{ "_id": "6ad71a0769e274306bae780a", "Package": "PheCAP", "Type": "Package", "Title": "High-Throughput Phenotyping with EHR using a Common Automated\nPipeline", "Version": "1.2.2", "Authors@R": "c(\nperson(\"Yichi\", \"Zhang\", role = \"aut\"),\nperson(\"Chuan\", \"Hong\", role = \"aut\"),\nperson(\"Tianxi\", \"Cai\", role = \"aut\"),\nperson(family = \"PARSE LTD\", role = c(\"aut\", \"cre\"), email = \"software@parse-health.org\")\n)", "Description": "Implement surrogate-assisted feature extraction (SAFE) and\ncommon machine learning approaches to train and validate\nphenotyping models. Background and details about the methods\ncan be found at Zhang et al. (2019)\n, Yu et al. (2017)\n, and Liao et al. (2015)\n.", "URL": "https://celehs.github.io/PheCAP/, https://github.com/celehs/PheCAP", "BugReports": "https://github.com/celehs/PheCAP/issues", "License": "GPL-3", "Encoding": "UTF-8", "ByteCompile": "yes", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "LazyData": "true", "Config/pak/sysreqs": "libmysqlclient-dev", "Repository": "https://celehs.r-universe.dev", "Date/Publication": "2021-02-23 06:01:23 UTC", "RemoteUrl": "https://github.com/celehs/phecap", "RemoteRef": "HEAD", "RemoteSha": "7c18179625c93f1058533aafedcae9480409da06", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-20 07:32:18 UTC", "User": "root" }, "Author": "Yichi Zhang [aut],\nChuan Hong [aut],\nTianxi Cai [aut],\nPARSE LTD [aut, cre]", "Maintainer": "PARSE LTD ", "_user": "celehs", "_type": "src", "_file": "PheCAP_1.2.2.tar.gz", "_fileid": "https://r2.ropensci.org/0db2d78cb5d2553d1f6eb460863f200cbe9b3832c423de77ccccb25cf5ee2f7f", "_filesize": 3198615, "_sha256": "0db2d78cb5d2553d1f6eb460863f200cbe9b3832c423de77ccccb25cf5ee2f7f", "_expires": "2027-01-28T07:36:38.000Z", "_created": "2026-10-20T07:32:18.000Z", "_published": "2026-10-20T07:36:39.824Z", "_upstream": "https://github.com/celehs/phecap", "_status": "success", "_maintainer": { "name": "PARSE LTD", "email": "software@parse-health.org", "login": "celehs", "description": "Translational Data Science Center for a Learning Health System", "uuid": 44823506 }, "_jobs": [ { "job": 118509820821, "time": 148, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12247554234" }, { "job": 118509820807, "time": 139, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12248445081" }, { "job": 118509820909, "time": 203, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "" }, { "job": 118509820814, "time": 140, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12247124030" }, { "job": 118506994188, "time": 473, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12248021586" }, { "job": 118509820947, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12248256277" }, { "job": 118509820918, "time": 86, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12247653113" }, { "job": 118509820859, "time": 106, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12247609080" }, { "job": 118509821025, "time": 105, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12247034231" } ], "_buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637", "_commit": { "id": "7c18179625c93f1058533aafedcae9480409da06", "author": "Ming Yang ", "committer": "Ming Yang ", "message": "update website\n", "time": 1614060083 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "RMySQL", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "e1071", "role": "Suggests" }, { "package": "randomForestSRC", "role": "Suggests" }, { "package": "xgboost", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "celehs", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 22, "_contributors": [ { "user": "celehs", "count": 22, "uuid": 44823506 }, { "user": "mingstat", "count": 21, "uuid": 5520067 }, { "user": "chuanhong", "count": 7, "uuid": 9748986 } ], "_userbio": { "uuid": 44823506, "type": "user", "name": "CELEHS", "followers": 61, "description": "Translational Data Science Center for a Learning Health System" }, "_downloads": { "count": 272, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PheCAP" }, "_mentions": 1, "_devurl": "https://github.com/celehs/phecap", "_pkgdown": "https://celehs.github.io/PheCAP/", "_searchresults": 11, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/PheCAP.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/celehs/phecap", "_realowner": "celehs", "_cranurl": true, "_releases": [ { "version": "1.1.0", "date": "2020-05-02" }, { "version": "1.2.1", "date": "2020-09-17" } ], "_exports": [ "phecap_generate_dictionary_file", "phecap_perform_majority_voting", "phecap_plot_roc_curves", "phecap_predict_phenotype", "phecap_run_feature_extraction", "phecap_train_phenotyping_model", "phecap_validate_phenotyping_model", "PhecapData", "PhecapSurrogate" ], "_datasets": [ { "name": "ehr_data", "title": "A Synthetic EHR Dataset", "object": "ehr_data", "class": [ "data.frame" ], "fields": [], "rows": 10000, "table": true, "tojson": true } ], "_help": [ { "page": "PheCAP-package", "title": "High-Throughput Phenotyping with EHR using a Common Automated Pipeline", "topics": [ "PheCAP-package", "PheCAP" ] }, { "page": "ehr_data", "title": "A Synthetic EHR Dataset", "topics": [ "ehr_data" ] }, { "page": "phecap_generate_dictionary_file", "title": "Generate a Dictionary File for Note Parsing", "topics": [ "phecap_generate_dictionary_file" ] }, { "page": "phecap_perform_majority_voting", "title": "Perform Majority Voting on the CUIs from Multiple Knowledge Sources", "topics": [ "phecap_perform_majority_voting" ] }, { "page": "phecap_plot_roc_curves", "title": "Plot ROC and Related Curves for Phenotyping Models", "topics": [ "phecap_plot_roc_curves" ] }, { "page": "phecap_predict_phenotype", "title": "Predict Phenotype", "topics": [ "phecap_predict_phenotype" ] }, { "page": "phecap_run_feature_extraction", "title": "Run Surrogate-Assisted Feature Extraction (SAFE)", "topics": [ "phecap_run_feature_extraction" ] }, { "page": "phecap_train_phenotyping_model", "title": "Train Phenotyping Model using the Training Labels", "topics": [ "phecap_train_phenotyping_model" ] }, { "page": "phecap_validate_phenotyping_model", "title": "Validate the Phenotyping Model using the Validation Labels", "topics": [ "phecap_validate_phenotyping_model" ] }, { "page": "PhecapData", "title": "Define or Read Datasets for Phenotyping", "topics": [ "PhecapData" ] }, { "page": "PhecapSurrogate", "title": "Define a Surrogate Variable used in Surrogate-Assisted Feature Extraction (SAFE)", "topics": [ "PhecapSurrogate" ] } ], "_readme": "https://github.com/celehs/phecap/raw/HEAD/README.md", "_rundeps": [ "codetools", "DBI", "foreach", "glmnet", "iterators", "lattice", "Matrix", "Rcpp", "RcppEigen", "RMySQL", "shape", "survival" ], "_vignettes": [ { "source": "example1.Rmd", "filename": "example1.html", "title": "Example 1: Simulated Data", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-03-29 06:38:24", "modified": "2020-09-17 02:45:44", "commits": 4 }, { "source": "example2.Rmd", "filename": "example2.html", "title": "Example 2: Real EHR Data", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-03-29 06:38:24", "modified": "2020-09-17 02:45:44", "commits": 4 }, { "source": "main.Rmd", "filename": "main.html", "title": "Main Steps", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-03-19 03:18:57", "modified": "2020-09-17 02:45:44", "commits": 3 }, { "source": "NER-MetaMAP.Rmd", "filename": "NER-MetaMAP.html", "title": "NER using MetaMAP", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-03-29 01:39:47", "modified": "2020-09-17 02:45:44", "commits": 10 }, { "source": "NLP-NILE.Rmd", "filename": "NLP-NILE.html", "title": "Running NLP using NILE", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-03-29 01:39:47", "modified": "2020-09-17 09:01:38", "commits": 13 } ], "_score": 6.08278537031645, "_indexed": true, "_nocasepkg": "phecap", "_universes": [ "celehs" ], "_binaries": [ { "r": "4.5.3", "os": "mac", "version": "1.2.2", "date": "2026-09-20T07:53:36.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/012072cf2e38fcc72832504503bf291f6c4eff4d853181d5858e55326b646a7a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/35497751551" }, { "r": "4.7.0", "os": "linux", "version": "1.2.2", "date": "2026-10-20T07:34:36.000Z", "distro": "resolute", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/7d90ebc69501fcb54d7bc24e49029763ee4f5f44ed0124826432883762e4353c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.6.1", "os": "linux", "version": "1.2.2", "date": "2026-10-20T07:34:38.000Z", "distro": "resolute", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/84e9f6b935e29688f028885d9fc5339f4264be9f71db513365c8a36eb0efcc31", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.6.1", "os": "mac", "version": "1.2.2", "date": "2026-10-20T07:34:37.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/cc35e52d19e0abc9c21b9b3c2789f847ae286c8ab2aa60215259cc83cf142694", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.2", "date": "2026-10-20T07:34:38.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/fcac279fe79627095a6e025f9687455cf56f8f4565b06873f998afaab586f8f7", "status": "success", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.7.0", "os": "win", "version": "1.2.2", "date": "2026-10-20T07:33:35.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/a497fc3de75025b0658a9780bcaf4e1e384413b8df6a3286fd4453201c172266", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.5.3", "os": "win", "version": "1.2.2", "date": "2026-10-20T07:33:49.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/2bd19e9f5ae578db2ca250557b16590692f315c2d1b1fc647e667f7a33f5f489", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" }, { "r": "4.6.1", "os": "win", "version": "1.2.2", "date": "2026-10-20T07:33:48.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "https://r2.ropensci.org/76af57bf765db7d681df9863bb39c009f9ecf3bdb8b03325475a6b1f5f05d922", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/39386312637" } ] }