{ "_id": "6a115dc5acfb0bcc41cec92d", "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": "2026-05-23 07:53:34 UTC", "User": "root" }, "Author": "Yichi Zhang [aut],\nChuan Hong [aut],\nTianxi Cai [aut],\nPARSE LTD [aut, cre]", "Maintainer": "PARSE LTD ", "MD5sum": "8efa66347752cee78b1c68e911748e84", "_user": "celehs", "_type": "src", "_file": "PheCAP_1.2.2.tar.gz", "_fileid": "b78c5e5e04a1a8c72fafbd69be1a0f90225c374ea9d651912e034390721b2294", "_filesize": 3198030, "_sha256": "b78c5e5e04a1a8c72fafbd69be1a0f90225c374ea9d651912e034390721b2294", "_created": "2026-05-23T07:53:34.000Z", "_published": "2026-05-23T07:56:53.190Z", "_distro": "noble", "_jobs": [ { "job": 77507577957, "time": 153, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175456379" }, { "job": 77507577954, "time": 156, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175456651" }, { "job": 77507577960, "time": 108, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175451979" }, { "job": 77507577949, "time": 92, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175450475" }, { "job": 77507294804, "time": 323, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175441661" }, { "job": 77507577950, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175455173" }, { "job": 77507577963, "time": 114, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175452437" }, { "job": 77507577970, "time": 105, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175452976" }, { "job": 77507577956, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175453037" } ], "_buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/celehs/phecap", "_commit": { "id": "7c18179625c93f1058533aafedcae9480409da06", "author": "Ming Yang ", "committer": "Ming Yang ", "message": "update website\n", "time": 1614060083 }, "_maintainer": { "name": "PARSE LTD", "email": "software@parse-health.org", "login": "celehs", "description": "Translational Data Science Center for a Learning Health System", "uuid": 44823506 }, "_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", "description": "Translational Data Science Center for a Learning Health System" }, "_downloads": { "count": 265, "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": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PheCAP.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": [ "patient_id", "label", "main_ICD", "main_NLP", "healthcare_utilization", "COD1", "COD2", "COD3", "COD4", "COD5", "COD6", "COD7", "COD8", "COD9", "COD10", "NLP1", "NLP2", "NLP3", "NLP4", "NLP5", "NLP6", "NLP7", "NLP8", "NLP9", "NLP10", "NLP11", "NLP12", "NLP13", "NLP14", "NLP15", "NLP16", "NLP17", "NLP18", "NLP19", "NLP20", "NLP21", "NLP22", "NLP23", "NLP24", "NLP25", "NLP26", "NLP27", "NLP28", "NLP29", "NLP30", "NLP31", "NLP32", "NLP33", "NLP34", "NLP35", "NLP36", "NLP37", "NLP38", "NLP39", "NLP40", "NLP41", "NLP42", "NLP43", "NLP44", "NLP45", "NLP46", "NLP47", "NLP48", "NLP49", "NLP50", "NLP51", "NLP52", "NLP53", "NLP54", "NLP55", "NLP56", "NLP57", "NLP58", "NLP59", "NLP60", "NLP61", "NLP62", "NLP63", "NLP64", "NLP65", "NLP66", "NLP67", "NLP68", "NLP69", "NLP70", "NLP71", "NLP72", "NLP73", "NLP74", "NLP75", "NLP76", "NLP77", "NLP78", "NLP79", "NLP80", "NLP81", "NLP82", "NLP83", "NLP84", "NLP85", "NLP86", "NLP87", "NLP88", "NLP89", "NLP90", "NLP91", "NLP92", "NLP93", "NLP94", "NLP95", "NLP96", "NLP97", "NLP98", "NLP99", "NLP100", "NLP101", "NLP102", "NLP103", "NLP104", "NLP105", "NLP106", "NLP107", "NLP108", "NLP109", "NLP110", "NLP111", "NLP112", "NLP113", "NLP114", "NLP115", "NLP116", "NLP117", "NLP118", "NLP119", "NLP120", "NLP121", "NLP122", "NLP123", "NLP124", "NLP125", "NLP126", "NLP127", "NLP128", "NLP129", "NLP130", "NLP131", "NLP132", "NLP133", "NLP134", "NLP135", "NLP136", "NLP137", "NLP138", "NLP139", "NLP140", "NLP141", "NLP142", "NLP143", "NLP144", "NLP145", "NLP146", "NLP147", "NLP148", "NLP149", "NLP150", "NLP151", "NLP152", "NLP153", "NLP154", "NLP155", "NLP156", "NLP157", "NLP158", "NLP159", "NLP160", "NLP161", "NLP162", "NLP163", "NLP164", "NLP165", "NLP166", "NLP167", "NLP168", "NLP169", "NLP170", "NLP171", "NLP172", "NLP173", "NLP174", "NLP175", "NLP176", "NLP177", "NLP178", "NLP179", "NLP180", "NLP181", "NLP182", "NLP183", "NLP184", "NLP185", "NLP186", "NLP187", "NLP188", "NLP189", "NLP190", "NLP191", "NLP192", "NLP193", "NLP194", "NLP195", "NLP196", "NLP197", "NLP198", "NLP199", "NLP200", "NLP201", "NLP202", "NLP203", "NLP204", "NLP205", "NLP206", "NLP207", "NLP208", "NLP209", "NLP210", "NLP211", "NLP212", "NLP213", "NLP214", "NLP215", "NLP216", "NLP217", "NLP218", "NLP219", "NLP220", "NLP221", "NLP222", "NLP223", "NLP224", "NLP225", "NLP226", "NLP227", "NLP228", "NLP229", "NLP230", "NLP231", "NLP232", "NLP233", "NLP234", "NLP235", "NLP236", "NLP237", "NLP238", "NLP239", "NLP240", "NLP241", "NLP242", "NLP243", "NLP244", "NLP245", "NLP246", "NLP247", "NLP248", "NLP249", "NLP250", "NLP251", "NLP252", "NLP253", "NLP254", "NLP255", "NLP256", "NLP257", "NLP258", "NLP259", "NLP260", "NLP261", "NLP262", "NLP263", "NLP264", "NLP265", "NLP266", "NLP267", "NLP268", "NLP269", "NLP270", "NLP271", "NLP272", "NLP273", "NLP274", "NLP275", "NLP276", "NLP277", "NLP278", "NLP279", "NLP280", "NLP281", "NLP282", "NLP283", "NLP284", "NLP285", "NLP286", "NLP287", "NLP288", "NLP289", "NLP290", "NLP291", "NLP292", "NLP293", "NLP294", "NLP295", "NLP296", "NLP297", "NLP298", "NLP299", "NLP300", "NLP301", "NLP302", "NLP303", "NLP304", "NLP305", "NLP306", "NLP307", "NLP308", "NLP309", "NLP310", "NLP311", "NLP312", "NLP313", "NLP314", "NLP315", "NLP316", "NLP317", "NLP318", "NLP319", "NLP320", "NLP321", "NLP322", "NLP323", "NLP324", "NLP325", "NLP326", "NLP327", "NLP328", "NLP329", "NLP330", "NLP331", "NLP332", "NLP333", "NLP334", "NLP335", "NLP336", "NLP337", "NLP338", "NLP339", "NLP340", "NLP341", "NLP342", "NLP343", "NLP344", "NLP345", "NLP346", "NLP347", "NLP348", "NLP349", "NLP350", "NLP351", "NLP352", "NLP353", "NLP354", "NLP355", "NLP356", "NLP357", "NLP358", "NLP359", "NLP360", "NLP361", "NLP362", "NLP363", "NLP364", "NLP365", "NLP366", "NLP367", "NLP368", "NLP369", "NLP370", "NLP371", "NLP372", "NLP373", "NLP374", "NLP375", "NLP376", "NLP377", "NLP378", "NLP379", "NLP380", "NLP381", "NLP382", "NLP383", "NLP384", "NLP385", "NLP386", "NLP387", "NLP388", "NLP389", "NLP390", "NLP391", "NLP392", "NLP393", "NLP394", "NLP395", "NLP396", "NLP397", "NLP398", "NLP399", "NLP400", "NLP401", "NLP402", "NLP403", "NLP404", "NLP405", "NLP406", "NLP407", "NLP408", "NLP409", "NLP410", "NLP411", "NLP412", "NLP413", "NLP414", "NLP415", "NLP416", "NLP417", "NLP418", "NLP419", "NLP420", "NLP421", "NLP422", "NLP423", "NLP424", "NLP425", "NLP426", "NLP427", "NLP428", "NLP429", "NLP430", "NLP431", "NLP432", "NLP433", "NLP434", "NLP435", "NLP436", "NLP437", "NLP438", "NLP439", "NLP440", "NLP441", "NLP442", "NLP443", "NLP444", "NLP445", "NLP446", "NLP447", "NLP448", "NLP449", "NLP450", "NLP451", "NLP452", "NLP453", "NLP454", "NLP455", "NLP456", "NLP457", "NLP458", "NLP459", "NLP460", "NLP461", "NLP462", "NLP463", "NLP464", "NLP465", "NLP466", "NLP467", "NLP468", "NLP469", "NLP470", "NLP471", "NLP472", "NLP473", "NLP474", "NLP475", "NLP476", "NLP477", "NLP478", "NLP479", "NLP480", "NLP481", "NLP482", "NLP483", "NLP484", "NLP485", "NLP486", "NLP487", "NLP488", "NLP489", "NLP490", "NLP491", "NLP492", "NLP493", "NLP494", "NLP495", "NLP496", "NLP497", "NLP498", "NLP499", "NLP500", "NLP501", "NLP502", "NLP503", "NLP504", "NLP505", "NLP506", "NLP507", "NLP508", "NLP509", "NLP510", "NLP511", "NLP512", "NLP513", "NLP514", "NLP515", "NLP516", "NLP517", "NLP518", "NLP519", "NLP520", "NLP521", "NLP522", "NLP523", "NLP524", "NLP525", "NLP526", "NLP527", "NLP528", "NLP529", "NLP530", "NLP531", "NLP532", "NLP533", "NLP534", "NLP535", "NLP536", "NLP537", "NLP538", "NLP539", "NLP540", "NLP541", "NLP542", "NLP543", "NLP544", "NLP545", "NLP546", "NLP547", "NLP548", "NLP549", "NLP550", "NLP551", "NLP552", "NLP553", "NLP554", "NLP555", "NLP556", "NLP557", "NLP558", "NLP559", "NLP560", "NLP561", "NLP562", "NLP563", "NLP564", "NLP565", "NLP566", "NLP567", "NLP568", "NLP569", "NLP570", "NLP571", "NLP572", "NLP573", "NLP574" ], "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": 6.041392685158225, "_indexed": true, "_nocasepkg": "phecap", "_universes": [ "celehs" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.2", "date": "2026-05-23T07:55:55.000Z", "distro": "noble", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "9dd04c881b0048da6d41b1b0e9deaa2babe23aeb39a910e3ecd64b795bc15132", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.6.0", "os": "linux", "version": "1.2.2", "date": "2026-05-23T07:55:59.000Z", "distro": "noble", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "eb0285f1f28984146b73027fac8723e58e45a0ff84d238e64e7f7c4664a69d13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.5.3", "os": "mac", "version": "1.2.2", "date": "2026-05-23T07:55:23.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "53aa850dad4252a7275a162b0da5e2cd96f61ec98a323f073eb1f7a96c966363", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.6.0", "os": "mac", "version": "1.2.2", "date": "2026-05-23T07:55:06.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "fbe3f245dbaf2f43a872688b33dae88e3ee96dfa055e845d7f4a0451e0f867bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.2", "date": "2026-05-23T07:56:17.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "5b9b1858839531d88016c5f0b2dfb1696cca5237e6453e48cb879113cb99b40d", "status": "success", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.7.0", "os": "win", "version": "1.2.2", "date": "2026-05-23T07:55:10.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "66c6469e3c3f606be7961ad2698e40554b6bc7573adbd897d2117642be8d52ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.5.3", "os": "win", "version": "1.2.2", "date": "2026-05-23T07:55:22.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "07fd90061f9c3cc4c743205c6d9fd7320526b6e37da5eb342eff6e442e374a11", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" }, { "r": "4.6.0", "os": "win", "version": "1.2.2", "date": "2026-05-23T07:55:08.000Z", "commit": "7c18179625c93f1058533aafedcae9480409da06", "fileid": "fd0eaee4b219f01effa2df79c7ca916b7ecc5dd2dc4a9583294f9d7cdd7cec53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/celehs/actions/runs/26327332309" } ] }