Man pages for sebastiz/EndoMineR
Functions to mine endoscopic and associated pathology datasets
| 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... |
