{ "_id": "6ae3c3aa3d0f299392dd1e95", "Type": "Package", "Package": "PheVis", "Title": "Automatic Phenotyping of Electronic Health Record at Visit\nResolution", "Version": "1.0.5", "Date": "2026-10-29", "Authors@R": "c(person(given = \"Thomas\",\nfamily = \"Ferte\",\nrole = c(\"aut\", \"cre\"),\nemail = \"thomas.ferte@u-bordeaux.fr\"),\nperson(given = \"Boris P.\",\nfamily = \"Hejblum\",\nrole = \"aut\",\nemail = \"boris.hejblum@u-bordeaux.fr\"))", "Description": "Using Electronic Health Record (EHR) is difficult because\nmost of the time the true characteristic of the patient is not\navailable. Instead we can retrieve the International\nClassification of Disease code related to the disease of\ninterest or we can count the occurrence of the Unified Medical\nLanguage System. None of them is the true phenotype which needs\nchart review to identify. However chart review is time\nconsuming and costly. 'PheVis' is an algorithm which is\nphenotyping (i.e identify a characteristic) at the visit level\nin an unsupervised fashion. It can be used for chronic or acute\ndiseases. An example of how to use 'PheVis' is available in the\nvignette. Basically there are two functions that are to be\nused: `train_phevis()` which trains the algorithm and\n`test_phevis()` which get the predicted probabilities. The\ndetailed method is described in Ferté et al. (2021)\n.", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 22:01:49 UTC", "User": "root" }, "Author": "Thomas Ferte [aut, cre], Boris P. Hejblum [aut]", "Maintainer": "Thomas Ferte ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-10-29 21:14:35 UTC", "RemoteUrl": "https://github.com/cran/PheVis", "RemoteRef": "HEAD", "RemoteSha": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "_user": "cran", "_type": "src", "_file": "PheVis_1.0.5.tar.gz", "_fileid": "https://r2.ropensci.org/31935de102310fee8468f3f80fb063ee706b31d36a26927deafd14259297abd8", "_filesize": 566016, "_sha256": "31935de102310fee8468f3f80fb063ee706b31d36a26927deafd14259297abd8", "_expires": "2027-02-06T22:07:36.000Z", "_created": "2026-10-29T22:01:49.000Z", "_published": "2026-10-29T22:07:38.519Z", "_upstream": "https://github.com/cran/PheVis", "_status": "success", "_maintainer": { "name": "Thomas Ferte", "email": "thomas.ferte@u-bordeaux.fr", "login": "thomasferte", "description": "", "uuid": 57225742 }, "_jobs": [ { "job": 123759310341, "time": 178, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "12935618454" }, { "job": 123759310335, "time": 181, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12936557497" }, { "job": 123759310385, "time": 149, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12935578502" }, { "job": 123759310344, "time": 169, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12935524972" }, { "job": 123757462605, "time": 240, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12936711719" }, { "job": 123759310314, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12936756780" }, { "job": 123759310416, "time": 294, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12936084250" }, { "job": 123759310355, "time": 167, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12936462705" }, { "job": 123759310342, "time": 298, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12935844495" }, { "job": 123759310471, "time": 149, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12936846483" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067", "_commit": { "id": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "author": "Thomas Ferte ", "committer": "cran-robot ", "message": "version 1.0.5\n", "time": 1793308475 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.3", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "PRROC", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-44", "n": 1 } ], "_tags": [ { "name": "1.0.5", "date": "2026-10-29" } ], "_stars": 1, "_contributors": [ { "user": "thomasferte", "count": 5, "uuid": 57225742 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 314, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PheVis" }, "_searchresults": 4, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/PheVis.html", "extra/readme.html", "extra/readme.md" ], "_realowner": "thomasferte", "_cranurl": false, "_releases": [ { "version": "1.0.1", "date": "2021-02-16" }, { "version": "1.0.2", "date": "2021-02-23" }, { "version": "1.0.3", "date": "2023-09-21" }, { "version": "1.0.4", "date": "2023-10-20" }, { "version": "1.0.5", "date": "2026-10-29" } ], "_exports": [ "ggindividual_plot", "test_phevis", "train_phevis" ], "_datasets": [ { "name": "data_perf", "title": "Control data for test", "object": "data_perf", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "data_phevis", "title": "PheVis simulated dataset", "object": "data_phevis", "class": [ "data.frame" ], "fields": [ "subject", "time", "PR_state", "mainICD", "mainCUI", "var1", "var2", "var3", "var4", "var5", "var6", "var7", "var8", "var9", "var10" ], "rows": 19659, "table": true, "tojson": true } ], "_help": [ { "page": "boot_df", "title": "boot_df", "topics": [ "boot_df" ] }, { "page": "build_qantsur", "title": "build_qantsur", "topics": [ "build_qantsur" ] }, { "page": "build_quali", "title": "build_quali", "topics": [ "build_quali" ] }, { "page": "check_arg_test_phevis", "title": "check_arg_test_phevis", "topics": [ "check_arg_test_phevis" ] }, { "page": "check_arg_train_phevis", "title": "check_arg_train_phevis", "topics": [ "check_arg_train_phevis" ] }, { "page": "cum_lag", "title": "cum_lag", "topics": [ "cum_lag" ] }, { "page": "data_perf", "title": "Control data for test", "topics": [ "data_perf" ] }, { "page": "data_phevis", "title": "PheVis simulated dataset", "topics": [ "data_phevis" ] }, { "page": "expcorrectC", "title": "expcorrectC", "topics": [ "expcorrectC" ] }, { "page": "fct_surrogate_quanti", "title": "fct_surrogate_quanti", "topics": [ "fct_surrogate_quanti" ] }, { "page": "ggindividual_plot", "title": "ggindividual_plot", "topics": [ "ggindividual_plot" ] }, { "page": "matrix_exp_smooth", "title": "matrix_exp_smooth", "topics": [ "matrix_exp_smooth" ] }, { "page": "noising", "title": "noising", "topics": [ "noising" ] }, { "page": "norm_var", "title": "norm_var", "topics": [ "norm_var" ] }, { "page": "phenorm_longit_fit", "title": "phenorm_longit_fit", "topics": [ "phenorm_longit_fit" ] }, { "page": "phenorm_longit_simpl", "title": "phenorm_longit_simpl", "topics": [ "phenorm_longit_simpl" ] }, { "page": "pred_lme4model", "title": "pred_lme4model", "topics": [ "pred_lme4model" ] }, { "page": "pretty_cv.glmnet", "title": "pretty_cv.glmnet", "topics": [ "pretty_cv.glmnet" ] }, { "page": "roll_time_sum", "title": "roll_time_sum", "topics": [ "roll_time_sum" ] }, { "page": "rolling_var", "title": "rolling_var", "topics": [ "rolling_var" ] }, { "page": "safe_selection", "title": "safe_selection", "topics": [ "safe_selection" ] }, { "page": "sur_exp_smooth", "title": "sur_exp_smooth", "topics": [ "sur_exp_smooth" ] }, { "page": "test_phevis", "title": "test_phevis", "topics": [ "test_phevis" ] }, { "page": "train_phevis", "title": "train_phevis", "topics": [ "train_phevis" ] } ], "_readme": "https://github.com/cran/PheVis/raw/HEAD/README.md", "_rundeps": [ "boot", "cli", "codetools", "cpp11", "dplyr", "evaluate", "farver", "foreach", "generics", "ggplot2", "glmnet", "glue", "gridExtra", "gtable", "highr", "isoband", "iterators", "knitr", "labeling", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "minqa", "nlme", "nloptr", "pillar", "pkgconfig", "purrr", "R6", "randomForest", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "reformulas", "rlang", "S7", "scales", "shape", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "TutoPheVis.Rmd", "filename": "TutoPheVis.html", "title": "Tuto PheVis", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Toy dataset", "Train PheVis", "Test PheVis", "Results", "train_model", "test_model", "plot predictions", "Performances" ], "created": "2021-02-16 08:20:02", "modified": "2026-10-29 21:14:35", "commits": 2 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "phevis", "_universes": [ "cran" ], "_indexurl": "https://thomasferte.r-universe.dev/PheVis", "_previous": "1.0.4", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-10-29T22:04:25.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/08f31fefb625b143e184eaf29653f85f8e6c815431fa241d70bb9e1704111ac1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-10-29T22:04:06.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/fbfb71b5b9a948cd9c9683463aef810b2bdc1a785c5cec2f82e77646d652a3fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.6.1", "os": "linux", "version": "1.0.5", "date": "2026-10-29T22:03:53.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/f5d73333930889444fd6c33429114a59611263408128b733033768ee206160c5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.6.1", "os": "linux", "version": "1.0.5", "date": "2026-10-29T22:04:00.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/f512bc3175532d7cf34a612ff44ef67bb61a4255a0414287e2d7e53e18089a07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.5", "date": "2026-10-29T22:04:06.000Z", "arch": "emscripten", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/12e84d9300fe5f297b853d24c5d9f17b2f4f51a5fed5061d56077a840e6b73f0", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.7.0", "os": "win", "version": "1.0.5", "date": "2026-10-29T22:05:47.000Z", "arch": "aarch64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/454e67e7020eac5a48ab62f1c1945a167cb0449ebdeabf86369f1dd795cb029b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.7.0", "os": "win", "version": "1.0.5", "date": "2026-10-29T22:03:15.000Z", "arch": "x86_64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/69aefde20d579cd501aaf44b74f200c4d20e562c7c17339abac84b98a1dc930b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.6.1", "os": "win", "version": "1.0.5", "date": "2026-10-29T22:06:01.000Z", "arch": "aarch64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/091577c5ce9b1f1f2a5e6e21bce3ace5def22957302d7951b26ac91829abe399", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" }, { "r": "4.6.1", "os": "win", "version": "1.0.5", "date": "2026-10-29T22:03:13.000Z", "arch": "x86_64", "commit": "d6c44d3e4da401df8a1fd014e92218bdcb7c4bfa", "fileid": "https://r2.ropensci.org/01f1f47117ff2cfe15b892f63fae558ff2f885662f34c0b12ac777d08e03248c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40962114067" } ] }