{ "_id": "6a103ac9acfb0bcc41c9b491", "Package": "mectx", "Type": "Package", "Title": "MEchanistic Clustering - Treatment eXposure Framework", "Version": "1.1.1", "Authors@R": "c(person(given = \"Dipankor\",\nfamily = \"Dhrubo\",\nemail = \"dhrubo.2@osu.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Daniel\",\nfamily = \"Spakowicz\",\nrole = c(\"aut\"),\nemail = \"daniel.spakowicz@osumc.edu\",\ncomment = c(ORCID = \"0000-0003-2314-6435\")))", "Description": "Implements the MEC-TX (MEchanistic Clustering - Treatment\neXposure) framework for encoding, clustering, and survival\nanalysis of real-world oncology treatment timelines. Provides\nfunctions for normalising medication records, computing\ntreatment intervals, performing k-means clustering in PCA\nspace, assigning line-of-therapy labels, and comparing survival\noutcomes across treatment groups. Designed for use with\nregistry-based cohorts such as the ORIEN AVATAR dataset.\nMethods follow the digital-twin framework described in Dhrubo\nand Spakowicz (2026) .\ntreatment timelines using the MEC-TX digital-twin framework.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Date": "2026-04-27", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 20:50:20 UTC", "User": "root" }, "Author": "Dipankor Dhrubo [aut, cre], Daniel Spakowicz [aut] (ORCID:\n)", "Maintainer": "Dipankor Dhrubo ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-11 20:09:26 UTC", "RemoteUrl": "https://github.com/cran/mectx", "RemoteRef": "HEAD", "RemoteSha": "71351649ec6489fabb1bb7bf4afe8b868e6ea2f3", "MD5sum": "4edd3bcbff37c7be13b005a398a6175d", "_user": "cran", "_type": "src", "_file": "mectx_1.1.1.tar.gz", "_fileid": "e17e30984f3ed5170e1847d0d81f21ae4f1c77977efd9a01f70438db14662190", 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"tx_duration", "tx_focus_dt", "tx_intervals", "tx_lines", "tx_normalize", "tx_pooled_analysis" ], "_help": [ { "page": "cox_forest_plot_from_df", "title": "Cox Proportional Hazards Forest Plot", "topics": [ "cox_forest_plot_from_df" ] }, { "page": "dominant_exclusive", "title": "Assign Mutually Exclusive Dominant Treatment Regimen Per Patient", "topics": [ "dominant_exclusive" ] }, { "page": "get_focus_cohort", "title": "Extract Focus Cohort Sample IDs", "topics": [ "get_focus_cohort" ] }, { "page": "km_panel_from_df", "title": "Kaplan-Meier Survival Panel with Optional Risk Table", "topics": [ "km_panel_from_df" ] }, { "page": "plot_timeline_for_k", "title": "Treatment Timeline Facet Plot by Cluster Assignment", "topics": [ "plot_timeline_for_k" ] }, { "page": "prep_segs", "title": "Recode and clip treatment segments to canonical types Validates a raw segments data frame, recodes free-text treatment type labels to the eight canonical MEC-TX types via regex, and clips segment start/end times to '[0, horizon_years]'. Zero-duration segments (after clipping) and rows with 'NA' in 'sample', 't0', or 't1' are dropped. Called upstream by 'plot_timeline_for_k()' and 'timeline_panel()' - not intended for direct use.", "topics": [ "prep_segs" ] }, { "page": "standardise_status", "title": "Standardise Survival Status Column to 0/1 Integer", "topics": [ "standardise_status" ] }, { "page": "timeline_panel", "title": "Treatment Timeline Panel for Selected Patients", "topics": [ "timeline_panel" ] }, { "page": "treatment_shares", "title": "Compute per-patient treatment type durations and shares Takes a clipped and recoded segments data frame (output of 'prep_segs') and computes per-patient treatment duration and share for each of the eight canonical treatment types. Returns a wide-format tibble with one row per patient. Called upstream by 'timeline_panel' and 'plot_timeline_for_k' - not intended for direct use.", "topics": [ "treatment_shares" ] }, { "page": "tx_cluster_surv", "title": "Cluster Treatment Timelines and Attach Survival Data", "topics": [ "tx_cluster_surv" ] }, { "page": "tx_compare_groups", "title": "Flexible Survival Comparison by Grouping Variable or Custom Groups", "topics": [ "tx_compare_groups" ] }, { "page": "tx_duration", "title": "Treatment Duration Analysis by Grouping Variable", "topics": [ "tx_duration" ] }, { "page": "tx_focus_dt", "title": "Digital Twin Focus Analysis for a Specific Treatment Type", "topics": [ "tx_focus_dt" ] }, { "page": "tx_intervals", "title": "Convert Normalised Treatment Timeline to Treatment Intervals", "topics": [ "tx_intervals" ] }, { "page": "tx_lines", "title": "Detect Lines of Therapy from Treatment Timelines", "topics": [ "tx_lines" ] }, { "page": "tx_normalize", "title": "Normalise Raw Medication Data into a Grid-Based Treatment Timeline", "topics": [ "tx_normalize" ] }, { "page": "tx_pooled_analysis", "title": "Pooled Treatment Cohort Analysis", "topics": [ "tx_pooled_analysis" ] } ], "_readme": "https://github.com/cran/mectx/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "broom", "cli", "cpp11", "dplyr", "farver", "forcats", "generics", "ggnewscale", "ggplot2", "glue", "gtable", "here", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "openssl", "patchwork", "pillar", "pkgconfig", "png", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RcppTOML", "reticulate", "rlang", "rprojroot", "RSpectra", "S7", "scales", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "umap", "utf8", "vctrs", "viridisLite", "withr" ], "_score": 1.6989700043360187, "_indexed": true, "_nocasepkg": "mectx", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-05-11T20:52:52.000Z", "distro": "noble", "commit": "71351649ec6489fabb1bb7bf4afe8b868e6ea2f3", "fileid": "605ae254b3411cf3323b7977493aed2736daae471d1ee992bcd8334e74036b5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25695887385" }, { "r": "4.6.0", "os": "linux", "version": "1.1.1", "date": "2026-05-11T20:52:54.000Z", "distro": "noble", "commit": "71351649ec6489fabb1bb7bf4afe8b868e6ea2f3", "fileid": "9d4547fd2c58c910c7079ecb5c1ebec92417336aa41676e2235284f2cbe1b1ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25695887385" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-05-22T11:15:05.000Z", "commit": "71351649ec6489fabb1bb7bf4afe8b868e6ea2f3", "fileid": "5f07309ccf2fba81f3a87412c0a0f5401c2dca72090d42c97f6ef41168b3bd33", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25695887385" } ] }