{ "_id": "69d62d2510581d1350debc4a", "Package": "EndoMineR", "Title": "Functions to mine endoscopic and associated pathology datasets", "Version": "2.0.1.9000", "Authors@R": "person(\"Sebastian\", \"Zeki\", email = \"sebastiz@hotmail.com\",\nrole = c(\"aut\", \"cre\"))", "Description": "This script comprises the functions that are used to clean\nup endoscopic reports and pathology reports as well as many of\nthe scripts used for analysis. The scripts assume the endoscopy\nand histopathology data set is merged already but it can also\nbe used of course with the unmerged datasets.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/EndoMineR,\nhttps://github.com/ropensci/EndoMineR", "BugReports": "https://github.com/ropensci/EndoMineR/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2024-09-02 10:10:04 UTC", "RemoteUrl": "https://github.com/ropensci/EndoMineR", "RemoteRef": "master", "RemoteSha": "2b3603a27687321e409a4a0fcf343ae2843ff889", "NeedsCompilation": "no", "Packaged": { "Date": "2026-04-08 09:06:34 UTC", "User": "root" }, "Author": "Sebastian Zeki [aut, cre]", 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Column mutators" ], "topics": [ "ListLookup" ] }, { "page": "LocationList", "title": "Use list of upper and lower GI standard locations", "concept": [ "NLP - Lexicons" ], "topics": [ "LocationList" ] }, { "page": "LocationListLower", "title": "Use list of standard locations for lower GI endoscopy", "concept": [ "NLP - Lexicons" ], "topics": [ "LocationListLower" ] }, { "page": "LocationListUniversal", "title": "Use list of standard locations for upper GI endoscopy", "concept": [ "NLP - Lexicons" ], "topics": [ "LocationListUniversal" ] }, { "page": "LocationListUpper", "title": "Use list of standard locations for upper GI endoscopy", "concept": [ "NLP - Lexicons" ], "topics": [ "LocationListUpper" ] }, { "page": "MetricByEndoscopist", "title": "Plot a metric by endoscopist", "concept": [ "Grouping by endoscopist" ], "topics": [ "MetricByEndoscopist" ] }, { "page": "Myendo", "title": "Fake Endoscopies", "topics": [ "Myendo" ] }, { "page": "MyImgLibrary", "title": "Clean html endoscopic 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per patient", "concept": [ "Basic Analysis - Surveillance Functions" ], "topics": [ "SurveilFirstTest" ] }, { "page": "SurveilLastTest", "title": "Extract the last test done by a patient only", "concept": [ "Basic Analysis - Surveillance Functions" ], "topics": [ "SurveilLastTest" ] }, { "page": "SurveilTimeByRow", "title": "Extract the time difference between each test in days", "concept": [ "Basic Analysis - Surveillance Functions" ], "topics": [ "SurveilTimeByRow" ] }, { "page": "SurveySankey", "title": "Create a Sankey plot for patient flow", "concept": [ "Patient Flow functions" ], "topics": [ "SurveySankey" ] }, { "page": "textPrep", "title": "Combine all the text cleaning and extraction functions into one", "concept": [ "NLP - Text Cleaning and Extraction" ], "topics": [ "textPrep" ] }, { "page": "theme_Publication", "title": "Set the publication theme for all the ggplots", "concept": [ "Data Presentation helpers" ], "topics": [ "theme_Publication" ] }, { "page": "TheOGDReportFinal", "title": "Fake Upper GI Endoscopy Set", "topics": [ "TheOGDReportFinal" ] }, { "page": "TimeToStatus", "title": "Extract the time to an event", "concept": [ "Basic Analysis - Surveillance Functions" ], "topics": [ "TimeToStatus" ] }, { "page": "vColon", "title": "Fake Lower GI Endoscopy Set including Pathology", "topics": [ "vColon" ] }, { "page": "WordsToNumbers", "title": "Convetr words to numbers especially for the histopathology text", "concept": [ "NLP - Lexicons" ], "topics": [ "WordsToNumbers" ] } ], "_readme": "https://github.com/ropensci/EndoMineR/raw/master/README.md", "_rundeps": [ "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", "farver", "fastmap", "fontawesome", "forcats", "foreign", "Formula", "fs", 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"Analysis.Rmd", "filename": "Analysis.html", "title": "Analysis", "author": "Sebastian Zeki", "engine": "knitr::rmarkdown", "headings": [ "2. Assessment of quality functions", "a) Documentation Quality", "b) Endoscopic Quality", "Sedation Usage", "4.Patient flow functions", "Sankey plots", "Circos plots" ], "created": "2017-12-22 12:04:29", "modified": "2019-10-03 11:13:02", "commits": 23 }, { "source": "Barretts.Rmd", "filename": "Barretts.html", "title": "Barrett's Oesophagus", "author": "Sebastian Zeki", "engine": "knitr::rmarkdown", "headings": [ "Specific diseases - Barrett's oesophagus", "1. 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