interstitial lung disease
'J84116', #Cryptogenic organizing pneumonia
'J84117', #Desquamative interstitial pneumonia
'J8417', #Oth interstit pulmon dis w fibrosis in dis classd elswhr
'J842', #Lymphoid interstitial pneumonia
'J8481', #Lymphangioleiomyomatosis
'J8482', #Adult pulmonary Langerhans cell histiocytosis
'J8489', #Other specified interstitial pulmonary diseases
'J849', #Interstitial pulmonary disease, unspecified
'J850', #Gangrene and necrosis of lung
'J869', #Pyothorax without fistula
'J920', #Pleural plaque with presence of asbestos
'J929', #Pleural plaque without asbestos
'J930', #Spontaneous tension pneumothorax
'J9312', #Secondary spontaneous pneumothorax
'J9381', #Chronic pneumothorax
'J9382', #Other air leak
'J9383', #Other pneumothorax
'J940', #Chylous effusion
'J941', #Fibrothorax
'J942', #Hemothorax
'J948', #Other specified pleural conditions
'J949', #Pleural condition, unspecified
'J9600', #Acute respiratory failure, unsp w hypoxia or hypercapnia
'J9601', #Acute respiratory failure with hypoxia
'J9602', #Acute respiratory failure with hypercapnia
'J9610', #Chronic respiratory failure, unsp w hypoxia or hypercapnia
'J9612', #Chronic respiratory failure with hypercapnia
'J9620', #Acute and chr resp failure, unsp w hypoxia or hypercapnia
'J9621', #Acute and chronic respiratory failure with hypoxia
'J9622', #Acute and chronic respiratory failure with hypercapnia
'J9690', #Respiratory failure, unsp, unsp w hypoxia or hypercapnia
'J9692', #Respiratory failure, unspecified with hypercapnia
'J9801', #Acute bronchospasm
'J9819', #Other pulmonary collapse
'J982', #Interstitial emphysema
'J983', #Compensatory emphysema
'J984', #Other disorders of lung
'J9851', #Mediastinitis
'J986', #Disorders of diaphragm
'J988', #Other specified respiratory disorders
'J99', #Respiratory disorders in diseases classified elsewhere
'N390', #Urinary tract infection, site not specified
'R040', #Epistaxis
'R041', #Hemorrhage from throat
'R048', #Hemorrhage from other sites in respiratory passages
'R0489', #Hemorrhage from other sites in respiratory passages
'R049', #Hemorrhage from respiratory passages, unspecified
'R091', #Pleurisy
'R0981', #Nasal congestion
'D649', #Anemia, unspecified
'D72829', #Elevated white blood cell count, unspecified
'E871', #Hypo-osmolality and hyponatremia
'I517', #Cardiomegaly
'J90', #Pleural effusion, not elsewhere classified
'J918', #Pleural effusion in other conditions classified elsewhere
'J939', #Pneumothorax, unspecified
'J9811', #Atelectasis
'R000', #Tachycardia, unspecified
'R0902', #Hypoxemia
'R220', #Localized swelling, mass and lump, head
'R221', #Localized swelling, mass and lump, neck
'R222', #Localized swelling, mass and lump, trunk
'R59', #Enlarged lymph nodes
'R590', #Localized enlarged lymph nodes
'R591', #Generalized enlarged lymph nodes
'R599', #Enlarged lymph nodes, unspecified
'R911', #Solitary pulmonary nodule
'R918' #Other nonspecific abnormal finding of lung field
))
# Procedure codes:
pr_codes_icd9 <- c()
pr_codes_icd10 <- c()
pr_codes_cpt <- c()
# Medication codes
rx_codes <- c()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.