{ "_id": "6a59c93f09eb0996dd68dcea", "Package": "apmx", "Type": "Package", "Title": "Automated Population Pharmacokinetic Dataset Assembly", "Version": "1.1.1", "Date": "2024-01-05", "Authors@R": "c(\nperson(\"Stephen\", \"Amori\", email=\"stephen.amori@amadorbio.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Ethan\", \"DellaMaestra\", email=\"ethan.dellamaestra@amadorbio.com\", role = c(\"aut\")),\nperson(\"Michael\", \"Dick\", email=\"michael.dick@amadorbio.com\", role=c(\"aut\")),\nperson(\"Daniel\", \"Litow\", role = c(\"ctb\")),\nperson(\"Jonah\", \"Lyon\", role = c(\"ctb\"))\n)", "Maintainer": "Stephen Amori ", "Description": "Automated methods to assemble population PK\n(pharmacokinetic) and PKPD (pharmacodynamic) datasets for\nanalysis in 'NONMEM' (non-linear mixed effects modeling) by\nBauer (2019) . The package includes\nfunctions to build datasets from SDTM (study data tabulation\nmodule) ,\nADaM (analysis dataset module)\n, or other\ndataset formats. The package will combine population datasets,\nadd covariates, and create documentation to support regulatory\nsubmission and internal communication.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.0", "URL": "https://github.com/stephen-amori/apmx", "BugReports": "https://github.com/stephen-amori/apmx/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev make libharfbuzz-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev", "Repository": "https://stephen-amori.r-universe.dev", "Date/Publication": "2024-01-18 21:04:58 UTC", "RemoteUrl": "https://github.com/stephen-amori/apmx", "RemoteRef": "HEAD", "RemoteSha": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-17 06:14:33 UTC", "User": "root" }, "Author": "Stephen Amori [aut, cre, cph],\nEthan DellaMaestra [aut],\nMichael Dick [aut],\nDaniel Litow [ctb],\nJonah Lyon [ctb]", "_user": "stephen-amori", "_type": "src", "_file": "apmx_1.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/86ac723ae4ea5a59e8ae7e8bd963637804a88b58a21c653efd1f3d25f6b01b37", "_filesize": 350487, "_sha256": "86ac723ae4ea5a59e8ae7e8bd963637804a88b58a21c653efd1f3d25f6b01b37", "_expires": "2026-10-25T06:18:38.000Z", "_created": "2026-07-17T06:14:33.000Z", "_published": "2026-07-17T06:18:39.850Z", "_jobs": [ { "job": 87818722579, "time": 175, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8398737050" }, { "job": 87818722566, "time": 207, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8398746126" }, { "job": 87818722580, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8398732074" }, { "job": 87818722577, "time": 128, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8398719055" }, { "job": 87818124156, "time": 256, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8398686784" }, { "job": 87818722578, "time": 152, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8398729912" }, { "job": 87818722565, "time": 110, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8398718836" }, { "job": 87818722590, "time": 135, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8398726677" }, { "job": 87818722603, "time": 130, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8398724856" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371", "_status": "success", "_upstream": "https://github.com/stephen-amori/apmx", "_commit": { "id": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "author": "Stephen Amori ", "committer": "Stephen Amori ", "message": "uploaded pkgdown.yml\n", "time": 1705611898 }, "_maintainer": { "name": "Stephen Amori", "email": "stephen.amori@amadorbio.com", "login": "stephen-amori", "description": "", "uuid": 128187850 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.00", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "this.path", "role": "Imports" }, { "package": "flextable", "role": "Imports" }, { "package": "officer", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "arsenal", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" } ], "_owner": "stephen-amori", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 7, "_contributors": [ { "user": "stephen-amori", "count": 31, "uuid": 128187850 }, { "user": "michaeld96", "count": 2, "uuid": 44264982 } ], "_userbio": { "uuid": 128187850, "type": "user", "name": "Stephen Amori", "followers": 2 }, "_downloads": { "count": 267, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/apmx" }, "_devurl": "https://github.com/stephen-amori/apmx", "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/apmx.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/stephen-amori/apmx", "_realowner": "stephen-amori", "_cranurl": true, "_releases": [ { "version": "1.1.1", "date": "2024-01-09" } ], "_exports": [ "cov_apply", "cov_find", "pk_build", "pk_combine", "pk_define", "pk_summarize", "pk_write", "variable_list_create", "version_log" ], "_datasets": [ { "name": "DM", "title": "DM", "object": "DM", "class": [ "data.frame" ], "fields": [ "STUDYID", "SITEID", "SUBJID", "USUBJID", "SCRFL", "ICFDT", "ICFDTC", "DOBDT", "AGE", "SEX", "RACE", "ETHNIC" ], "rows": 22, "table": true, "tojson": true }, { "name": "EX", "title": "EX", "object": "EX", "class": [ "data.frame" ], "fields": [ "STUDYID", "SITEID", "USUBJID", "EXCAT", "VISIT", "EXSTDY", "VISCRFN", "EXTRT", "EXDOSE", "EXDOSU", "EXROUTE", "EXDOSFRQ", "EXDT", "EXDTC", "EXTM", "EXTMC", "EXSTDTC", "EXTPT", "EXTPTNUM" ], "rows": 42, "table": true, "tojson": true }, { "name": "LB", "title": "LB", "object": "LB", "class": [ "data.frame" ], "fields": [ "STUDYID", "SITEID", "USUBJID", "LBCAT", "LBCOMPFL", "LBDT", "LBVST", "VISCRFN", "LBTPT", "LBTPTN", "LBPARAMCD", "LBPARAM", "LBPARAMN", "LBORRES", "LBORRESC", "LBORRESU" ], "rows": 2159, "table": true, "tojson": true }, { "name": "PC", "title": "PC", "object": "PC", "class": [ "data.frame" ], "fields": [ "STUDYID", "SITEID", "USUBJID", "PCCAT", "PCTEST", "VISIT", "PCDY", "VISCRFN", "PCTPT", "PCTPTN", "PCSTAT", "PCDT", "PCTM", "PCTMC", "PCDTC", "PCORRES", "PCORRESU", "PCSTRESN", "PCSTRESC", "PCSTRESU", "PCLLOQ" ], "rows": 420, "table": true, "tojson": true }, { "name": "VL", "title": "VL", "object": "VL", "class": [ "data.frame" ], "fields": [ "Variable", "Categorization", "Description", "Comment" ], "rows": 66, "table": true, "tojson": true } ], "_help": [ { "page": "cov_apply", "title": "Apply covariates to PK(PD) dataset", "topics": [ "cov_apply" ] }, { "page": "cov_find", "title": "Find covariates of particular types", "topics": [ "cov_find" ] }, { "page": "DM", "title": "DM", "topics": [ "DM" ] }, { "page": "EX", "title": "EX", "topics": [ "EX" ] }, { "page": "LB", "title": "LB", "topics": [ "LB" ] }, { "page": "PC", "title": "PC", "topics": [ "PC" ] }, { "page": "pk_build", "title": "Create a NONMEM PK(PD) dataset", "topics": [ "pk_build" ] }, { "page": "pk_combine", "title": "combine study level datasets to form population dataset", "topics": [ "pk_combine" ] }, { "page": "pk_define", "title": "Create definition file from published dataset", "topics": [ "pk_define" ] }, { "page": "pk_summarize", "title": "Produce summary tables for a PK(PD) dataset", "topics": [ "pk_summarize" ] }, { "page": "pk_write", "title": "Write PK(PD) dataset to specified location", "topics": [ "pk_write" ] }, { "page": "variable_list_create", "title": "Create a dataframe with standard variable names and definitions", "topics": [ "variable_list_create" ] }, { "page": "version_log", "title": "Create and maintain a dataset version log", "topics": [ "version_log" ] }, { "page": "VL", "title": "VL", "topics": [ "VL" ] } ], "_readme": "https://github.com/stephen-amori/apmx/raw/HEAD/README.md", "_rundeps": [ "arsenal", "askpass", "base64enc", "bslib", "cachem", "cli", "cpp11", "data.table", "digest", "dplyr", "evaluate", "fastmap", "flextable", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "glue", "highr", "htmltools", "jquerylib", "jsonlite", "knitr", "lifecycle", "magrittr", "memoise", "mime", "officer", "openssl", "pillar", "pkgconfig", "purrr", "R6", "ragg", "rappdirs", "Rcpp", "rlang", "rmarkdown", "sass", "stringi", "stringr", "sys", "systemfonts", "textshaping", "this.path", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "uuid", "vctrs", "withr", "xfun", "xml2", "yaml", "zip" ], "_vignettes": [ { "source": "Dataset_assembly_and_documentation_for_PK_and_PKPD_analysis.Rmd", "filename": "Dataset_assembly_and_documentation_for_PK_and_PKPD_analysis.html", "title": "PKPD_analysis", "engine": "knitr::rmarkdown", "headings": [ "PK(PD) dataset assembly with the apmx library", "Prepare workspace and load data", "Background", "Dose event preparation", "PK observation event preparation", "Simple dataset assembly", "Covariate preparation", "PD observation preparation", "Full dataset assembly", "Other covariate methods", "Errors and warnings", "Errors", "Warnings", "Time imputations", "Dataset combination", "Dataset documentation" ], "created": "2023-12-15 15:17:16", "modified": "2023-12-15 15:17:16", "commits": 1 } ], "_score": 4.544068044350276, "_indexed": true, "_nocasepkg": "apmx", "_universes": [ "stephen-amori" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-07-17T06:17:02.000Z", "distro": "resolute", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/31efb23764dceb7e145203e632e8c8dbaf407414ad394a015f84ffd9b3bb497f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1", "date": "2026-07-17T06:17:43.000Z", "distro": "resolute", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/f7ee49f105ad496635d7d3824e830bd66aefe51ec8567824db7acf4fb5d229b1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-07-17T06:17:01.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/871b1aa3cf3d0cc8526eaeba9b36ac9000fd47b635a3d49bfc82c129db47d48b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.6.1", "os": "mac", "version": "1.1.1", "date": "2026-07-17T06:16:18.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/9eb56a84290ed5b55c201a55b088875b86cdef6b811cf887acd7fa6173bdfa82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-07-17T06:17:19.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/133fd549db8c0a5d19bd08f0e76e447888a240950ebf2504f0e28b87841c32ac", "status": "success", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-07-17T06:15:45.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/880c1698fe8a146a82b83ebe87bb3ca8339d81f738e7c06abeed4f785a515662", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-07-17T06:16:16.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/9f6a80ad333a68fb758cb802f82bab0062ddeb3331679b4b51f37ee1bbd286ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" }, { "r": "4.6.1", "os": "win", "version": "1.1.1", "date": "2026-07-17T06:16:11.000Z", "commit": "571d5287014e59cbf57e6ba6e4fe4018dbd493bf", "fileid": "https://r2.ropensci.org/3932ea044cd544278697b60bb93c9520aae0e7b408e13061bd954d8d71cbcdca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephen-amori/actions/runs/29559281371" } ] }