Package: EndoMineR 2.0.1.9000

Sebastian Zeki

EndoMineR: Functions to mine endoscopic and associated pathology datasets

This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.

Authors:Sebastian Zeki [aut, cre]

EndoMineR_2.0.1.9000.tar.gz
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|EndoMineR.html✨
EndoMineR/json (API)
NEWS

# Install 'EndoMineR' in R:

install.packages('EndoMineR', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/endominer/issues

Datasets:

ColonFinal - Fake Lower GI Endoscopy Set
Myendo - Fake Endoscopies
Mypath - Fake Pathology report
PathDataFrameFinal - Fake Upper GI Pathology Set
PathDataFrameFinalColon - Fake Lower GI Pathology Set
TheOGDReportFinal - Fake Upper GI Endoscopy Set
vColon - Fake Lower GI Endoscopy Set including Pathology

On CRAN:

endoscopy gastroenterology peer-reviewed semi-structured-data text-mining

55 exports 12 stars 1.45 score 133 dependencies

Last updated 1 years agofrom:6d63f07bfb (on master)

Exports:Barretts_FUType Barretts_PathStage Barretts_PragueScore BarrettsAll BarrettsBxQual BarrettsParisEMR BiopsyIndex CategoricalByEndoscopist ColumnCleanUp dev_ExtrapolateOPCS4Prep DictionaryInPlaceReplace EndoBasicGraph Endomerge2 EndoPaste EndoscEndoscopist EndoscInstrument EndoscMeds EndoscopyEvent EntityPairs_OneSentence EntityPairs_TwoSentence Eosinophilics EventList Extractor ExtrapolatefromDictionary GISymptomsList GRS_Type_Assess_By_Unit HistolBxSize HistolNumbOfBx HistolType HistolTypeAndSite HowManyOverTime IBD_Scores ListLookup LocationList LocationListLower LocationListUniversal LocationListUpper MetricByEndoscopist MyImgLibrary NegativeRemove NegativeRemoveWrapper PatientFlow_CircosPlots PatientFlowIndividual RFACath sanity scale_colour_Publication scale_fill_Publication SurveilFirstTest SurveilLastTest SurveilTimeByRow SurveySankey textPrep theme_Publication TimeToStatus WordsToNumbers

Dependencies:askpass backports base64enc BH bit bit64 blob broom bslib cachem callr cellranger checkmate cli clipr cluster colorspace conflicted cpp11 crayon curl data.table DBI dbplyr DiagrammeR digest dplyr dtplyr evaluate fansi farver fastmap fontawesome forcats foreign Formula fs fuzzyjoin gargle generics geosphere ggplot2 ggthemes glue googledrive googlesheets4 gridExtra gtable haven here highr Hmisc hms htmlTable htmltools htmlwidgets httr ids igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv mime modelr munsell nlme NLP nnet openssl pander pillar pkgconfig prettyunits processx progress ps purrr R6 ragg rappdirs RColorBrewer Rcpp readr readxl rematch rematch2 reprex rlang rmarkdown rpart rprojroot rstudioapi rvest sass scales selectr slam sp stringdist stringi stringr sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tm tzdb utf8 uuid vctrs viridis viridisLite visNetwork vroom withr xfun xml2 yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Analysis

Sebastian Zeki

Rendered fromAnalysis.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2019-10-03
Started: 2017-12-22

Barrett's Oesophagus

Sebastian Zeki

Rendered fromBarretts.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2019-10-03
Started: 2017-12-22

Data

Sebastian Zeki

Rendered fromData.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2019-10-03
Started: 2018-03-01

EndoMineR

Sebastian Zeki r Sys.Date()

Rendered fromEndoMineR.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2021-01-30
Started: 2017-09-08

Polyps

Sebastian Zeki

Rendered fromPolyps.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2019-10-03
Started: 2019-04-26

Citation

Development and contributors

Readme and manuals

Help Manual

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

Package: EndoMineR 2.0.1.9000

EndoMineR: Functions to mine endoscopic and associated pathology datasets

Analysis

Barrett's Oesophagus

Data

EndoMineR

Polyps

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)