R/ssd_codes/append.R
In aarmiller/codeBuildr: This package provides functions for loading project codes
## Codes for append
# Description:
desc <- "Appendicitis"
# Diagnosis codes:
# tmp <- read_csv("~/Documents/GitHub/delay_dx/params/ssd_codes/append/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 <- as.character((c('27651', #Dehydration
'33819', #Acute pain NEC
'5362', #Persistent vomiting
'56400', #Constipation NOS
'56409', #Constipation NEC
'5679', #Peritonitis NOS
'56942', #Anal or rectal pain
'6258', #Fem genital symptoms NEC
'6259', #Fem genital symptoms NOS
'7245', #Backache NOS
'7806', #Fever and other physiologic disturbances of temperature regulation
'78060', #Fever NOS
'78079', #Malaise and fatigue NEC
'7830', #Anorexia
'78650', #Chest pain NOS
'78659', #Chest pain NEC
'78701', #Nausea with vomiting
'78702', #Nausea alone
'78703', #Vomiting alone
'7873', #Flatul/eructat/gas pain
'78791', #Diarrhea
'78799', #Digestve syst symptm NEC
'7881', #Dysuria
'78900', #Abdmnal pain unspcf site
'78901', #Abdmnal pain rt upr quad
'78902', #Abdmnal pain lft up quad
'78903', #Abdmnal pain rt lwr quad
'78904', #Abdmnal pain lt lwr quad
'78905', #Abdmnal pain periumbilic
'78906', #Abdmnal pain epigastric
'78907', #Abdmnal pain generalized
'78909', #Abdmnal pain oth spcf st
'78963', #Abdmnal tndr rt lwr quad
'00845', #Int inf clstrdium dfcile
'0088', #Viral enteritis NOS
'0090', #Infectious enteritis NOS
'0340', #Strep sore throat
'0389', #Septicemia NOS
'07999', #Viral infection NOS
'462', #Acute pharyngitis
'486', #Pneumonia, organism NOS
'4871', #Flu w resp manifest NEC
'59080', #Pyelonephritis NOS
'5950', #Acute cystitis
'5990', #Urin tract infection NOS
'7908', #Viremia NOS
'99591', #Sepsis
'07882', #Epidemic vomiting synd
'2892', #Mesenteric lymphadenitis
'53011', #Reflux esophagitis
'53081', #Esophageal reflux
'53500', #Acute gastrtis w/o hmrhg
'53510', #Atrph gastrtis w/o hmrhg
'53550', #Gstr/ddnts NOS w/o hmrhg
'5368', #Stomach function dis NEC
'55090', #Unilat inguinal hernia
'5531', #Umbilical hernia
'55320', #Ventral hernia NOS
'55329', #Ventral hernia NEC
'5533', #Diaphragmatic hernia
'5570', #Ac vasc insuff intestine
'5589', #Noninf gastroenterit NEC
'5601', #Paralytic ileus
'56089', #Intestinal obstruct NEC
'5609', #Intestinal obstruct NOS
'56210', #Dvrtclo colon w/o hmrhg
'56211', #Dvrtcli colon w/o hmrhg
'5641', #Irritable bowel syndrome
'56949', #Rectal & anal dis NEC
'56989', #Intestinal disorders NEC
'5699', #Intestinal disorder NOS
'5718', #Chronic liver dis NEC
'5719', #Chronic liver dis NOS
'5738', #Liver disorders NEC
'5739', #Liver disorder NOS
'57410', #Cholelith w cholecys NEC
'57420', #Cholelithiasis NOS
'5750', #Acute cholecystitis
'57510', #Cholecystitis NOS
'57511', #Chronic cholecystitis
'5758', #Dis of gallbladder NEC
'9974', #Digestive system complications
'2189', #Uterine leiomyoma NOS
'5920', #Calculus of kidney
'5921', #Calculus of ureter
'5932', #Cyst of kidney, acquired
'59382', #Ureteral fistula
'59389', #Renal & ureteral dis NEC
'5939', #Renal & ureteral dis NOS
'6089', #Male genital dis NOS
'6149', #Fem pelv inflam dis NOS
'6169', #Female gen inflam NOS
'6173', #Pelv perit endometriosis
'6179', #Endometriosis NOS
'6200', #Follicular cyst of ovary
'6202', #Ovarian cyst NEC/NOS
'6206', #Broad ligament lacer syn
'6208', #Noninfl dis ova/adnx NEC
'V7241', #Pregnancy test negative
'28860', #Leukocytosis NOS
'56882', #Peritoneal effusion
'59970', #Hematuria NOS
'59972', #Microscopic hematuria
'78820', #Retention urine NOS
'7891', #Hepatomegaly
'7892', #Splenomegaly
'78930', #Abdmnal mass unspcf site
'78933', #Abdmnal mass rt lwr quad
'78939', #Abdmnal mass oth spcf st
'78959', #Ascites NEC
'7934', #Nonsp abn find-gi tract
'7936', #Nonsp abn fnd-abdom area
'7948' #Abn liver function study
)))
icd10_codes <- as.character((c('K5289', #Other specified noninfective gastroenteritis and colitis
'K5900', #Constipation, unspecified
'K5909', #Other constipation
'M5489', #Other dorsalgia
'M549', #Dorsalgia, unspecified
'R0782', #Intercostal pain
'R0789', #Other chest pain
'R079', #Chest pain, unspecified
'R1010', #Upper abdominal pain, unspecified
'R1011', #Right upper quadrant pain
'R1012', #Left upper quadrant pain
'R1013', #Epigastric pain
'R102', #Pelvic and perineal pain
'R1030', #Lower abdominal pain, unspecified
'R1031', #Right lower quadrant pain
'R1032', #Left lower quadrant pain
'R1033', #Periumbilical pain
'R10813', #Right lower quadrant abdominal tenderness
'R1084', #Generalized abdominal pain
'R109', #Unspecified abdominal pain
'R110', #Nausea
'R1110', #Vomiting, unspecified
'R1111', #Vomiting without nausea
'R1112', #Projectile vomiting
'R112', #Nausea with vomiting, unspecified
'R140', #Abdominal distension (gaseous)
'R141', #Gas pain
'R142', #Eructation
'R143', #Flatulence
'R194', #Change in bowel habit
'R197', #Diarrhea, unspecified
'R198', #Oth symptoms and signs involving the dgstv sys and abdomen
'R300', #Dysuria
'R309', #Painful micturition, unspecified
'R509', #Fever, unspecified
'R52', #Pain, unspecified
'R531', #Weakness
'R5381', #Other malaise
'R5383', #Other fatigue
'R630', #Anorexia
'A047', #Enterocolitis due to Clostridium difficile
'A084', #Viral intestinal infection, unspecified
'A088', #Other specified intestinal infections
'A09', #Infectious gastroenteritis and colitis, unspecified
'A419', #Sepsis, unspecified organism
'B349', #Viral infection, unspecified
'B9789', #Oth viral agents as the cause of diseases classd elswhr
'J020', #Streptococcal pharyngitis
'J029', #Acute pharyngitis, unspecified
'J0300', #Acute streptococcal tonsillitis, unspecified
'J111', #Flu due to unidentified influenza virus w oth resp manifest
'J189', #Pneumonia, unspecified organism
'N3000', #Acute cystitis without hematuria
'N3001', #Acute cystitis with hematuria
'N390', #Urinary tract infection, site not specified
'N739', #Female pelvic inflammatory disease, unspecified
'E860', #Dehydration
'I880', #Nonspecific mesenteric lymphadenitis
'K210', #Gastro-esophageal reflux disease with esophagitis
'K219', #Gastro-esophageal reflux disease without esophagitis
'K2900', #Acute gastritis without bleeding
'K2950', #Unspecified chronic gastritis without bleeding
'K2970', #Gastritis, unspecified, without bleeding
'K2990', #Gastroduodenitis, unspecified, without bleeding
'K30', #Functional dyspepsia
'K4090', #Unil inguinal hernia, w/o obst or gangr, not spcf as recur
'K429', #Umbilical hernia without obstruction or gangrene
'K439', #Ventral hernia without obstruction or gangrene
'K449', #Diaphragmatic hernia without obstruction or gangrene
'K529', #Noninfective gastroenteritis and colitis, unspecified
'K550', #Acute vascular disorders of intestine
'K560', #Paralytic ileus
'K5660', #Unspecified intestinal obstruction
'K5669', #Other intestinal obstruction
'K567', #Ileus, unspecified
'K5730', #Dvrtclos of lg int w/o perforation or abscess w/o bleeding
'K5732', #Dvtrcli of lg int w/o perforation or abscess w/o bleeding
'K5790', #Dvrtclos of intest, part unsp, w/o perf or abscess w/o bleed
'K5792', #Dvtrcli of intest, part unsp, w/o perf or abscess w/o bleed
'K580', #Irritable bowel syndrome with diarrhea
'K589', #Irritable bowel syndrome without diarrhea
'K6289', #Other specified diseases of anus and rectum
'K634', #Enteroptosis
'K6389', #Other specified diseases of intestine
'K639', #Disease of intestine, unspecified
'K761', #Chronic passive congestion of liver
'K7689', #Other specified diseases of liver
'K769', #Liver disease, unspecified
'K8010', #Calculus of gallbladder w chronic cholecyst w/o obstruction
'K8018', #Calculus of gallbladder w oth cholecystitis w/o obstruction
'K8020', #Calculus of gallbladder w/o cholecystitis w/o obstruction
'K810', #Acute cholecystitis
'K811', #Chronic cholecystitis
'K819', #Cholecystitis, unspecified
'K828', #Other specified diseases of gallbladder
'D259', #Leiomyoma of uterus, unspecified
'N200', #Calculus of kidney
'N201', #Calculus of ureter
'N281', #Cyst of kidney, acquired
'N2889', #Other specified disorders of kidney and ureter
'N289', #Disorder of kidney and ureter, unspecified
'N809', #Endometriosis, unspecified
'N830', #Follicular cyst of ovary
'N8320', #Unspecified ovarian cysts
'N83201', #Unspecified ovarian cyst, right side
'N8329', #Other ovarian cysts
'N838', #Oth noninflammatory disord of ovary, fallop and broad ligmt
'N9489', #Oth cond assoc w female genital organs and menstrual cycle
'Z3202', #Encounter for pregnancy test, result negative
'D72829', #Elevated white blood cell count, unspecified
'K659', #Peritonitis, unspecified
'N803', #Endometriosis of pelvic peritoneum
'N9983', #Residual ovary syndrome
'R10823', #Right lower quadrant rebound abdominal tenderness
'R160', #Hepatomegaly, not elsewhere classified
'R161', #Splenomegaly, not elsewhere classified
'R188', #Other ascites
'R1900', #Intra-abd and pelvic swelling, mass and lump, unsp site
'R1903', #Right lower quadrant abdominal swelling, mass and lump
'R1909', #Other intra-abdominal and pelvic swelling, mass and lump
'R312', #Other microscopic hematuria
'R319', #Hematuria, unspecified
'R339', #Retention of urine, unspecified
'R933', #Abnormal findings on dx imaging of prt digestive tract
'R935', #Abn findings on dx imaging of abd regions, inc retroperiton
'R945' #Abnormal results of liver function studies
)))
# 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.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## Codes for append
# Description:
desc <- "Appendicitis"
# Diagnosis codes:
# tmp <- read_csv("~/Documents/GitHub/delay_dx/params/ssd_codes/append/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 <- as.character((c('27651', #Dehydration
'33819', #Acute pain NEC
'5362', #Persistent vomiting
'56400', #Constipation NOS
'56409', #Constipation NEC
'5679', #Peritonitis NOS
'56942', #Anal or rectal pain
'6258', #Fem genital symptoms NEC
'6259', #Fem genital symptoms NOS
'7245', #Backache NOS
'7806', #Fever and other physiologic disturbances of temperature regulation
'78060', #Fever NOS
'78079', #Malaise and fatigue NEC
'7830', #Anorexia
'78650', #Chest pain NOS
'78659', #Chest pain NEC
'78701', #Nausea with vomiting
'78702', #Nausea alone
'78703', #Vomiting alone
'7873', #Flatul/eructat/gas pain
'78791', #Diarrhea
'78799', #Digestve syst symptm NEC
'7881', #Dysuria
'78900', #Abdmnal pain unspcf site
'78901', #Abdmnal pain rt upr quad
'78902', #Abdmnal pain lft up quad
'78903', #Abdmnal pain rt lwr quad
'78904', #Abdmnal pain lt lwr quad
'78905', #Abdmnal pain periumbilic
'78906', #Abdmnal pain epigastric
'78907', #Abdmnal pain generalized
'78909', #Abdmnal pain oth spcf st
'78963', #Abdmnal tndr rt lwr quad
'00845', #Int inf clstrdium dfcile
'0088', #Viral enteritis NOS
'0090', #Infectious enteritis NOS
'0340', #Strep sore throat
'0389', #Septicemia NOS
'07999', #Viral infection NOS
'462', #Acute pharyngitis
'486', #Pneumonia, organism NOS
'4871', #Flu w resp manifest NEC
'59080', #Pyelonephritis NOS
'5950', #Acute cystitis
'5990', #Urin tract infection NOS
'7908', #Viremia NOS
'99591', #Sepsis
'07882', #Epidemic vomiting synd
'2892', #Mesenteric lymphadenitis
'53011', #Reflux esophagitis
'53081', #Esophageal reflux
'53500', #Acute gastrtis w/o hmrhg
'53510', #Atrph gastrtis w/o hmrhg
'53550', #Gstr/ddnts NOS w/o hmrhg
'5368', #Stomach function dis NEC
'55090', #Unilat inguinal hernia
'5531', #Umbilical hernia
'55320', #Ventral hernia NOS
'55329', #Ventral hernia NEC
'5533', #Diaphragmatic hernia
'5570', #Ac vasc insuff intestine
'5589', #Noninf gastroenterit NEC
'5601', #Paralytic ileus
'56089', #Intestinal obstruct NEC
'5609', #Intestinal obstruct NOS
'56210', #Dvrtclo colon w/o hmrhg
'56211', #Dvrtcli colon w/o hmrhg
'5641', #Irritable bowel syndrome
'56949', #Rectal & anal dis NEC
'56989', #Intestinal disorders NEC
'5699', #Intestinal disorder NOS
'5718', #Chronic liver dis NEC
'5719', #Chronic liver dis NOS
'5738', #Liver disorders NEC
'5739', #Liver disorder NOS
'57410', #Cholelith w cholecys NEC
'57420', #Cholelithiasis NOS
'5750', #Acute cholecystitis
'57510', #Cholecystitis NOS
'57511', #Chronic cholecystitis
'5758', #Dis of gallbladder NEC
'9974', #Digestive system complications
'2189', #Uterine leiomyoma NOS
'5920', #Calculus of kidney
'5921', #Calculus of ureter
'5932', #Cyst of kidney, acquired
'59382', #Ureteral fistula
'59389', #Renal & ureteral dis NEC
'5939', #Renal & ureteral dis NOS
'6089', #Male genital dis NOS
'6149', #Fem pelv inflam dis NOS
'6169', #Female gen inflam NOS
'6173', #Pelv perit endometriosis
'6179', #Endometriosis NOS
'6200', #Follicular cyst of ovary
'6202', #Ovarian cyst NEC/NOS
'6206', #Broad ligament lacer syn
'6208', #Noninfl dis ova/adnx NEC
'V7241', #Pregnancy test negative
'28860', #Leukocytosis NOS
'56882', #Peritoneal effusion
'59970', #Hematuria NOS
'59972', #Microscopic hematuria
'78820', #Retention urine NOS
'7891', #Hepatomegaly
'7892', #Splenomegaly
'78930', #Abdmnal mass unspcf site
'78933', #Abdmnal mass rt lwr quad
'78939', #Abdmnal mass oth spcf st
'78959', #Ascites NEC
'7934', #Nonsp abn find-gi tract
'7936', #Nonsp abn fnd-abdom area
'7948' #Abn liver function study
)))
icd10_codes <- as.character((c('K5289', #Other specified noninfective gastroenteritis and colitis
'K5900', #Constipation, unspecified
'K5909', #Other constipation
'M5489', #Other dorsalgia
'M549', #Dorsalgia, unspecified
'R0782', #Intercostal pain
'R0789', #Other chest pain
'R079', #Chest pain, unspecified
'R1010', #Upper abdominal pain, unspecified
'R1011', #Right upper quadrant pain
'R1012', #Left upper quadrant pain
'R1013', #Epigastric pain
'R102', #Pelvic and perineal pain
'R1030', #Lower abdominal pain, unspecified
'R1031', #Right lower quadrant pain
'R1032', #Left lower quadrant pain
'R1033', #Periumbilical pain
'R10813', #Right lower quadrant abdominal tenderness
'R1084', #Generalized abdominal pain
'R109', #Unspecified abdominal pain
'R110', #Nausea
'R1110', #Vomiting, unspecified
'R1111', #Vomiting without nausea
'R1112', #Projectile vomiting
'R112', #Nausea with vomiting, unspecified
'R140', #Abdominal distension (gaseous)
'R141', #Gas pain
'R142', #Eructation
'R143', #Flatulence
'R194', #Change in bowel habit
'R197', #Diarrhea, unspecified
'R198', #Oth symptoms and signs involving the dgstv sys and abdomen
'R300', #Dysuria
'R309', #Painful micturition, unspecified
'R509', #Fever, unspecified
'R52', #Pain, unspecified
'R531', #Weakness
'R5381', #Other malaise
'R5383', #Other fatigue
'R630', #Anorexia
'A047', #Enterocolitis due to Clostridium difficile
'A084', #Viral intestinal infection, unspecified
'A088', #Other specified intestinal infections
'A09', #Infectious gastroenteritis and colitis, unspecified
'A419', #Sepsis, unspecified organism
'B349', #Viral infection, unspecified
'B9789', #Oth viral agents as the cause of diseases classd elswhr
'J020', #Streptococcal pharyngitis
'J029', #Acute pharyngitis, unspecified
'J0300', #Acute streptococcal tonsillitis, unspecified
'J111', #Flu due to unidentified influenza virus w oth resp manifest
'J189', #Pneumonia, unspecified organism
'N3000', #Acute cystitis without hematuria
'N3001', #Acute cystitis with hematuria
'N390', #Urinary tract infection, site not specified
'N739', #Female pelvic inflammatory disease, unspecified
'E860', #Dehydration
'I880', #Nonspecific mesenteric lymphadenitis
'K210', #Gastro-esophageal reflux disease with esophagitis
'K219', #Gastro-esophageal reflux disease without esophagitis
'K2900', #Acute gastritis without bleeding
'K2950', #Unspecified chronic gastritis without bleeding
'K2970', #Gastritis, unspecified, without bleeding
'K2990', #Gastroduodenitis, unspecified, without bleeding
'K30', #Functional dyspepsia
'K4090', #Unil inguinal hernia, w/o obst or gangr, not spcf as recur
'K429', #Umbilical hernia without obstruction or gangrene
'K439', #Ventral hernia without obstruction or gangrene
'K449', #Diaphragmatic hernia without obstruction or gangrene
'K529', #Noninfective gastroenteritis and colitis, unspecified
'K550', #Acute vascular disorders of intestine
'K560', #Paralytic ileus
'K5660', #Unspecified intestinal obstruction
'K5669', #Other intestinal obstruction
'K567', #Ileus, unspecified
'K5730', #Dvrtclos of lg int w/o perforation or abscess w/o bleeding
'K5732', #Dvtrcli of lg int w/o perforation or abscess w/o bleeding
'K5790', #Dvrtclos of intest, part unsp, w/o perf or abscess w/o bleed
'K5792', #Dvtrcli of intest, part unsp, w/o perf or abscess w/o bleed
'K580', #Irritable bowel syndrome with diarrhea
'K589', #Irritable bowel syndrome without diarrhea
'K6289', #Other specified diseases of anus and rectum
'K634', #Enteroptosis
'K6389', #Other specified diseases of intestine
'K639', #Disease of intestine, unspecified
'K761', #Chronic passive congestion of liver
'K7689', #Other specified diseases of liver
'K769', #Liver disease, unspecified
'K8010', #Calculus of gallbladder w chronic cholecyst w/o obstruction
'K8018', #Calculus of gallbladder w oth cholecystitis w/o obstruction
'K8020', #Calculus of gallbladder w/o cholecystitis w/o obstruction
'K810', #Acute cholecystitis
'K811', #Chronic cholecystitis
'K819', #Cholecystitis, unspecified
'K828', #Other specified diseases of gallbladder
'D259', #Leiomyoma of uterus, unspecified
'N200', #Calculus of kidney
'N201', #Calculus of ureter
'N281', #Cyst of kidney, acquired
'N2889', #Other specified disorders of kidney and ureter
'N289', #Disorder of kidney and ureter, unspecified
'N809', #Endometriosis, unspecified
'N830', #Follicular cyst of ovary
'N8320', #Unspecified ovarian cysts
'N83201', #Unspecified ovarian cyst, right side
'N8329', #Other ovarian cysts
'N838', #Oth noninflammatory disord of ovary, fallop and broad ligmt
'N9489', #Oth cond assoc w female genital organs and menstrual cycle
'Z3202', #Encounter for pregnancy test, result negative
'D72829', #Elevated white blood cell count, unspecified
'K659', #Peritonitis, unspecified
'N803', #Endometriosis of pelvic peritoneum
'N9983', #Residual ovary syndrome
'R10823', #Right lower quadrant rebound abdominal tenderness
'R160', #Hepatomegaly, not elsewhere classified
'R161', #Splenomegaly, not elsewhere classified
'R188', #Other ascites
'R1900', #Intra-abd and pelvic swelling, mass and lump, unsp site
'R1903', #Right lower quadrant abdominal swelling, mass and lump
'R1909', #Other intra-abdominal and pelvic swelling, mass and lump
'R312', #Other microscopic hematuria
'R319', #Hematuria, unspecified
'R339', #Retention of urine, unspecified
'R933', #Abnormal findings on dx imaging of prt digestive tract
'R935', #Abn findings on dx imaging of abd regions, inc retroperiton
'R945' #Abnormal results of liver function studies
)))
# Procedure codes:
pr_codes_icd9 <- c()
pr_codes_icd10 <- c()
pr_codes_cpt <- c()
# Medication codes
rx_codes <- c()
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