R/Lexicons.R
In sebastiz/EndoMineR_devlop: Functions to mine endoscopic and associated pathology datasets
########## Lexicons ##########
#' Extract pathology type
#'
#' This standardizes terms to describe the pathology tissue type being exmained
#' @keywords Pathology type
#' @export
#' @examples #No examples as just returns a list
HistolType <- function() {
#First standardise the terms
tissue<-list("Resection" = "Resection",
"bx|biopsies"="Biopsy",
"(endoscopic mucosal resection)|(endoscopic mucosectomy)"="EMR",
"endoscopic submucosal (dissection|resection)"="ESD",
"nodul"="nodul",
"polyp "="polyp")
#To get the list as a list of values only in a regex use
#paste0(unlist(HistolType(),use.names=F),collapse="|")
return(tissue)
}
#' Use list of standard locations
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationList<-function(){
All<-append(LocationListLower(), LocationListUpper())
All<-append(All,LocationListUniversal())
#To get the list as a list of values only in a regex use
#paste0(unlist(All,use.names=F),collapse="|")
return(All)
}
#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListUpper<-function(){
upper<-list("duodenum|d2|D2|duodenal" = "Duodenum",
"gastric|stomach"="Stomach",
"antrum|antral"="Antrum",
"ogj|goj|gastrooesophageal"="GOJ",
"fundal|fundus"="stomach",
"pyloric"="Pylorus",
"gastric cardia"="Cardia",
"oesophagus|oesophageal"="Oesophagus")
#To get the list as a list of values only in a regex use
#paste0(unlist(upper,use.names=F),collapse="|")
return(upper)
}
#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListUniversal<-function(){
universal<-list("Anastomosis" = "Ascending ")
return(universal)
#If need to use then use
#paste0(unlist(universal,use.names=F),collapse="|")
}
#' Use list of standard locations for lower GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListLower<-function(){
lower<-list("asce |ascending|(ascend[^a-z])|( colon r )|(r colon)|(asc )|(right colon)" = "Ascending ",
"descending|(descen[^a-z])|(desc[^a-z])|(des[^a-z])|(colon l)|(l colon)|(left colon)" = "Descending ",
"sigmoid|(sigm[^a-z])|sigmo "= "Sigmoid ",
"rectal|rectum|(rectum[a-z])|rect "="Rectum ",
"transverse|(transv[^a-z])|tranv |trans "="Transverse ",
"caecum|caecal"="Caecum ",
"splenic"="Splenic ",
"(ileum )|( ileal )"="Ileum ",
"rectosigmoid"="Rectosigmoid ",
"(ileocaecal\\s*)|icv|(ileo-caecum)"="Ileocaecal",
"(hep[^a-z])|([Hh]epatic)"="Hepatic ",
"colonic|colon |(col[^a-z])"="Colon ",
"term |terminal"="Terminal",
"TI "="Terminal",
"caec"="Caecum ",
"[Ss]ig "="Sigmoid ",
"ileo\\s*-\\s*anal|ileo\\s*anal "="Ileoanal ",
"(pre\\s*pouch)|(pre-[Pp]ouch)"="PrePouch",
"pouch"="Pouch",
"term |terminal"="Terminal")
#To get the list as a list of values only in a regex use
#paste0(unlist(lower,use.names=F),collapse="|")
return(lower)
}
#' Use list of catheters used in radiofrequency ablation
#'
#' The takes a list of catheters used in radiofrequency ablation
#'
#' @keywords RFA
#' @export
#' @examples #No example needed
RFACath<-function(){
tofind <-
paste(
c(
"90","360","HALO60"," 60","TTS",
"[Cc]hannel","APC"
),
collapse = "|"
)
return(tofind)
}
#' Event list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#' @export
#'
EventList<-function(){
Event <- list("radiofrequency ablation" = "RFA",
"(argon plasma coagulation)|apc" = "APC",
"halo| rfa" = "RFA",
"dilatation|dilated"="dilat",
" emr"="EMR",
"(endoscopic mucosal resection)|(endoscopic mucosectomy)"="EMR",
"clip"="clip",
"grasp"="grasp",
"iodine"="iodine",
"acetic"="acetic",
"NAC"="NAC",
"Brushings"="brushings"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(Event,use.names=F),collapse="|")
return(Event)
}
#' Temporal list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Temporal extraction
#' @examples # unique(unlist(Temporal(), use.names = FALSE))
#' @export
#'
TemporalList<-function(){
Temporal <- list("Past" = "Past",
"Present" = "Present",
"Future" = "Future"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(Temporal,use.names=F),collapse="|")
return(Temporal)
}
#' Biopsy index list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
BiopsyIndex<-function(){
BiopsyIndexList <- list("ileum:biopsy"="C11",
"ileocaecal:biopsy"="C10",
"caecum:biopsy"="C9",
"ascending:biopsy"="C8",
"hepatic:biopsy"="C7",
"transverse:biopsy"="C6",
"splenic:biopsy"="C5",
"descending:biopsy"="C4",
"sigmoid:biopsy"="C3",
"rectosigmoid:biopsy"="C2",
"rectum:biopsy"="C1",
"ileoanal:biopsy"="S1",
"prepouch:biopsy"="S2",
"pouch:biopsy"="S3",
"duodenum:biopsy"="O5",
"antrum:biopsy"="O4",
"stomach:biopsy"="O3",
"goj:biopsy"="O1",
"cardia:biopsy"="O2",
"oesophagus:biopsy"="O1",
"colon:biopsy"="colon",
"oesophagus:emr"="O1",
"goj:emr"="O1",
"stomach:emr"="O3",
"duodenum:emr"="O5")
#To get the list as a list of values only in a regex use
#paste0(unlist(BiopsyIndex,use.names=F),collapse="|")
return(BiopsyIndexList)
}
#' GISymptoms
#'
#' This function returns all the Common GI symptoms. They are simply listed as is without grouping
#' or mapping. They have been derived from a manual list with synonyms derived from the UMLS Methatharus
#' using the browser.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
GISymptomsList<-function(){
Symptoms <- list("abdomen pain"="abdomen pain",
"abdomen; pain, epigastric"="abdomen; pain, epigastric",
"abdominal pain"="abdominal pain",
"abdominal pain epigastric"="abdominal pain epigastric",
"abdominal pain in the central upper belly"="abdominal pain in the central upper belly",
"abdominal pain nos"="abdominal pain nos",
"abdominal pain, epigastric"="abdominal pain, epigastric",
"abdominal pain, unspecified site"="abdominal pain, unspecified site",
"abdominal pains"="abdominal pains",
"abdominal wind"="abdominal wind",
"abdominal; pain"="abdominal; pain",
"abdominalgia"="abdominalgia",
"acid reflux"="acid reflux",
"acidity"="acidity",
"alteration in bowel elimination: incontinence"="alteration in bowel elimination: incontinence",
"altered blood in stool"="altered blood in stool",
"altered blood passed per rectum"="altered blood passed per rectum",
"anal incontinence"="anal incontinence",
"anal pain"="anal pain",
"anus pain"="anus pain",
"anus pains"="anus pains",
"anus; pain"="anus; pain",
"ap - abdominal pain"="ap - abdominal pain",
"bad breath"="bad breath",
"bad breath - halitosis"="bad breath - halitosis",
"bad breath halitosis"="bad breath halitosis",
"bad or foul breath"="bad or foul breath",
"bad/foul;breath"="bad/foul;breath",
"being sick"="being sick",
"belch"="belch",
"belching"="belching",
"belching symptom"="belching symptom",
"belching symptoms"="belching symptoms",
"belching, burping"="belching, burping",
"belchings"="belchings",
"bellyache"="bellyache",
"black stool"="black stool",
"black stools"="black stools",
"black, tarry stool"="black, tarry stool",
"bleeding per rectum"="bleeding per rectum",
"bleeding rectal"="bleeding rectal",
"bleeding rectum"="bleeding rectum",
"bleeding-rectal"="bleeding-rectal",
"bleeding;anal"="bleeding;anal",
"bleeding;rectal"="bleeding;rectal",
"blood per rectum"="blood per rectum",
"blood; vomiting"="blood; vomiting",
"bowel incontinena"="bowel incontinena",
"bowel incontinence"="bowel incontinence",
"bowel incontinent"="bowel incontinent",
"bowel loose movements"="bowel loose movements",
"bowels loose movement"="bowels loose movement",
"bowels: incontinent"="bowels: incontinent",
"brash"="brash",
"breath odor"="breath odor",
"breath odor abnormal"="breath odor abnormal",
"breath odor nos"="breath odor nos",
"breath odors"="breath odors",
"breath odour"="breath odour",
"breath odour nos"="breath odour nos",
"breath smells offensive"="breath smells offensive",
"breath smells unpleasant"="breath smells unpleasant",
"breath; foul"="breath; foul",
"burning reflux"="burning reflux",
"burp"="burp",
"burping"="burping",
"burps"="burps",
"c/o - cough"="c/o - cough",
"can't get food down"="can't get food down",
"cannot get food down"="cannot get food down",
"chest pain"="chest pain",
"chest pain nos"="chest pain nos",
"chest pain or discomfort"="chest pain or discomfort",
"chest pain or discomfort reported as pain"="chest pain or discomfort reported as pain",
"chest pain, nos"="chest pain, nos",
"chest pain, pleuritic"="chest pain, pleuritic",
"chest pain, unspecified"="chest pain, unspecified",
"chest pains"="chest pains",
"chest; pain"="chest; pain",
"clear throat"="clear throat",
"clearing throat"="clearing throat",
"clearings throat"="clearings throat",
"complaining of cough"="complaining of cough",
"cough"="cough",
"cough symptom"="cough symptom",
"cough symptoms"="cough symptoms",
"cough, nos"="cough, nos",
"coughing"="coughing",
"coughing - function"="coughing - function",
"coughing symptom"="coughing symptom",
"coughs"="coughs",
"d - diarrhea"="d - diarrhea",
"d - diarrhoea"="d - diarrhoea",
"dark stools"="dark stools",
"deglutition disorder"="deglutition disorder",
"deglutition disorders"="deglutition disorders",
"diarrhea"="diarrhea",
"diarrhea nos"="diarrhea nos",
"diarrhea running"="diarrhea running",
"diarrhea symptom"="diarrhea symptom",
"diarrhea symptoms"="diarrhea symptoms",
"diarrhea, nos"="diarrhea, nos",
"diarrhea, unspecified"="diarrhea, unspecified",
"diarrheas"="diarrheas",
"diarrhoea"="diarrhoea",
"diarrhoea nos"="diarrhoea nos",
"diarrhoea symptom"="diarrhoea symptom",
"diarrhoea symptoms"="diarrhoea symptoms",
"difficult swallowing"="difficult swallowing",
"difficult; swallowing"="difficult; swallowing",
"difficulties swallowing"="difficulties swallowing",
"difficulty in swallowing"="difficulty in swallowing",
"difficulty in swallowing nos"="difficulty in swallowing nos",
"difficulty swallowing"="difficulty swallowing",
"difficulty;swallowing"="difficulty;swallowing",
"disorder deglutition"="disorder deglutition",
"disorders, deglutition"="disorders, deglutition",
"dry heave"="dry heave",
"dry heaves"="dry heaves",
"dysphagia"="dysphagia",
"dysphagia, nos"="dysphagia, nos",
"dysphagia, unspecified"="dysphagia, unspecified",
"dysphagias"="dysphagias",
"emesis"="emesis",
"emesis bloody"="emesis bloody",
"epigastralgia"="epigastralgia",
"epigastric abdominal pain"="epigastric abdominal pain",
"epigastric ache"="epigastric ache",
"epigastric pain"="epigastric pain",
"epigastric; pain"="epigastric; pain",
"epigastrium pain"="epigastrium pain",
"eructate"="eructate",
"eructation"="eructation",
"eructation, function"="eructation, function",
"eructations"="eructations",
"excessive farting"="excessive farting",
"excessive passing of gas"="excessive passing of gas",
"faecal incontinence"="faecal incontinence",
"fart"="fart",
"farting"="farting",
"farts"="farts",
"faucitis"="faucitis",
"fecal incontinence"="fecal incontinence",
"fecal incontinence nos"="fecal incontinence nos",
"feces incontinence"="feces incontinence",
"feces incontinence of"="feces incontinence of",
"feces; incontinence"="feces; incontinence",
"fetor ex ore"="fetor ex ore",
"fetor oris"="fetor oris",
"finding of vomiting"="finding of vomiting",
"flatulence"="flatulence",
"flatulence symptom"="flatulence symptom",
"flatus"="flatus",
"flatus, function"="flatus, function",
"foetor ex ore"="foetor ex ore",
"foul breath"="foul breath",
"foul; breath"="foul; breath",
"frequent stools"="frequent stools",
"full of wind"="full of wind",
"gas passing"="gas passing",
"gas raising"="gas raising",
"gaseous regurgitation"="gaseous regurgitation",
"gaseousness"="gaseousness",
"gastric contents; regurgitation"="gastric contents; regurgitation",
"gastrointestinal disorder hematemesis"="gastrointestinal disorder hematemesis",
"gut pain"="gut pain",
"haematemesis"="haematemesis",
"haematemesis/vomiting blood"="haematemesis/vomiting blood",
"haemorrhage of rectum"="haemorrhage of rectum",
"haemorrhage rectal"="haemorrhage rectal",
"haemorrhage rectum"="haemorrhage rectum",
"halitoses"="halitoses",
"halitosis"="halitosis",
"heart burn"="heart burn",
"heartburn"="heartburn",
"heartburn symptom"="heartburn symptom",
"heaving"="heaving",
"hematemeses"="hematemeses",
"hematemesis"="hematemesis",
"hematemesis was observed"="hematemesis was observed",
"hematemesis/vomiting blood"="hematemesis/vomiting blood",
"hemorrhage of rectum"="hemorrhage of rectum",
"hemorrhage rectal"="hemorrhage rectal",
"hemorrhage rectum"="hemorrhage rectum",
"hemorrhage; rectum"="hemorrhage; rectum",
"incontinence (fecal)"="incontinence (fecal)",
"incontinence bowel"="incontinence bowel",
"incontinence faecal"="incontinence faecal",
"incontinence fecal"="incontinence fecal",
"incontinence of bowel"="incontinence of bowel",
"incontinence of faeces"="incontinence of faeces",
"incontinence of feces"="incontinence of feces",
"incontinence of feces (finding)"="incontinence of feces (finding)",
"incontinence of stool"="incontinence of stool",
"incontinence stool"="incontinence stool",
"incontinence, bowel"="incontinence, bowel",
"incontinence, fecal"="incontinence, fecal",
"incontinence; fecal"="incontinence; fecal",
"incontinence;bowel"="incontinence;bowel",
"incontinence;faeces"="incontinence;faeces",
"incontinent bowel"="incontinent bowel",
"incontinent of bowels"="incontinent of bowels",
"incontinent of faeces"="incontinent of faeces",
"incontinent of feces"="incontinent of feces",
"incontinent of stool"="incontinent of stool",
"intestinal gas excretion"="intestinal gas excretion",
"involuntary stool"="involuntary stool",
"loose bowel motion"="loose bowel motion",
"loose bowel motions"="loose bowel motions",
"loose bowel movement"="loose bowel movement",
"loose stools"="loose stools",
"loss of bowel control"="loss of bowel control",
"melaena"="melaena",
"melena"="melena",
"melena (disorder)"="melena (disorder)",
"melena/black tarry stools"="melena/black tarry stools",
"melenas"="melenas",
"nausea"="nausea",
"nonspecific chest pain"="nonspecific chest pain",
"observation of cough"="observation of cough",
"observation of diarrhea"="observation of diarrhea",
"observation of diarrhoea"="observation of diarrhoea",
"observation of vomiting"="observation of vomiting",
"odor breath"="odor breath",
"odor of breath"="odor of breath",
"odor of breath fetor oris"="odor of breath fetor oris",
"odour breath"="odour breath",
"of bowel incontinence"="of bowel incontinence",
"ozostomia"="ozostomia",
"pain abdominal"="pain abdominal",
"pain anal"="pain anal",
"pain anus"="pain anus",
"pain chest"="pain chest",
"pain epigastric"="pain epigastric",
"pain in chest"="pain in chest",
"pain in stomach"="pain in stomach",
"pain in the pharynx"="pain in the pharynx",
"pain in throat"="pain in throat",
"pain pharynx"="pain pharynx",
"pain pleural"="pain pleural",
"pain thoracic"="pain thoracic",
"pain throat"="pain throat",
"pain, abdominal"="pain, abdominal",
"pain, chest"="pain, chest",
"pain, pleuritic"="pain, pleuritic",
"pain; abdominal"="pain; abdominal",
"pain; anus"="pain; anus",
"pain; chest"="pain; chest",
"pain; epigastric"="pain; epigastric",
"pain; pharynx"="pain; pharynx",
"pain; pleura"="pain; pleura",
"pain; thorax"="pain; thorax",
"pain; throat"="pain; throat",
"pain;abdominal"="pain;abdominal",
"pain;anal"="pain;anal",
"pain;chest"="pain;chest",
"pain;epigastric"="pain;epigastric",
"pain;throat"="pain;throat",
"pains, abdominal"="pains, abdominal",
"pains, chest"="pains, chest",
"pass wind"="pass wind",
"passage of gas by anus"="passage of gas by anus",
"passing flatus"="passing flatus",
"passing wind"="passing wind",
"pharyngeal pain"="pharyngeal pain",
"pharynx discomfort"="pharynx discomfort",
"pharynx; pain"="pharynx; pain",
"pleura; pain"="pleura; pain",
"pleural pain"="pleural pain",
"pleuralgia"="pleuralgia",
"pleuritic chest pain"="pleuritic chest pain",
"pleuritic pain"="pleuritic pain",
"pleurodynia"="pleurodynia",
"pleurodynia nos"="pleurodynia nos",
"poor swallowing"="poor swallowing",
"pr - bleeding per rectum"="pr - bleeding per rectum",
"pr - blood per rectum"="pr - blood per rectum",
"prb - rectal bleeding"="prb - rectal bleeding",
"proctorrhagia"="proctorrhagia",
"pyroses"="pyroses",
"pyrosis"="pyrosis",
"rb - rectal bleeding"="rb - rectal bleeding",
"rectal bleed"="rectal bleed",
"rectal bleeding"="rectal bleeding",
"rectal blood loss"="rectal blood loss",
"rectal discharge incontinent of stool"="rectal discharge incontinent of stool",
"rectal discharge incontinent of stool (physical finding)"="rectal discharge incontinent of stool (physical finding)",
"rectal haemorrhage"="rectal haemorrhage",
"rectal hemorrhage"="rectal hemorrhage",
"rectal pain"="rectal pain",
"rectorrhagia"="rectorrhagia",
"rectum bleeding"="rectum bleeding",
"rectum hemorrhage"="rectum hemorrhage",
"rectum; hemorrhage"="rectum; hemorrhage",
"reflux"="reflux",
"reflux, nos"="reflux, nos",
"refluxed"="refluxed",
"refluxing"="refluxing",
"refluxs"="refluxs",
"regurgitation"="regurgitation",
"regurgitation of gastric content"="regurgitation of gastric content",
"regurgitation; gastric contents"="regurgitation; gastric contents",
"reported chest pain"="reported chest pain",
"retch"="retch",
"retching"="retching",
"rndx bowel incontinence"="rndx bowel incontinence",
"rndx bowel incontinence (diagnosis)"="rndx bowel incontinence (diagnosis)",
"rndx diarrhea"="rndx diarrhea",
"ructus"="ructus",
"runs"="runs",
"smelly breath"="smelly breath",
"sore symptom throat"="sore symptom throat",
"sore symptoms throat"="sore symptoms throat",
"sore throat"="sore throat",
"sore throat nos"="sore throat nos",
"sore throat symptom"="sore throat symptom",
"sore throat, nos"="sore throat, nos",
"sore throat;"="sore throat;",
"sore throats"="sore throats",
"sorethroat"="sorethroat",
"spitting up"="spitting up",
"stomach pain"="stomach pain",
"stomatodysodia"="stomatodysodia",
"stool black"="stool black",
"stool color black"="stool color black",
"stool incontinence"="stool incontinence",
"stool soiling"="stool soiling",
"stool tarry"="stool tarry",
"stool(s);black"="stool(s);black",
"stool(s);tarry"="stool(s);tarry",
"stools loose"="stools loose",
"stools.incontinent"="stools.incontinent",
"swallowing difficult"="swallowing difficult",
"swallowing difficulties"="swallowing difficulties",
"swallowing difficulty"="swallowing difficulty",
"swallowing disorder"="swallowing disorder",
"swallowing disorders"="swallowing disorders",
"swallowing; difficult"="swallowing; difficult",
"symptoms diarrhea"="symptoms diarrhea",
"symptoms vomiting"="symptoms vomiting",
"tarry stool"="tarry stool",
"tarry stools"="tarry stools",
"the runs"="the runs",
"the trots"="the trots",
"thoracalgia"="thoracalgia",
"thoracic pain"="thoracic pain",
"thoracodynia"="thoracodynia",
"thorax pain"="thorax pain",
"thorax painful"="thorax painful",
"thorax; pain"="thorax; pain",
"throat clearing"="throat clearing",
"throat discomfort"="throat discomfort",
"throat pain"="throat pain",
"throat sore"="throat sore",
"throat soreness"="throat soreness",
"throat, sore"="throat, sore",
"throw up"="throw up",
"throwing up"="throwing up",
"unable to restrain bowel movement"="unable to restrain bowel movement",
"unable to restrain bowel movement (symptom)"="unable to restrain bowel movement (symptom)",
"unspecified abdominal pain"="unspecified abdominal pain",
"unspecified chest pain"="unspecified chest pain",
"vomit"="vomit",
"vomited"="vomited",
"vomiting"="vomiting",
"vomiting blood"="vomiting blood",
"vomiting disorder"="vomiting disorder",
"vomiting nos"="vomiting nos",
"vomiting of blood"="vomiting of blood",
"vomiting out blood"="vomiting out blood",
"vomiting symptom"="vomiting symptom",
"vomiting symptoms"="vomiting symptoms",
"vomiting was observed"="vomiting was observed",
"vomiting, nos"="vomiting, nos",
"vomiting, unspecified"="vomiting, unspecified",
"vomiting; blood"="vomiting; blood",
"vomiting;blood"="vomiting;blood",
"vomits"="vomits",
"vomitting blood"="vomitting blood",
"vomiturition"="vomiturition",
"waterbrash"="waterbrash",
"waterbrash symptom"="waterbrash symptom",
"watery stool"="watery stool",
"watery stools"="watery stools",
"wind"="wind",
"wind - flatus"="wind - flatus",
"wind symptom"="wind symptom",
"winding"="winding",
"c/o - nausea"="c/o - nausea",
"feel sick"="feel sick",
"feeling bilious"="feeling bilious",
"feeling queasy"="feeling queasy",
"feeling sick"="feeling sick",
"nausea nos"="nausea nos",
"nausea symptom"="nausea symptom",
"nausea symptoms"="nausea symptoms",
"nausea"="nausea",
"nauseas"="nauseas",
"nauseated"="nauseated",
"nauseating"="nauseating",
"nauseous"="nauseous",
"observation of nausea"="observation of nausea",
"queasy"="queasy",
"rndx nausea"="rndx nausea",
"sick feeling"="sick feeling",
"symptom nausea"="symptom nausea",
"symptoms nausea"="symptoms nausea")
#To get the list as a list of values only in a regex use
#paste0(unlist(WordsToNumbers,use.names=F),collapse="|")
return(Symptoms)
}
#' Words to numbers
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
WordsToNumbers<-function(){
NumberConv <- list("[Oo]ne "="1",
"[Ss]ingle "="1",
"[Tt]wo "="2",
"[Tt]hree "= "3",
"[Ff]our "= "4",
"[Ff]ive "= "5",
"[Ss]ix "="6",
"[Ss]even "= "7",
"[Ee]ight "= "8",
"[Nn]ine "= "9",
"[Tt]en "= "10",
"[Ee]leven "= "11",
"[Tt]welve "= "12",
"[Tt]hirteen "= "13",
"[Ff]ourteen "= "14",
"[Ff]ifteen "= "15",
"[Ss]ixteen "= "16"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(WordsToNumbers,use.names=F),collapse="|")
return(NumberConv)
}
#' #' Validate columns
#' #'
#' #' This is an attempt to determine whether functions are accurate in their extraction
#' #' It is part of a validation pipeline to make sure the data outputted from a function
#' #' is accurate
#' #' It essentially is a comparison of actual vs expected output. The intention is to
#' #' then quantify the output of a function for a specific dataset.
#' #'
#' #' @param dataframe dataframe
#' #' @param testcolumn The dataframe column to run the function on
#' #' @param pHospitalNum the hospital number of the patient so can be identified
#' #' @importFrom openxlsx write.xlsx
#' #' @keywords validation
#' #' @export
#' #' @examples #ValidationR(HistolBxSize,myHistol$histology_report)
#'
#' sensAndSpecificMultip<-function(FUN =funct,dataframe,Column,pHospitalNum){
#' dd<-funct(dataframe,Column)
#' #Now just want the columns that have changed or have been added from the original as well
#' #as well as the columns that sound very similar to the original
#' #ie need to get the original column called Column as well as the new column created (can
#' # I get this from the diff between two data frames? dd-dataframe??)
#' #This gets the new column name from the dataframe that the function has run
#' MyNegsFiltered$FindingsAlgoNegs<-as.list(strsplit(MyNegsFiltered$FindingsAlgoNegs, ";"))
#' MyNegsFiltered$negativeresults<-as.list(strsplit(MyNegsFiltered$negativeresults, ";"))
#' #pHospitalNum
#' ff<-setdiff(union(names(dataframe), names(dd)), names(dataframe))
#' ff<-data.frame(dd[,Column],dd[,ff],dd[,pHospitalNum])
#' write.xlsx(ff, paste0(getwd(),"/MyValidation.xlsx"))
#' }
#' #dataframe[,pHospitalNum],
#' #' Validate columns
#' #'
#' #' This is an attempt to determine whether functions are accurate in their extraction
#' #' It is part of a validation pipeline to make sure the data outputted from a function
#' #' is accurate
#' #' It essentially is a comparison of actual vs expected output where there are multiple
#' #' outputs in the column
#' #' The intention is to then quantify the output of a function for a specific dataset.
#' #'
#' #' @param dataframe dataframe
#' #' @param testcolumn The dataframe column to run the function on
#' #' @param pHospitalNum the hospital number of the patient so can be identified
#' #' @importFrom openxlsx write.xlsx
#' #' @keywords validation
#' #' @export
#' #' @examples #ValidationR(HistolBxSize,myHistol$histology_report)
#'
#' ValidationR<-function(FUN =funct,dataframe,Column,pHospitalNum){
#' dd<-funct(dataframe,Column)
#' #Now just want the columns that have changed or have been added from the original as well
#' #as well as the columns that sound very similar to the original
#' #ie need to get the original column called Column as well as the new column created (can
#' # I get this from the diff between two data frames? dd-dataframe??)
#' #This gets the new column name from the dataframe that the function has run
#' MyNegsFiltered$FindingsAlgoNegs<-as.list(strsplit(MyNegsFiltered$FindingsAlgoNegs, ";"))
#' MyNegsFiltered$negativeresults<-as.list(strsplit(MyNegsFiltered$negativeresults, ";"))
#' #pHospitalNum
#' ff<-setdiff(union(names(dataframe), names(dd)), names(dataframe))
#' ff<-data.frame(dd[,Column],dd[,ff],dd[,pHospitalNum])
#' write.xlsx(ff, paste0(getwd(),"/MyValidation.xlsx"))
#' }
#' #dataframe[,pHospitalNum],
#'
sebastiz/EndoMineR_devlop documentation built on May 29, 2019, 7:33 a.m.
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########## Lexicons ##########
#' Extract pathology type
#'
#' This standardizes terms to describe the pathology tissue type being exmained
#' @keywords Pathology type
#' @export
#' @examples #No examples as just returns a list
HistolType <- function() {
#First standardise the terms
tissue<-list("Resection" = "Resection",
"bx|biopsies"="Biopsy",
"(endoscopic mucosal resection)|(endoscopic mucosectomy)"="EMR",
"endoscopic submucosal (dissection|resection)"="ESD",
"nodul"="nodul",
"polyp "="polyp")
#To get the list as a list of values only in a regex use
#paste0(unlist(HistolType(),use.names=F),collapse="|")
return(tissue)
}
#' Use list of standard locations
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationList<-function(){
All<-append(LocationListLower(), LocationListUpper())
All<-append(All,LocationListUniversal())
#To get the list as a list of values only in a regex use
#paste0(unlist(All,use.names=F),collapse="|")
return(All)
}
#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListUpper<-function(){
upper<-list("duodenum|d2|D2|duodenal" = "Duodenum",
"gastric|stomach"="Stomach",
"antrum|antral"="Antrum",
"ogj|goj|gastrooesophageal"="GOJ",
"fundal|fundus"="stomach",
"pyloric"="Pylorus",
"gastric cardia"="Cardia",
"oesophagus|oesophageal"="Oesophagus")
#To get the list as a list of values only in a regex use
#paste0(unlist(upper,use.names=F),collapse="|")
return(upper)
}
#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListUniversal<-function(){
universal<-list("Anastomosis" = "Ascending ")
return(universal)
#If need to use then use
#paste0(unlist(universal,use.names=F),collapse="|")
}
#' Use list of standard locations for lower GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the TermStandardLocator as well
#' as extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @export
#' @examples #No example needed
LocationListLower<-function(){
lower<-list("asce |ascending|(ascend[^a-z])|( colon r )|(r colon)|(asc )|(right colon)" = "Ascending ",
"descending|(descen[^a-z])|(desc[^a-z])|(des[^a-z])|(colon l)|(l colon)|(left colon)" = "Descending ",
"sigmoid|(sigm[^a-z])|sigmo "= "Sigmoid ",
"rectal|rectum|(rectum[a-z])|rect "="Rectum ",
"transverse|(transv[^a-z])|tranv |trans "="Transverse ",
"caecum|caecal"="Caecum ",
"splenic"="Splenic ",
"(ileum )|( ileal )"="Ileum ",
"rectosigmoid"="Rectosigmoid ",
"(ileocaecal\\s*)|icv|(ileo-caecum)"="Ileocaecal",
"(hep[^a-z])|([Hh]epatic)"="Hepatic ",
"colonic|colon |(col[^a-z])"="Colon ",
"term |terminal"="Terminal",
"TI "="Terminal",
"caec"="Caecum ",
"[Ss]ig "="Sigmoid ",
"ileo\\s*-\\s*anal|ileo\\s*anal "="Ileoanal ",
"(pre\\s*pouch)|(pre-[Pp]ouch)"="PrePouch",
"pouch"="Pouch",
"term |terminal"="Terminal")
#To get the list as a list of values only in a regex use
#paste0(unlist(lower,use.names=F),collapse="|")
return(lower)
}
#' Use list of catheters used in radiofrequency ablation
#'
#' The takes a list of catheters used in radiofrequency ablation
#'
#' @keywords RFA
#' @export
#' @examples #No example needed
RFACath<-function(){
tofind <-
paste(
c(
"90","360","HALO60"," 60","TTS",
"[Cc]hannel","APC"
),
collapse = "|"
)
return(tofind)
}
#' Event list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#' @export
#'
EventList<-function(){
Event <- list("radiofrequency ablation" = "RFA",
"(argon plasma coagulation)|apc" = "APC",
"halo| rfa" = "RFA",
"dilatation|dilated"="dilat",
" emr"="EMR",
"(endoscopic mucosal resection)|(endoscopic mucosectomy)"="EMR",
"clip"="clip",
"grasp"="grasp",
"iodine"="iodine",
"acetic"="acetic",
"NAC"="NAC",
"Brushings"="brushings"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(Event,use.names=F),collapse="|")
return(Event)
}
#' Temporal list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Temporal extraction
#' @examples # unique(unlist(Temporal(), use.names = FALSE))
#' @export
#'
TemporalList<-function(){
Temporal <- list("Past" = "Past",
"Present" = "Present",
"Future" = "Future"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(Temporal,use.names=F),collapse="|")
return(Temporal)
}
#' Biopsy index list
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
BiopsyIndex<-function(){
BiopsyIndexList <- list("ileum:biopsy"="C11",
"ileocaecal:biopsy"="C10",
"caecum:biopsy"="C9",
"ascending:biopsy"="C8",
"hepatic:biopsy"="C7",
"transverse:biopsy"="C6",
"splenic:biopsy"="C5",
"descending:biopsy"="C4",
"sigmoid:biopsy"="C3",
"rectosigmoid:biopsy"="C2",
"rectum:biopsy"="C1",
"ileoanal:biopsy"="S1",
"prepouch:biopsy"="S2",
"pouch:biopsy"="S3",
"duodenum:biopsy"="O5",
"antrum:biopsy"="O4",
"stomach:biopsy"="O3",
"goj:biopsy"="O1",
"cardia:biopsy"="O2",
"oesophagus:biopsy"="O1",
"colon:biopsy"="colon",
"oesophagus:emr"="O1",
"goj:emr"="O1",
"stomach:emr"="O3",
"duodenum:emr"="O5")
#To get the list as a list of values only in a regex use
#paste0(unlist(BiopsyIndex,use.names=F),collapse="|")
return(BiopsyIndexList)
}
#' GISymptoms
#'
#' This function returns all the Common GI symptoms. They are simply listed as is without grouping
#' or mapping. They have been derived from a manual list with synonyms derived from the UMLS Methatharus
#' using the browser.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
GISymptomsList<-function(){
Symptoms <- list("abdomen pain"="abdomen pain",
"abdomen; pain, epigastric"="abdomen; pain, epigastric",
"abdominal pain"="abdominal pain",
"abdominal pain epigastric"="abdominal pain epigastric",
"abdominal pain in the central upper belly"="abdominal pain in the central upper belly",
"abdominal pain nos"="abdominal pain nos",
"abdominal pain, epigastric"="abdominal pain, epigastric",
"abdominal pain, unspecified site"="abdominal pain, unspecified site",
"abdominal pains"="abdominal pains",
"abdominal wind"="abdominal wind",
"abdominal; pain"="abdominal; pain",
"abdominalgia"="abdominalgia",
"acid reflux"="acid reflux",
"acidity"="acidity",
"alteration in bowel elimination: incontinence"="alteration in bowel elimination: incontinence",
"altered blood in stool"="altered blood in stool",
"altered blood passed per rectum"="altered blood passed per rectum",
"anal incontinence"="anal incontinence",
"anal pain"="anal pain",
"anus pain"="anus pain",
"anus pains"="anus pains",
"anus; pain"="anus; pain",
"ap - abdominal pain"="ap - abdominal pain",
"bad breath"="bad breath",
"bad breath - halitosis"="bad breath - halitosis",
"bad breath halitosis"="bad breath halitosis",
"bad or foul breath"="bad or foul breath",
"bad/foul;breath"="bad/foul;breath",
"being sick"="being sick",
"belch"="belch",
"belching"="belching",
"belching symptom"="belching symptom",
"belching symptoms"="belching symptoms",
"belching, burping"="belching, burping",
"belchings"="belchings",
"bellyache"="bellyache",
"black stool"="black stool",
"black stools"="black stools",
"black, tarry stool"="black, tarry stool",
"bleeding per rectum"="bleeding per rectum",
"bleeding rectal"="bleeding rectal",
"bleeding rectum"="bleeding rectum",
"bleeding-rectal"="bleeding-rectal",
"bleeding;anal"="bleeding;anal",
"bleeding;rectal"="bleeding;rectal",
"blood per rectum"="blood per rectum",
"blood; vomiting"="blood; vomiting",
"bowel incontinena"="bowel incontinena",
"bowel incontinence"="bowel incontinence",
"bowel incontinent"="bowel incontinent",
"bowel loose movements"="bowel loose movements",
"bowels loose movement"="bowels loose movement",
"bowels: incontinent"="bowels: incontinent",
"brash"="brash",
"breath odor"="breath odor",
"breath odor abnormal"="breath odor abnormal",
"breath odor nos"="breath odor nos",
"breath odors"="breath odors",
"breath odour"="breath odour",
"breath odour nos"="breath odour nos",
"breath smells offensive"="breath smells offensive",
"breath smells unpleasant"="breath smells unpleasant",
"breath; foul"="breath; foul",
"burning reflux"="burning reflux",
"burp"="burp",
"burping"="burping",
"burps"="burps",
"c/o - cough"="c/o - cough",
"can't get food down"="can't get food down",
"cannot get food down"="cannot get food down",
"chest pain"="chest pain",
"chest pain nos"="chest pain nos",
"chest pain or discomfort"="chest pain or discomfort",
"chest pain or discomfort reported as pain"="chest pain or discomfort reported as pain",
"chest pain, nos"="chest pain, nos",
"chest pain, pleuritic"="chest pain, pleuritic",
"chest pain, unspecified"="chest pain, unspecified",
"chest pains"="chest pains",
"chest; pain"="chest; pain",
"clear throat"="clear throat",
"clearing throat"="clearing throat",
"clearings throat"="clearings throat",
"complaining of cough"="complaining of cough",
"cough"="cough",
"cough symptom"="cough symptom",
"cough symptoms"="cough symptoms",
"cough, nos"="cough, nos",
"coughing"="coughing",
"coughing - function"="coughing - function",
"coughing symptom"="coughing symptom",
"coughs"="coughs",
"d - diarrhea"="d - diarrhea",
"d - diarrhoea"="d - diarrhoea",
"dark stools"="dark stools",
"deglutition disorder"="deglutition disorder",
"deglutition disorders"="deglutition disorders",
"diarrhea"="diarrhea",
"diarrhea nos"="diarrhea nos",
"diarrhea running"="diarrhea running",
"diarrhea symptom"="diarrhea symptom",
"diarrhea symptoms"="diarrhea symptoms",
"diarrhea, nos"="diarrhea, nos",
"diarrhea, unspecified"="diarrhea, unspecified",
"diarrheas"="diarrheas",
"diarrhoea"="diarrhoea",
"diarrhoea nos"="diarrhoea nos",
"diarrhoea symptom"="diarrhoea symptom",
"diarrhoea symptoms"="diarrhoea symptoms",
"difficult swallowing"="difficult swallowing",
"difficult; swallowing"="difficult; swallowing",
"difficulties swallowing"="difficulties swallowing",
"difficulty in swallowing"="difficulty in swallowing",
"difficulty in swallowing nos"="difficulty in swallowing nos",
"difficulty swallowing"="difficulty swallowing",
"difficulty;swallowing"="difficulty;swallowing",
"disorder deglutition"="disorder deglutition",
"disorders, deglutition"="disorders, deglutition",
"dry heave"="dry heave",
"dry heaves"="dry heaves",
"dysphagia"="dysphagia",
"dysphagia, nos"="dysphagia, nos",
"dysphagia, unspecified"="dysphagia, unspecified",
"dysphagias"="dysphagias",
"emesis"="emesis",
"emesis bloody"="emesis bloody",
"epigastralgia"="epigastralgia",
"epigastric abdominal pain"="epigastric abdominal pain",
"epigastric ache"="epigastric ache",
"epigastric pain"="epigastric pain",
"epigastric; pain"="epigastric; pain",
"epigastrium pain"="epigastrium pain",
"eructate"="eructate",
"eructation"="eructation",
"eructation, function"="eructation, function",
"eructations"="eructations",
"excessive farting"="excessive farting",
"excessive passing of gas"="excessive passing of gas",
"faecal incontinence"="faecal incontinence",
"fart"="fart",
"farting"="farting",
"farts"="farts",
"faucitis"="faucitis",
"fecal incontinence"="fecal incontinence",
"fecal incontinence nos"="fecal incontinence nos",
"feces incontinence"="feces incontinence",
"feces incontinence of"="feces incontinence of",
"feces; incontinence"="feces; incontinence",
"fetor ex ore"="fetor ex ore",
"fetor oris"="fetor oris",
"finding of vomiting"="finding of vomiting",
"flatulence"="flatulence",
"flatulence symptom"="flatulence symptom",
"flatus"="flatus",
"flatus, function"="flatus, function",
"foetor ex ore"="foetor ex ore",
"foul breath"="foul breath",
"foul; breath"="foul; breath",
"frequent stools"="frequent stools",
"full of wind"="full of wind",
"gas passing"="gas passing",
"gas raising"="gas raising",
"gaseous regurgitation"="gaseous regurgitation",
"gaseousness"="gaseousness",
"gastric contents; regurgitation"="gastric contents; regurgitation",
"gastrointestinal disorder hematemesis"="gastrointestinal disorder hematemesis",
"gut pain"="gut pain",
"haematemesis"="haematemesis",
"haematemesis/vomiting blood"="haematemesis/vomiting blood",
"haemorrhage of rectum"="haemorrhage of rectum",
"haemorrhage rectal"="haemorrhage rectal",
"haemorrhage rectum"="haemorrhage rectum",
"halitoses"="halitoses",
"halitosis"="halitosis",
"heart burn"="heart burn",
"heartburn"="heartburn",
"heartburn symptom"="heartburn symptom",
"heaving"="heaving",
"hematemeses"="hematemeses",
"hematemesis"="hematemesis",
"hematemesis was observed"="hematemesis was observed",
"hematemesis/vomiting blood"="hematemesis/vomiting blood",
"hemorrhage of rectum"="hemorrhage of rectum",
"hemorrhage rectal"="hemorrhage rectal",
"hemorrhage rectum"="hemorrhage rectum",
"hemorrhage; rectum"="hemorrhage; rectum",
"incontinence (fecal)"="incontinence (fecal)",
"incontinence bowel"="incontinence bowel",
"incontinence faecal"="incontinence faecal",
"incontinence fecal"="incontinence fecal",
"incontinence of bowel"="incontinence of bowel",
"incontinence of faeces"="incontinence of faeces",
"incontinence of feces"="incontinence of feces",
"incontinence of feces (finding)"="incontinence of feces (finding)",
"incontinence of stool"="incontinence of stool",
"incontinence stool"="incontinence stool",
"incontinence, bowel"="incontinence, bowel",
"incontinence, fecal"="incontinence, fecal",
"incontinence; fecal"="incontinence; fecal",
"incontinence;bowel"="incontinence;bowel",
"incontinence;faeces"="incontinence;faeces",
"incontinent bowel"="incontinent bowel",
"incontinent of bowels"="incontinent of bowels",
"incontinent of faeces"="incontinent of faeces",
"incontinent of feces"="incontinent of feces",
"incontinent of stool"="incontinent of stool",
"intestinal gas excretion"="intestinal gas excretion",
"involuntary stool"="involuntary stool",
"loose bowel motion"="loose bowel motion",
"loose bowel motions"="loose bowel motions",
"loose bowel movement"="loose bowel movement",
"loose stools"="loose stools",
"loss of bowel control"="loss of bowel control",
"melaena"="melaena",
"melena"="melena",
"melena (disorder)"="melena (disorder)",
"melena/black tarry stools"="melena/black tarry stools",
"melenas"="melenas",
"nausea"="nausea",
"nonspecific chest pain"="nonspecific chest pain",
"observation of cough"="observation of cough",
"observation of diarrhea"="observation of diarrhea",
"observation of diarrhoea"="observation of diarrhoea",
"observation of vomiting"="observation of vomiting",
"odor breath"="odor breath",
"odor of breath"="odor of breath",
"odor of breath fetor oris"="odor of breath fetor oris",
"odour breath"="odour breath",
"of bowel incontinence"="of bowel incontinence",
"ozostomia"="ozostomia",
"pain abdominal"="pain abdominal",
"pain anal"="pain anal",
"pain anus"="pain anus",
"pain chest"="pain chest",
"pain epigastric"="pain epigastric",
"pain in chest"="pain in chest",
"pain in stomach"="pain in stomach",
"pain in the pharynx"="pain in the pharynx",
"pain in throat"="pain in throat",
"pain pharynx"="pain pharynx",
"pain pleural"="pain pleural",
"pain thoracic"="pain thoracic",
"pain throat"="pain throat",
"pain, abdominal"="pain, abdominal",
"pain, chest"="pain, chest",
"pain, pleuritic"="pain, pleuritic",
"pain; abdominal"="pain; abdominal",
"pain; anus"="pain; anus",
"pain; chest"="pain; chest",
"pain; epigastric"="pain; epigastric",
"pain; pharynx"="pain; pharynx",
"pain; pleura"="pain; pleura",
"pain; thorax"="pain; thorax",
"pain; throat"="pain; throat",
"pain;abdominal"="pain;abdominal",
"pain;anal"="pain;anal",
"pain;chest"="pain;chest",
"pain;epigastric"="pain;epigastric",
"pain;throat"="pain;throat",
"pains, abdominal"="pains, abdominal",
"pains, chest"="pains, chest",
"pass wind"="pass wind",
"passage of gas by anus"="passage of gas by anus",
"passing flatus"="passing flatus",
"passing wind"="passing wind",
"pharyngeal pain"="pharyngeal pain",
"pharynx discomfort"="pharynx discomfort",
"pharynx; pain"="pharynx; pain",
"pleura; pain"="pleura; pain",
"pleural pain"="pleural pain",
"pleuralgia"="pleuralgia",
"pleuritic chest pain"="pleuritic chest pain",
"pleuritic pain"="pleuritic pain",
"pleurodynia"="pleurodynia",
"pleurodynia nos"="pleurodynia nos",
"poor swallowing"="poor swallowing",
"pr - bleeding per rectum"="pr - bleeding per rectum",
"pr - blood per rectum"="pr - blood per rectum",
"prb - rectal bleeding"="prb - rectal bleeding",
"proctorrhagia"="proctorrhagia",
"pyroses"="pyroses",
"pyrosis"="pyrosis",
"rb - rectal bleeding"="rb - rectal bleeding",
"rectal bleed"="rectal bleed",
"rectal bleeding"="rectal bleeding",
"rectal blood loss"="rectal blood loss",
"rectal discharge incontinent of stool"="rectal discharge incontinent of stool",
"rectal discharge incontinent of stool (physical finding)"="rectal discharge incontinent of stool (physical finding)",
"rectal haemorrhage"="rectal haemorrhage",
"rectal hemorrhage"="rectal hemorrhage",
"rectal pain"="rectal pain",
"rectorrhagia"="rectorrhagia",
"rectum bleeding"="rectum bleeding",
"rectum hemorrhage"="rectum hemorrhage",
"rectum; hemorrhage"="rectum; hemorrhage",
"reflux"="reflux",
"reflux, nos"="reflux, nos",
"refluxed"="refluxed",
"refluxing"="refluxing",
"refluxs"="refluxs",
"regurgitation"="regurgitation",
"regurgitation of gastric content"="regurgitation of gastric content",
"regurgitation; gastric contents"="regurgitation; gastric contents",
"reported chest pain"="reported chest pain",
"retch"="retch",
"retching"="retching",
"rndx bowel incontinence"="rndx bowel incontinence",
"rndx bowel incontinence (diagnosis)"="rndx bowel incontinence (diagnosis)",
"rndx diarrhea"="rndx diarrhea",
"ructus"="ructus",
"runs"="runs",
"smelly breath"="smelly breath",
"sore symptom throat"="sore symptom throat",
"sore symptoms throat"="sore symptoms throat",
"sore throat"="sore throat",
"sore throat nos"="sore throat nos",
"sore throat symptom"="sore throat symptom",
"sore throat, nos"="sore throat, nos",
"sore throat;"="sore throat;",
"sore throats"="sore throats",
"sorethroat"="sorethroat",
"spitting up"="spitting up",
"stomach pain"="stomach pain",
"stomatodysodia"="stomatodysodia",
"stool black"="stool black",
"stool color black"="stool color black",
"stool incontinence"="stool incontinence",
"stool soiling"="stool soiling",
"stool tarry"="stool tarry",
"stool(s);black"="stool(s);black",
"stool(s);tarry"="stool(s);tarry",
"stools loose"="stools loose",
"stools.incontinent"="stools.incontinent",
"swallowing difficult"="swallowing difficult",
"swallowing difficulties"="swallowing difficulties",
"swallowing difficulty"="swallowing difficulty",
"swallowing disorder"="swallowing disorder",
"swallowing disorders"="swallowing disorders",
"swallowing; difficult"="swallowing; difficult",
"symptoms diarrhea"="symptoms diarrhea",
"symptoms vomiting"="symptoms vomiting",
"tarry stool"="tarry stool",
"tarry stools"="tarry stools",
"the runs"="the runs",
"the trots"="the trots",
"thoracalgia"="thoracalgia",
"thoracic pain"="thoracic pain",
"thoracodynia"="thoracodynia",
"thorax pain"="thorax pain",
"thorax painful"="thorax painful",
"thorax; pain"="thorax; pain",
"throat clearing"="throat clearing",
"throat discomfort"="throat discomfort",
"throat pain"="throat pain",
"throat sore"="throat sore",
"throat soreness"="throat soreness",
"throat, sore"="throat, sore",
"throw up"="throw up",
"throwing up"="throwing up",
"unable to restrain bowel movement"="unable to restrain bowel movement",
"unable to restrain bowel movement (symptom)"="unable to restrain bowel movement (symptom)",
"unspecified abdominal pain"="unspecified abdominal pain",
"unspecified chest pain"="unspecified chest pain",
"vomit"="vomit",
"vomited"="vomited",
"vomiting"="vomiting",
"vomiting blood"="vomiting blood",
"vomiting disorder"="vomiting disorder",
"vomiting nos"="vomiting nos",
"vomiting of blood"="vomiting of blood",
"vomiting out blood"="vomiting out blood",
"vomiting symptom"="vomiting symptom",
"vomiting symptoms"="vomiting symptoms",
"vomiting was observed"="vomiting was observed",
"vomiting, nos"="vomiting, nos",
"vomiting, unspecified"="vomiting, unspecified",
"vomiting; blood"="vomiting; blood",
"vomiting;blood"="vomiting;blood",
"vomits"="vomits",
"vomitting blood"="vomitting blood",
"vomiturition"="vomiturition",
"waterbrash"="waterbrash",
"waterbrash symptom"="waterbrash symptom",
"watery stool"="watery stool",
"watery stools"="watery stools",
"wind"="wind",
"wind - flatus"="wind - flatus",
"wind symptom"="wind symptom",
"winding"="winding",
"c/o - nausea"="c/o - nausea",
"feel sick"="feel sick",
"feeling bilious"="feeling bilious",
"feeling queasy"="feeling queasy",
"feeling sick"="feeling sick",
"nausea nos"="nausea nos",
"nausea symptom"="nausea symptom",
"nausea symptoms"="nausea symptoms",
"nausea"="nausea",
"nauseas"="nauseas",
"nauseated"="nauseated",
"nauseating"="nauseating",
"nauseous"="nauseous",
"observation of nausea"="observation of nausea",
"queasy"="queasy",
"rndx nausea"="rndx nausea",
"sick feeling"="sick feeling",
"symptom nausea"="symptom nausea",
"symptoms nausea"="symptoms nausea")
#To get the list as a list of values only in a regex use
#paste0(unlist(WordsToNumbers,use.names=F),collapse="|")
return(Symptoms)
}
#' Words to numbers
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' It is used in the Barretts_EventType. This does not include EMR as this is
#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @export
#' @examples # unique(unlist(EventList(), use.names = FALSE))
#'
WordsToNumbers<-function(){
NumberConv <- list("[Oo]ne "="1",
"[Ss]ingle "="1",
"[Tt]wo "="2",
"[Tt]hree "= "3",
"[Ff]our "= "4",
"[Ff]ive "= "5",
"[Ss]ix "="6",
"[Ss]even "= "7",
"[Ee]ight "= "8",
"[Nn]ine "= "9",
"[Tt]en "= "10",
"[Ee]leven "= "11",
"[Tt]welve "= "12",
"[Tt]hirteen "= "13",
"[Ff]ourteen "= "14",
"[Ff]ifteen "= "15",
"[Ss]ixteen "= "16"
)
#To get the list as a list of values only in a regex use
#paste0(unlist(WordsToNumbers,use.names=F),collapse="|")
return(NumberConv)
}
#' #' Validate columns
#' #'
#' #' This is an attempt to determine whether functions are accurate in their extraction
#' #' It is part of a validation pipeline to make sure the data outputted from a function
#' #' is accurate
#' #' It essentially is a comparison of actual vs expected output. The intention is to
#' #' then quantify the output of a function for a specific dataset.
#' #'
#' #' @param dataframe dataframe
#' #' @param testcolumn The dataframe column to run the function on
#' #' @param pHospitalNum the hospital number of the patient so can be identified
#' #' @importFrom openxlsx write.xlsx
#' #' @keywords validation
#' #' @export
#' #' @examples #ValidationR(HistolBxSize,myHistol$histology_report)
#'
#' sensAndSpecificMultip<-function(FUN =funct,dataframe,Column,pHospitalNum){
#' dd<-funct(dataframe,Column)
#' #Now just want the columns that have changed or have been added from the original as well
#' #as well as the columns that sound very similar to the original
#' #ie need to get the original column called Column as well as the new column created (can
#' # I get this from the diff between two data frames? dd-dataframe??)
#' #This gets the new column name from the dataframe that the function has run
#' MyNegsFiltered$FindingsAlgoNegs<-as.list(strsplit(MyNegsFiltered$FindingsAlgoNegs, ";"))
#' MyNegsFiltered$negativeresults<-as.list(strsplit(MyNegsFiltered$negativeresults, ";"))
#' #pHospitalNum
#' ff<-setdiff(union(names(dataframe), names(dd)), names(dataframe))
#' ff<-data.frame(dd[,Column],dd[,ff],dd[,pHospitalNum])
#' write.xlsx(ff, paste0(getwd(),"/MyValidation.xlsx"))
#' }
#' #dataframe[,pHospitalNum],
#' #' Validate columns
#' #'
#' #' This is an attempt to determine whether functions are accurate in their extraction
#' #' It is part of a validation pipeline to make sure the data outputted from a function
#' #' is accurate
#' #' It essentially is a comparison of actual vs expected output where there are multiple
#' #' outputs in the column
#' #' The intention is to then quantify the output of a function for a specific dataset.
#' #'
#' #' @param dataframe dataframe
#' #' @param testcolumn The dataframe column to run the function on
#' #' @param pHospitalNum the hospital number of the patient so can be identified
#' #' @importFrom openxlsx write.xlsx
#' #' @keywords validation
#' #' @export
#' #' @examples #ValidationR(HistolBxSize,myHistol$histology_report)
#'
#' ValidationR<-function(FUN =funct,dataframe,Column,pHospitalNum){
#' dd<-funct(dataframe,Column)
#' #Now just want the columns that have changed or have been added from the original as well
#' #as well as the columns that sound very similar to the original
#' #ie need to get the original column called Column as well as the new column created (can
#' # I get this from the diff between two data frames? dd-dataframe??)
#' #This gets the new column name from the dataframe that the function has run
#' MyNegsFiltered$FindingsAlgoNegs<-as.list(strsplit(MyNegsFiltered$FindingsAlgoNegs, ";"))
#' MyNegsFiltered$negativeresults<-as.list(strsplit(MyNegsFiltered$negativeresults, ";"))
#' #pHospitalNum
#' ff<-setdiff(union(names(dataframe), names(dd)), names(dataframe))
#' ff<-data.frame(dd[,Column],dd[,ff],dd[,pHospitalNum])
#' write.xlsx(ff, paste0(getwd(),"/MyValidation.xlsx"))
#' }
#' #dataframe[,pHospitalNum],
#'
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