{ "_id": "6a290186732311cd87590d93", "Type": "Package", "Package": "PheVis", "Title": "Automatic Phenotyping of Electronic Health Record at Visit\nResolution", "Version": "1.0.4", "Date": "2023-10-20", "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 preprint by Ferté et al. (2020)\n.", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-10 06:08:51 UTC", "User": "root" }, "Author": "Thomas Ferte [aut, cre], Boris P. Hejblum [aut]", "Maintainer": "Thomas Ferte ", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://thomasferte.r-universe.dev", "Date/Publication": "2023-10-20 09:30:41 UTC", "RemoteUrl": "https://github.com/cran/PheVis", "RemoteRef": "HEAD", "RemoteSha": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "MD5sum": "97e5ad433cd761d68ff3fff051f5aa57", "_user": "thomasferte", "_type": "src", "_file": "PheVis_1.0.4.tar.gz", "_fileid": "376bbc490446ed06f1dcde90ad9bbfcec6f637fe4877397273cbf5e7220da3ee", "_filesize": 564315, "_sha256": "376bbc490446ed06f1dcde90ad9bbfcec6f637fe4877397273cbf5e7220da3ee", "_created": "2026-06-10T06:08:51.000Z", "_published": "2026-06-10T06:17:42.205Z", "_distro": "noble", "_jobs": [ { "job": 80493182771, "time": 179, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7527878358" }, { "job": 80493182848, "time": 183, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7527879057" }, { "job": 80493182808, "time": 208, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7527885921" }, { "job": 80493182804, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7527876161" }, { "job": 80493182782, "time": 163, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7527869468" }, { "job": 80493182792, "time": 479, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7527945535" }, { "job": 80493182793, "time": 197, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7527874475" }, { "job": 80493182784, "time": 376, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7527919926" }, { "job": 80492745801, "time": 211, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7527834495" }, { "job": 80493182786, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7527865172" }, { "job": 80493182858, "time": 169, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7527875379" }, { "job": 80493182769, "time": 176, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7527877205" }, { "job": 80493182794, "time": 151, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7527871259" } ], "_buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/PheVis", "_commit": { "id": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "author": "Thomas Ferte ", "committer": "cran-robot ", "message": "version 1.0.4\n", "time": 1697794241 }, "_maintainer": { "name": "Thomas Ferte", "email": "thomas.ferte@u-bordeaux.fr", "login": "thomasferte", "description": "", "uuid": 57225742 }, "_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": "purrr", "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": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "thomasferte", "count": 4, "uuid": 57225742 } ], "_userbio": { "uuid": 57225742, "type": "user", "name": "thomasferte" }, "_downloads": { "count": 185, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PheVis" }, "_searchresults": 3, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PheVis.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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" } ], "_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": "14.2.0-4ubuntu2~24.04.1", "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": "2021-02-16 08:20:02", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "phevis", "_universes": [ "thomasferte" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-06-10T06:11:19.000Z", "distro": "noble", "arch": "aarch64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "972c008df2579b563e1a8f935069d8ca41ac754ed777c817d6f8eee9320826ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-06-10T06:11:15.000Z", "distro": "noble", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "42438bc52a37f058277b9c560fd712467f776f2bbb9dbb48cca8311b08723b30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "linux", "version": "1.0.4", "date": "2026-06-10T06:11:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "b45a802f667cc1a218ac2b51fbb1f7bcdc54aa411cf228339a461d64b3487d4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "linux", "version": "1.0.4", "date": "2026-06-10T06:11:06.000Z", "distro": "noble", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "130248bbd291f6be0e0989f91e51dbe72ca4d854d60e84e911eb04f323c9fa99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-06-10T06:10:57.000Z", "arch": "aarch64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "3d316ea830d9ffa6a9290c1461ea661a96dda07111df9382e0408b0903995b92", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-06-10T06:14:31.000Z", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "17df8bee040c3dade52c98d73896ddbbd77113e801ad9831c3f2d6457b2ca4ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "mac", "version": "1.0.4", "date": "2026-06-10T06:11:10.000Z", "arch": "aarch64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "aa6781342b7737e8b55f28f30fb354ef69891439d6333fe1ee9ba82d113acf4e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "mac", "version": "1.0.4", "date": "2026-06-10T06:13:08.000Z", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "a635f0b4e32c28ed2516d31239120fa14baf96a41b1acf947cdcdc4f445a4625", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.4", "date": "2026-06-10T06:11:19.000Z", "arch": "emscripten", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "52d683e950b977e69da95ae7a85b0ddcab1270fcb4789f2097b20027ced21da3", "status": "success", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.7.0", "os": "win", "version": "1.0.4", "date": "2026-06-10T06:10:43.000Z", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "07c503c70d12f65473ecd7eff848894b9a0c62ee97bd3b0032652a1f1429166b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.5.3", "os": "win", "version": "1.0.4", "date": "2026-06-10T06:10:43.000Z", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "4a2c55a65abb1a432ed922470c3cdd7c9e4f2efebc8720e4e9e34ea004f0c328", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" }, { "r": "4.6.0", "os": "win", "version": "1.0.4", "date": "2026-06-10T06:10:14.000Z", "arch": "x86_64", "commit": "33d5ff29cce5105be54880a3d9fc308b7b653f86", "fileid": "5f0969efe75ee0fc06b7a58969c0e5542ef778c332ec950200516b9456973743", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/thomasferte/actions/runs/27256772524" } ] }