Package index
-
textPrep()
- Combine all the text cleaning and extraction functions into one
-
Extractor()
- Extract columns from the raw text
-
DictionaryInPlaceReplace()
- Dictionary In Place Replace
-
NegativeRemove()
- Remove negative and normal sentences
-
NegativeRemoveWrapper()
- Wrapper for Negative Remove
-
spellCheck()
- Find and Replace
-
ColumnCleanUp()
- Tidy up messy columns
-
ListLookup()
- Extract from report, using words from a list
-
EndoPaste()
- Paste endoscopy and histology results into one
-
Endomerge2()
- Merge endoscopy and histology data.
-
HistolType()
- Use list of pathology types
-
LocationList()
- Use list of upper and lower GI standard locations
-
LocationListUpper()
- Use list of standard locations for upper GI endoscopy
-
LocationListUniversal()
- Use list of standard locations for upper GI endoscopy
-
LocationListLower()
- Use list of standard locations for lower GI endoscopy
-
RFACath()
- Use list of catheters used in radiofrequency ablation
-
EventList()
- Use list of endoscopic events and procedures
-
BiopsyIndex()
- Index biopsy locations
-
GISymptomsList()
- Index of GI symptoms
-
WordsToNumbers()
- Convetr words to numbers especially for the histopathology text
-
ExtrapolatefromDictionary()
- Extrapolate from Dictionary
-
ListLookup()
- Extract from report, using words from a list
-
EntityPairs_OneSentence()
- See if words from two lists co-exist within a sentence
-
EntityPairs_TwoSentence()
- Look for relationships between site and event
-
MyImgLibrary()
- Clean html endoscopic images
Specific Text Cleaning - Endoscopy specific cleaning functions:
Functions to help clean endoscopy reports
-
EndoscEndoscopist()
- Clean endoscopist column
-
EndoscInstrument()
- Clean instrument column
-
EndoscMeds()
- Clean medication column
-
EndoscopyEvent()
- Extract the endoscopic event.
Specific Text Cleaning - Histology specific cleaning functions:
Functions to help clean histology text
-
HistolNumbOfBx()
- Extract the number of biopsies taken from the histology report
-
HistolBxSize()
- Determine the largest biopsy size from the histology report
-
HistolTypeAndSite()
- Extract the site a specimen was removed from as well as the type
-
MetricByEndoscopist()
- Plot a metric by endoscopist
-
CategoricalByEndoscopist()
- Group anything by Endoscopist and returns the table
-
SurveilTimeByRow()
- Extract the time difference between each test in days
-
SurveilLastTest()
- Extract the last test done by a patient only
-
SurveilFirstTest()
- Extracts the first test only per patient
-
TimeToStatus()
- Extract the time to an event
-
HowManyOverTime()
- Number of tests done per month and year by indication
-
BarrettsAll()
- Run all the basic Barrett's functions
-
BarrettsBxQual()
- Get the number of Barrett's biopsies taken
-
BarrettsParisEMR()
- Run the Paris classification versus worst histopath grade for Barrett's
-
Barretts_FUType()
- Determine the Follow up group
-
Barretts_PathStage()
- Get the worst pathological stage for Barrett's
-
Barretts_PragueScore()
- Extract the Prague score
-
GRS_Type_Assess_By_Unit()
- Create GRS metrics by endoscopist (X-ref with pathology)
-
SurveySankey()
- Create a Sankey plot for patient flow
-
PatientFlow_CircosPlots()
- Create a Circos plot for patient flow
-
PatientFlowIndividual()
- Create a plot over time of patient categorical findings as a line chart
-
sanity()
- Create a basic consort diagram from dataframes
-
theme_Publication()
- Set the publication theme for all the ggplots
-
scale_fill_Publication()
- Set the fills for all the ggplots
-
scale_colour_Publication()
- Set the colour theme for all the ggplots
-
EndoBasicGraph()
- Basic graph creation using the template specified in theme_Publication.