BarrettsAll | Run all the basic Barrett's functions |
BarrettsBxQual | Get the number of Barrett's biopsies taken |
Barretts_FUType | Determine the Follow up group |
BarrettsParisEMR | Run the Paris classification versus worst histopath grade for... |
Barretts_PathStage | Get the worst pathological stage for Barrett's |
Barretts_PragueScore | Extract the Prague score |
BiopsyIndex | Index biopsy locations |
CategoricalByEndoscopist | Group anything by Endoscopist and returns the table |
ColonFinal | Fake Lower GI Endoscopy Set |
ColumnCleanUp | Tidy up messy columns |
dev_ExtrapolateOPCS4Prep | OPCS-4 Coding |
DictionaryInPlaceReplace | Dictionary In Place Replace |
EndoBasicGraph | Basic graph creation using the template specified in... |
Endomerge2 | Merge endoscopy and histology data. |
EndoMineR | EndoMineR: A package for analysis of endoscopic and related... |
EndoPaste | Paste endoscopy and histology results into one |
EndoscEndoscopist | Clean endoscopist column |
EndoscInstrument | Clean instrument column |
EndoscMeds | Clean medication column |
EndoscopyEvent | Extract the endoscopic event. |
EntityPairs_OneSentence | See if words from two lists co-exist within a sentence |
EntityPairs_TwoSentence | Look for relationships between site and event |
Eosinophilics | Extract the Prague score |
EventList | Use list of endoscopic events and procedures |
Extractor | Extract columns from the raw text |
ExtrapolatefromDictionary | Extrapolate from Dictionary |
GISymptomsList | Index of GI symptoms |
GRS_Type_Assess_By_Unit | Create GRS metrics by endoscopist (X-ref with pathology) |
HistolBxSize | Determine the largest biopsy size from the histology report |
HistolNumbOfBx | Extract the number of biopsies taken from the histology... |
HistolType | Use list of pathology types |
HistolTypeAndSite | Extract the site a specimen was removed from as well as the... |
HowManyOverTime | Number of tests done per month and year by indication |
IBD_Scores | Cleans medication column if present |
ListLookup | Extract from report, using words from a list |
LocationList | Use list of upper and lower GI standard locations |
LocationListLower | Use list of standard locations for lower GI endoscopy |
LocationListUniversal | Use list of standard locations for upper GI endoscopy |
LocationListUpper | Use list of standard locations for upper GI endoscopy |
MetricByEndoscopist | Plot a metric by endoscopist |
Myendo | Fake Endoscopies |
MyImgLibrary | Clean html endoscopic images |
Mypath | Fake Pathology report |
NegativeRemove | Remove negative and normal sentences |
NegativeRemoveWrapper | Wrapper for Negative Remove |
PathDataFrameFinal | Fake Upper GI Pathology Set |
PathDataFrameFinalColon | Fake Lower GI Pathology Set |
PatientFlow_CircosPlots | Create a Circos plot for patient flow |
PatientFlowIndividual | Create a plot over time of patient categorical findings as a... |
RFACath | Use list of catheters used in radiofrequency ablation |
sanity | Create a basic consort diagram from dataframes |
scale_colour_Publication | Set the colour theme for all the ggplots |
scale_fill_Publication | Set the fills for all the ggplots |
spellCheck | Find and Replace |
SurveilFirstTest | Extracts the first test only per patient |
SurveilLastTest | Extract the last test done by a patient only |
SurveilTimeByRow | Extract the time difference between each test in days |
SurveySankey | Create a Sankey plot for patient flow |
textPrep | Combine all the text cleaning and extraction functions into... |
theme_Publication | Set the publication theme for all the ggplots |
TheOGDReportFinal | Fake Upper GI Endoscopy Set |
TimeToStatus | Extract the time to an event |
vColon | Fake Lower GI Endoscopy Set including Pathology |
WordsToNumbers | Convetr words to numbers especially for the histopathology... |
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