Man pages for sebastiz/EndoMineR_devlop
Functions to mine endoscopic and associated pathology datasets
| BarrettsBxQual | Barrett's number of biopsies |
| Barretts_FUType | Follow up group determination |
| BarrettsParisEMR | Paris vs histopath Barrett's |
| Barretts_PathStage | Worst pathological stage Barrett's |
| Barretts_PragueScore | Prague score extraction |
| BiopsyIndex | Biopsy index list |
| CategoricalByEndoscopist | This creates a proportion table for categorical variables by... |
| ColonFinal | Fake Lower GI Endoscopy Set |
| ColumnCleanUp | Tidies up messy columns |
| DictionaryInPlaceReplace | Dictionary In Place Replace |
| EndoDataVizEDA | Create a Circos plot for patient flow |
| EndoDataVizNum_xNum_y | Create non Numeric x versus y |
| EndoDataVizNum_y | Create non-Numeric x versus y |
| Endomerge2 | Endomerge |
| EndoMineR | EndoMineR: A package for analysis of endoscopic and related... |
| EndoPOS | Parts of speech tagging for reports |
| EndoscEndoscopist | Cleans endoscopist column if present |
| EndoscInstrument | Cleans instrument column if present |
| EndoscMeds | Cleans medication column if present |
| EndoscopyEvent | EndoscopyEvent |
| EntityPairs_OneSentence | EntityPairs_OneSentence |
| EntityPairs_TwoSentence | EntityPairs_TwoSentence |
| EventList | Event list |
| Extractor | Extracts the columns from the raw report |
| Extractor2 | Extractor2 |
| ExtrapolateEndoscopicICD10 | Primary Diagnosis from Endoscopy |
| ExtrapolatefromDictionary | Extrapolate from Dictionary |
| ExtrapolateOPCS4Prep | OPCS-4 Coding |
| GISymptomsList | GISymptoms |
| 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 histology report |
| HistolType | Extract pathology type |
| HistolTypeAndSite | HistolTypeAndSite |
| HowManyOverTime | Number of tests done per month and year by indication |
| ListLookup | Extract from report, using words from a list |
| LocationList | Use list of 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 |
| Mypath | Fake Pathology report |
| NegativeRemove | Removes negative and normal sentences |
| PathDataFrameFinal | Fake Upper GI Pathology Set |
| PathDataFrameFinalColon | Fake Lower GI Pathology Set |
| PatientFlow_CircosPlots | Create a Circos plot for patient flow |
| POS_Extract | Extract sentences with the POS tags desired |
| RFACath | Use list of catheters used in radiofrequency ablation |
| scale_colour_Publication | Sets the publication theme for all the ggplots |
| scale_fill_Publication | #' Sets the publication theme for all the ggplots #' #' |
| SensAndSpecif | Sensitivity and Specificity of text mining functions |
| spellCheck | Find and Replace function |
| 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 | #' Determine the patient metric of choice over time WORK IN... |
| TemporalList | Temporal list |
| textPrep | textPrep function |
| theme_Publication | #' Sets the publication theme for all the ggplots #' #' |
| TheOGDReportFinal | Fake Upper GI Endoscopy Set |
| TimeToStatus | Last status |
| vColon | Fake Lower GI Endoscopy Set including Pathology |
| WordsToNumbers | Words to numbers |
