{ "_id": "6a1f3164b401979e73427b3f", "Package": "AdhereR", "Type": "Package", "Title": "Adherence to Medications", "Version": "0.8.2", "Authors@R": "c(person(given=\"Dan\" ,family=\"Dediu\", role = c(\"aut\", \"cre\"),\nemail = \"ddediu@gmail.com\"),\nperson(given=\"Alexandra L.\" , family=\"Dima\", role = \"aut\",\nemail = \"alexadima@gmail.com\"),\nperson(given=\"Samuel\", family=\"Allemann\", role = \"aut\",\nemail = \"samuel.allemann@gmx.ch\"))", "Author": "Dan Dediu [aut, cre], Alexandra L. Dima [aut], Samuel Allemann\n[aut]", "Maintainer": "Dan Dediu ", "Description": "Computation of adherence to medications from Electronic\nHealth care Data and visualization of individual medication\nhistories and adherence patterns. The package implements a set\nof S3 classes and functions consistent with current adherence\nguidelines and definitions. It allows the computation of\ndifferent measures of adherence (as defined in the literature,\nbut also several original ones), their publication-quality\nplotting, the estimation of event duration and time to\ninitiation, the interactive exploration of patient medication\nhistory and the real-time estimation of adherence given various\nparameter settings. It scales from very small datasets stored\nin flat CSV files to very large databases and from\nsingle-thread processing on mid-range consumer laptops to\nparallel processing on large heterogeneous computing clusters.\nIt exposes a standardized interface allowing it to be used from\nother programming languages and platforms, such as Python.", "URL": "https://github.com/ddediu/AdhereR", "License": "GPL (>= 2)", "LazyData": "TRUE", "VignetteBuilder": "knitr, R.rsp", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libjpeg-dev libpng-dev librsvg2-dev libwebp-dev", "Repository": "https://ddediu.r-universe.dev", "Date/Publication": "2026-01-15 10:53:31 UTC", "RemoteUrl": "https://github.com/ddediu/adherer", "RemoteRef": "HEAD", "RemoteSha": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "RemoteSubdir": "AdhereR", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 08:01:36 UTC", "User": "root" }, "MD5sum": "9690b11e42833070b1fed610d8043a00", "_user": "ddediu", "_type": "src", "_file": "AdhereR_0.8.2.tar.gz", "_fileid": "402a5fb4d43009b3b5fb302aff09e2d90d3cb71e0845551bc51334025de92a27", "_filesize": 3374907, "_sha256": "402a5fb4d43009b3b5fb302aff09e2d90d3cb71e0845551bc51334025de92a27", "_created": "2026-05-15T08:01:36.000Z", "_published": "2026-06-02T19:39:16.081Z", "_distro": "noble", "_jobs": [ { "job": 79156491766, "time": 181, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7012877190" }, { "job": 79156491379, "time": 193, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7012879455" }, { "job": 79156491368, "time": 167, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7012869435" }, { "job": 79156491664, "time": 159, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7012869664" }, { "job": 79156490524, "time": 732, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7012833210" }, { "job": 79156490833, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367988136" }, { "job": 79156491308, "time": 143, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7012871724" }, { "job": 79156492178, "time": 152, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7012872484" }, { "job": 79156491824, "time": 114, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7012865818" } ], "_buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ddediu/adherer", "_commit": { "id": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "author": "Dan Dediu ", "committer": "GitHub ", "message": "Update ReadMe.md", "time": 1768474411 }, "_maintainer": { "name": "Dan Dediu", "email": "ddediu@gmail.com", "login": "ddediu", "uuid": 13965574 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "lubridate", "version": ">= 1.5", "role": "Imports" }, { "package": "parallel", "version": ">= 3.0", "role": "Imports" }, { "package": "data.table", "version": ">= 1.9", "role": "Imports" }, { "package": "rsvg", "version": ">= 1.3", "role": "Imports" }, { "package": "jpeg", "version": ">= 0.1", "role": "Imports" }, { "package": "png", "version": ">= 0.1", "role": "Imports" }, { "package": "webp", "version": ">= 1.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rmarkdown", "version": ">= 1.1", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.20", "role": "Suggests" }, { "package": "R.rsp", "version": ">= 0.40", "role": "Suggests" }, { "package": "base64", "version": ">= 2.0", "role": "Suggests" }, { "package": "viridisLite", "version": ">= 0.4", "role": "Suggests" }, { "package": "AdhereRViz", "version": ">= 0.2", "role": "Suggests" } ], "_owner": "ddediu", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 1 }, { "week": "2026-03", "n": 2 } ], "_tags": [ { "name": "v0.8.2", "date": "2026-01-15" } ], "_topics": [ "adherence-to-medications", "electronic-healthcare-data", "hadoop", "medical-databases", "medication-histories", "python", "sql", "visualisation" ], "_stars": 31, "_contributors": [ { "user": "ddediu", "count": 490, "uuid": 13965574 }, { "user": "masswear", "count": 116, "uuid": 8583228 }, { "user": "ciaranmci", "count": 1, "uuid": 44294573 }, { "user": "geraldinegomez", "count": 1, "uuid": 46997659 } ], "_userbio": { "uuid": 13965574, "type": "user", "name": "Dan Dediu", "description": "Software developer turned linguist, working mostly on understanding language evolution and linguistic diversity using databases, statistics and experiments." }, "_downloads": { "count": 707, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AdhereR" }, "_mentions": 5, "_devurl": "https://github.com/ddediu/adherer", "_searchresults": 69, "_rbuild": "4.6.0", "_assets": [ "extra/AdhereR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/ddediu/adherer", "_realowner": "ddediu", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2017-04-27" }, { "version": "0.2.0", "date": "2018-06-15" }, { "version": "0.3", "date": "2018-11-21" }, { "version": "0.3.1", "date": "2018-11-26" }, { "version": "0.4", "date": "2019-02-10" }, { "version": "0.4.1", "date": "2019-02-11" }, { "version": "0.5", "date": "2019-06-11" }, { "version": "0.6.0", "date": "2020-05-07" }, { "version": "0.6.1", "date": "2020-05-12" }, { "version": "0.7.0", "date": "2021-09-18" }, { "version": "0.8.0", "date": "2022-06-23" }, { "version": "0.8.1", "date": "2022-07-05" }, { "version": "0.8.2", "date": "2026-01-15" } ], "_exports": [ "callAdhereR", "CMA_per_episode", "CMA_polypharmacy", "CMA_sliding_window", "CMA0", "CMA1", "CMA2", "CMA3", "CMA4", "CMA5", "CMA6", "CMA7", "CMA8", "CMA9", "compute_event_durations", "compute.event.int.gaps", "compute.treatment.episodes", "cover_special_periods", "get.event.plotting.area", "get.legend.plotting.area", "get.plotted.events", "get.plotted.partial.cmas", "getCallerWrapperLocation", "getCMA", "getEventInfo", "getEventsToEpisodesMapping", "getEventsToSlidingWindowsMapping", "getInnerEventInfo", "getMGs", "last.plot.get.info", "map.event.coords.to.plot", "plot_interactive_cma", "prune_event_durations", "subsetCMA", "time_to_initiation" ], "_datasets": [ { "name": "durcomp.dispensing", "title": "Example dispensing events for 16 patients.", "object": "durcomp", "class": [ "data.table", "data.frame" ], "fields": [ "ID", "DATE.DISP", "ATC.CODE", "UNIT", "FORM", "TOTAL.DOSE" ], "rows": 1794, "table": true, "tojson": true }, { "name": "durcomp.hospitalisation", "title": "Example special periods for 10 patients.", "object": "durcomp", "class": [ "data.table", "data.frame" ], "fields": [ "ID", "DATE.IN", "DATE.OUT" ], "rows": 28, "table": true, "tojson": true }, { "name": "durcomp.prescribing", "title": "Example prescription events for 16 patients.", "object": "durcomp", "class": [ "data.table", "data.frame" ], "fields": [ "ID", "DATE.PRESC", "VISIT", "ATC.CODE", "FORM", "UNIT", "PRESC.DURATION", "DAILY.DOSE" ], "rows": 1502, "table": true, "tojson": true }, { "name": "med.events", "title": "Example medication events records for 100 patients.", "object": "medevents", "class": [ "data.frame" ], "fields": [ "PATIENT_ID", "DATE", "PERDAY", "CATEGORY", "DURATION" ], "rows": 1080, "table": true, "tojson": true }, { "name": "med.events.ATC", "title": "", "object": "medgroups", "class": [ "data.frame" ], "fields": [ "PATIENT_ID", "DATE", "DURATION", "PERDAY", "CATEGORY", "CATEGORY_L1", "CATEGORY_L2" ], "rows": 1564, "table": true, "tojson": true }, { "name": "med.groups", "title": "", "object": "medgroups", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "callAdhereR", "title": "callAdhereR.", "topics": [ "callAdhereR" ] }, { "page": "CMA_per_episode", "title": "CMA_per_episode constructor.", "topics": [ "CMA_per_episode" ] }, { "page": "CMA_polypharmacy", "title": "CMA constructor for polypharmacy.", "topics": [ "CMA_polypharmacy" ] }, { "page": "CMA_sliding_window", "title": "CMA_sliding_window constructor.", "topics": [ "CMA_sliding_window" ] }, { "page": "CMA0", "title": "CMA0 constructor.", "topics": [ "CMA0" ] }, { "page": "CMA1", "title": "CMA1 and CMA3 constructors.", "topics": [ "CMA1", "CMA3" ] }, { "page": "CMA2", "title": "CMA2 and CMA4 constructors.", "topics": [ "CMA2", "CMA4" ] }, { "page": "CMA5", "title": "CMA5 constructor.", "topics": [ "CMA5" ] }, { "page": "CMA6", "title": "CMA6 constructor.", "topics": [ "CMA6" ] }, { "page": "CMA7", "title": "CMA7 constructor.", "topics": [ "CMA7" ] }, { "page": "CMA8", "title": "CMA8 constructor.", "topics": [ "CMA8" ] }, { "page": "CMA9", "title": "CMA9 constructor.", "topics": [ "CMA9" ] }, { "page": "compute_event_durations", "title": "Computation of event durations.", "topics": [ "compute_event_durations" ] }, { "page": "compute.event.int.gaps", "title": "Gap Days and Event (prescribing or dispensing) Intervals.", "topics": [ "compute.event.int.gaps" ] }, { "page": "compute.treatment.episodes", "title": "Compute Treatment Episodes.", "topics": [ "compute.treatment.episodes" ] }, { "page": "cover_special_periods", "title": "Cover special periods.", "topics": [ "cover_special_periods" ] }, { "page": "durcomp.dispensing", "title": "Example dispensing events for 16 patients.", "topics": [ "durcomp.dispensing" ] }, { "page": "durcomp.hospitalisation", "title": "Example special periods for 10 patients.", "topics": [ "durcomp.hospitalisation" ] }, { "page": "durcomp.prescribing", "title": "Example prescription events for 16 patients.", "topics": [ "durcomp.prescribing" ] }, { "page": "get.event.plotting.area", "title": "Get the actual plotting area.", "topics": [ "get.event.plotting.area" ] }, { "page": "get.legend.plotting.area", "title": "Get the legend plotting area.", "topics": [ "get.legend.plotting.area" ] }, { "page": "get.plotted.events", "title": "Get info about the plotted events.", "topics": [ "get.plotted.events" ] }, { "page": "get.plotted.partial.cmas", "title": "Get info about the plotted partial CMAs.", "topics": [ "get.plotted.partial.cmas" ] }, { "page": "getCallerWrapperLocation", "title": "getCallerWrapperLocation.", "topics": [ "getCallerWrapperLocation" ] }, { "page": "getCMA", "title": "Access the actual CMA estimate from a CMA object.", "topics": [ "getCMA" ] }, { "page": "last.plot.get.info", "title": "Access last adherence plot info.", "topics": [ "last.plot.get.info" ] }, { "page": "map.event.coords.to.plot", "title": "Map from event to plot coordinates.", "topics": [ "map.event.coords.to.plot" ] }, { "page": "med.events", "title": "Example medication events records for 100 patients.", "topics": [ "med.events" ] }, { "page": "plot_interactive_cma", "title": "Interactive exploration and CMA computation.", "topics": [ "plot_interactive_cma" ] }, { "page": "plot.CMA_per_episode", "title": "Plot CMA_per_episode and CMA_sliding_window objects.", "topics": [ "plot.CMA_per_episode", "plot.CMA_sliding_window" ] }, { "page": "plot.CMA0", "title": "Plot CMA0 objects.", "topics": [ "plot.CMA0" ] }, { "page": "plot.CMA1", "title": "Plot CMA0-derived objects.", "topics": [ "plot.CMA1", "plot.CMA2", "plot.CMA3", "plot.CMA4", "plot.CMA5", "plot.CMA6", "plot.CMA7", "plot.CMA8", "plot.CMA9" ] }, { "page": "print.CMA0", "title": "Print CMA0 (and derived) objects.", "topics": [ "print.CMA0", "print.CMA1", "print.CMA2", "print.CMA3", "print.CMA4", "print.CMA5", "print.CMA6", "print.CMA7", "print.CMA8", "print.CMA9", "print.CMA_per_episode", "print.CMA_sliding_window" ] }, { "page": "prune_event_durations", "title": "Prune event durations.", "topics": [ "prune_event_durations" ] }, { "page": "time_to_initiation", "title": "Computation of initiation times.", "topics": [ "time_to_initiation" ] } ], "_rundeps": [ "cpp11", "data.table", "generics", "jpeg", "lubridate", "png", "rsvg", "timechange", "webp" ], "_vignettes": [ { "source": "AdhereR-overview.Rmd", "filename": "AdhereR-overview.html", "title": "AdhereR: Adherence to Medications", "author": "Alexandra L. Dima, Dan Dediu & Samuel Allemann", "engine": "knitr::rmarkdown", "headings": [ "Definitions", "Data preparation and example dataset", "Visualization of patient records", "Persistence -- treatment episodes", "Adherence -- continuous multiple interval measures of medication availability/gaps (CMA)", "The simple CMAs", "CMA1", "CMA2", "CMA3 and CMA4", "CMA5 and CMA6", "CMA7", "CMA8", "CMA9", "The iterated CMAs", "CMA per episode", "Sliding-window CMA", "Mapping events to episodes and sliding windows", "Interactive plotting", "Computing event duration from prescription, dispensing, and hospitalization data", "Computing time to initiation", "Defining medication groups", "Working with very large databases", "Using AdhereR from other programming languages and platforms", "AdhereR is pipe (%>% or |>)-friendly", "Modifying AdhereR plots a posteriori", "Plot CMA7 for patients 5 and 8:", "Access the plotting info:", "Let's add a vertical line for patient 8 between the medication change:", "Find the event where the medication changes:", "Half-way between the events where medication changes:", "Draw the line:", "Put a star * next to the 4th event of patient 5:", "Find the event:", "Plot the star:", "Add some random text over the figure:" ], "created": "2019-12-20 14:21:31", "modified": "2026-01-15 10:46:23", "commits": 5 }, { "source": "calling-AdhereR-from-python3.Rmd", "filename": "calling-AdhereR-from-python3.html", "title": "Calling AdhereR from Python 3", "author": "Dan Dediu", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Table of Contents", "General ideas", "Fundamentals of calling AdhereR from Python 3", "The Python 3 wrapper: the adherer module", "Making the adherer module visible to Python (aka installation)", "Importing the adherer module and initializations", "The class hierarchy", "The CallAdhereRError exception class", "The base class CMA0", "Class CMA1 and its daughter classes CMA2, CMA3 and CMA4", "Class CMA5 and its daughter classes CMA6, CMA7, CMA8 and CMA9", "Classes CMAPerEpisode and CMASlidingWindow", "Examples of use", "Basic usage", "Importing adherer and checking autodetection", "Export the test dataset from R and import it in Python", "Compute and plot test CMA", "Interactive plotting", "From a Jupyter Notebook", "Parallel processing (locally and on different machines)", "Single thread on the local machine", "R", "Python 3", "Multi-threaded on the local machine", "Parallel on remote machines over a network", "Some caveats for over-the-network distributed computation", "Appendix I: the communication protocol", "Context", "Protocol", "PARAMETERS[^1]", "COMMENTS", "SPECIAL PARAMETERS[^2]", "FUNCTIONS", "PLOTTING", "CMA1, CMA2, CMA3, CMA4", "CMA5, CMA6, CMA7, CMA8, CMA9", "CMA_per_episode", "CMA_sliding_window", "compute_event_int_gaps", "compute_treatment_episodes", "plot_interactive_cma", "Appendix II: the Python 3 code", "Notes" ], "created": "2019-12-20 14:21:31", "modified": "2026-01-15 10:46:23", "commits": 3 }, { "source": "adherer_with_databases.pdf.asis", "filename": "adherer_with_databases.pdf", "title": "Using AdhereR with various database technologies for processing very large datasets", "engine": "R.rsp::asis", "headings": [], "created": "2019-12-20 14:21:31", "modified": "2019-12-20 14:21:31", "commits": 1 } ], "_score": 7.761574548730516, "_indexed": true, "_nocasepkg": "adherer", "_universes": [ "ddediu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.2", "date": "2026-05-15T08:13:46.000Z", "distro": "noble", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "37163acb5aeb6bf0a4d49602d0a668643e86336976e24fd4b0e28ecba98d9a08", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.6.0", "os": "linux", "version": "0.8.2", "date": "2026-05-15T08:13:57.000Z", "distro": "noble", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "e682af89bb34f0fb5ce52afab89d1205eff4037ef4559f7af6ebab01bfe242fe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.5.3", "os": "mac", "version": "0.8.2", "date": "2026-05-15T08:13:07.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "a8797b02e867648f3153a68a30919d859796718d6bde5264fc172751aeabc486", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.6.0", "os": "mac", "version": "0.8.2", "date": "2026-05-15T08:13:06.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "2c4a846b31fb8ee441555b23a7f66b82f1835dcc53cd5c88a5b5ade641ffbba5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.7.0", "os": "win", "version": "0.8.2", "date": "2026-05-15T08:12:53.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "9e44f6aeedcad198f81ad9b223e6b09167c2d619fc18d19a4224eadf439181cc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.5.3", "os": "win", "version": "0.8.2", "date": "2026-05-15T08:13:05.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "d87da95a6ff9066ba9643e3000c0e494b774aedc3038cf3722e4b7dd4a4a1611", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.6.0", "os": "win", "version": "0.8.2", "date": "2026-05-15T08:12:24.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "c10d031198eeb04a9d3f2573560135a7b57e1796cfed7a0aa4bbb888ec388b81", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" }, { "r": "4.6.0", "os": "wasm", "version": "0.8.2", "date": "2026-06-02T19:38:59.000Z", "commit": "8ab25bc2ec79353dc70086b48bcf8a466bbceb09", "fileid": "3a37acf9cd68d5d697b20fbbdecbb5647ac170ab2bd1df32fef22ba5795b33cd", "status": "success", "buildurl": "https://github.com/r-universe/ddediu/actions/runs/25907117071" } ] }