{ "_id": "6a1d3a6f1d7bb097a0a3eacf", "Package": "ggPMX", "Title": "'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME\nModels", "Description": "At Novartis, we aimed at standardizing the set of\ndiagnostic plots used for modeling activities in order to\nreduce the overall effort required for generating such plots.\nFor this, we developed a guidance that proposes an adequate set\nof diagnostics and a toolbox, called 'ggPMX' to execute them.\n'ggPMX' is a toolbox that can generate all diagnostic plots at\na quality sufficient for publication and submissions using few\nlines of code. This package focuses on plots recommended by\nISoP . While not required, you can\nget/install the 'R' 'lixoftConnectors' package in the 'Monolix'\ninstallation, as described at the following url\n.\nWhen 'lixoftConnectors' is available, 'R' can use 'Monolix'\ndirectly to create the required Chart Data instead of exporting\nit from the 'Monolix' gui.", "Version": "1.3.1", "Authors@R": "c(\nperson(\"Amine\", \"Gassem\", email=\"contact@ag-study.com\", role=c(\"aut\")),\nperson(\"Bruno\", \"Bieth\", email=\"biethb@hotmail.com\", role=\"aut\"),\nperson(\"Irina\", \"Baltcheva\", email=\"irina.baltcheva@gmail.com\", role=\"aut\"),\nperson(\"Thomas\", \"Dumortier\", email=\" thomas.dumortier@novartis.com\", role=\"aut\"),\nperson(\"Christian\", \"Bartels\", email=\"christian.bartels@novartis.com\", role=\"aut\"),\nperson(\"Souvik\", \"Bhattacharya\", email=\"souvik.bhattacharya@novartis.com\", role=\"aut\"),\nperson(\"Inga\", \"Ludwig\", email=\"inga.ludwig@novartis.com\", role=\"aut\"),\nperson(\"Ines\", \"Paule\", email=\"ines.paule@novartis.com\", role=\"aut\"),\nperson(\"Didier\", \"Renard\", email=\"didier.renard@novartis.com\", role=\"aut\"),\nperson(\"Matthew\",\"Fidler\", role = c(\"aut\"), email = \"matt.fidler@novartis.com\", comment=c(ORCID=\"0000-0001-8538-6691\")),\nperson(\"Seid\", \"Hamzic\", email = \"se.hamzic@gmail.com\",role =\"aut\"),\nperson(\"Benjamin\", \"Guiastrennec\", email = \"guiastrennec@gmail.com\",role =\"ctb\"),\nperson(\"Kyle T\", \"Baron\", email = \"kyleb@metrumrg.com\",role =\"ctb\", comment = c(ORCID = \"0000-0001-7252-5656\")),\nperson(\"Qing Xi\", \"Ooi\", email=\"ooi.qingxi@gmail.com\", role=\"ctb\"),\nperson(\"Aleksandr\",\"Pogodaev\", role = c(\"aut\", \"cre\"), email = \"alex.pogodaev@novartis.com\", comment=c(ORCID=\"0000-0002-1371-207X\")),\nperson(\"Danielle\", \"Navarro\", role = c(\"aut\"), email = \"djnavarro@protonmail.com\"),\nperson(\"Ibtissem\", \"Rebai\", email=\"ibtissem.rebai@certara.com\", role=\"ctb\"),\nperson(\"Mahmoud\", \"Ali\", email=\"mahmoud.ali@certara.com\", role=\"ctb\"),\nperson(\"Novartis Pharma AG\", role = c(\"cph\"))\n)", "URL": "https://github.com/ggPMXdevelopment/ggPMX", "BugReports": "https://github.com/ggPMXdevelopment/ggPMX/issues", "License": "GPL-2", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev make\nlibicu-dev libuv1-dev libssl-dev libx11-dev", "Repository": "https://ggpmxdevelopment.r-universe.dev", "Date/Publication": "2025-09-02 11:58:04 UTC", "RemoteUrl": "https://github.com/ggpmxdevelopment/ggpmx", "RemoteRef": "HEAD", "RemoteSha": "dbc53ffdbf385920e8dc0fe1197408d54434b62e", "Packaged": { "Date": "2026-06-01 07:39:09 UTC", "User": "root" }, "Author": "Amine Gassem [aut],\nBruno Bieth [aut],\nIrina Baltcheva [aut],\nThomas Dumortier [aut],\nChristian Bartels [aut],\nSouvik Bhattacharya [aut],\nInga Ludwig [aut],\nInes Paule [aut],\nDidier Renard [aut],\nMatthew Fidler [aut] (ORCID: ),\nSeid Hamzic [aut],\nBenjamin Guiastrennec [ctb],\nKyle T Baron [ctb] (ORCID: ),\nQing Xi Ooi [ctb],\nAleksandr Pogodaev [aut, cre] (ORCID:\n),\nDanielle Navarro [aut],\nIbtissem Rebai [ctb],\nMahmoud Ali [ctb],\nNovartis Pharma AG [cph]", "Maintainer": "Aleksandr Pogodaev ", "MD5sum": "76009de0bb3e8767d4d6e7e0311b259b", "_user": "ggpmxdevelopment", "_type": "src", "_file": "ggPMX_1.3.1.tar.gz", "_fileid": "ea51310d259bd3d96808d0552d012af1bbe426174ad12e4617ae33aa5911fc93", "_filesize": 8138330, "_sha256": "ea51310d259bd3d96808d0552d012af1bbe426174ad12e4617ae33aa5911fc93", "_created": "2026-06-01T07:39:09.000Z", "_published": "2026-06-01T07:53:19.247Z", "_distro": "noble", "_jobs": [ { "job": 78807136299, "time": 490, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7325997808" }, { "job": 78807136347, "time": 602, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7326034044" }, { "job": 78807136300, "time": 443, 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"_commit": { "id": "dbc53ffdbf385920e8dc0fe1197408d54434b62e", "author": "ggPMXdevelopment <49687660+ggPMXdevelopment@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #405 from ggPMXdevelopment/develop\n\nBump to 1.3.1", "time": 1756814284 }, "_maintainer": { "name": "Aleksandr Pogodaev", "email": "alex.pogodaev@novartis.com", "orcid": "0000-0002-1371-207X" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "yaml", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "gtable", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "ggforce", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "zoo", "role": 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"version": "1.3.2", "date": "2025-09-05" } ], "_exports": [ "%>%", "abbrev", "check_shrink", "get_abbrev", "get_cats", "get_conts", "get_covariates", "get_data", "get_occ", "get_plot", "get_plot_config", "get_strats", "getPmxOption", "is.pmx_gpar", "load_config", "load_source", "param_table", "parse_mlxtran", "pk_occ", "pk_pd", "plot_names", "plot_pmx", "plots", "pmx", "pmx_bloq", "pmx_comp_shrink", "pmx_config", "pmx_copy", "pmx_cov", "pmx_endpoint", "pmx_filter", "pmx_get_configs", "pmx_gpar", "pmx_mlx", "pmx_mlxtran", "pmx_nlmixr", "pmx_nm", "pmx_plot", "pmx_plot_abs_iwres_ipred", "pmx_plot_abs_iwres_time", "pmx_plot_cats", "pmx_plot_cwres_cpred", "pmx_plot_cwres_pred", "pmx_plot_cwres_qq", "pmx_plot_cwres_time", "pmx_plot_dv_ipred", "pmx_plot_dv_pred", "pmx_plot_eta_box", "pmx_plot_eta_cats", "pmx_plot_eta_conts", "pmx_plot_eta_hist", "pmx_plot_eta_matrix", "pmx_plot_eta_qq", "pmx_plot_individual", "pmx_plot_iwres_dens", "pmx_plot_iwres_ipred", "pmx_plot_iwres_qq", "pmx_plot_iwres_time", "pmx_plot_npd_epred", "pmx_plot_npd_pred", "pmx_plot_npd_qq", "pmx_plot_npd_time", "pmx_plot_npde_pred", "pmx_plot_npde_qq", "pmx_plot_npde_time", "pmx_plot_saem_convergence", "pmx_plot_vpc", "pmx_register_plot", "pmx_report", "pmx_report_template", "pmx_settings", "pmx_shrink", "pmx_sim", "pmx_theme", "pmx_update", "pmx_vpc", "pmx_vpc_bin", "pmx_vpc_ci", "pmx_vpc_obs", "pmx_vpc_pi", "pmx_vpc_rug", "pmxOptions", "read_extfile", "set_abbrev", "set_data", "set_plot", "theophylline" ], "_help": [ { "page": "sub-.pmx_gpar", "title": "Method for subsetting \"pmx_gpar\" objects", "topics": [ "[.pmx_gpar" ] }, { "page": "abbrev", "title": "Give the whole abbreviation definition", "topics": [ "abbrev" ] }, { "page": "add_draft", "title": "Add draft layer annotation", "topics": [ "add_draft" ] }, { "page": "check_shrink", "title": "Performs checks of names in shrink list", "topics": [ "check_shrink" ] }, { "page": "distrib", "title": "creates a graphic distribution object", "concept": [ "plot_pmx" ], "topics": [ "distrib" ] }, { "page": "eta_cov", "title": "This creates an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkage..", "concept": [ "plot_pmx" ], "topics": [ "eta_cov" ] }, { "page": "eta_cov_plot", "title": "Eta Covariates plots", "concept": [ "eta_cov_plot" ], "topics": [ "dummy", "eta_cov_plot", "pmx_plot_eta_cats", "pmx_plot_eta_conts" ] }, { "page": "eta_distribution_plot", "title": "Eta distribution plots", "concept": [ "eta_distribution_plot" ], "topics": [ "eta_distribution_plot", "pmx_plot_eta_box", "pmx_plot_eta_hist" ] }, { "page": "eta_pairs", "title": "This creates an eta correlation which defines the relationship between parameters", "concept": [ "plot_pmx" ], "topics": [ "eta_pairs" ] }, { "page": "eval_sym_parent_env", "title": "Try to evaluate a symbol in the parent frame (on error return the symbol)", "topics": [ "eval_sym_parent_env" ] }, { "page": "get_abbrev", "title": "Get abbreviation definition by key", "topics": [ "get_abbrev" ] }, { "page": "get_cats", "title": "Get category covariates", "concept": [ "pmxclass" ], "topics": [ "get_cats" ] }, { "page": "get_conts", "title": "Get continuous covariates", "concept": [ "pmxclass" ], "topics": [ "get_conts" ] }, { "page": "get_covariates", "title": "Get covariates variables", "concept": [ "pmxclass" ], "topics": [ "get_covariates" ] }, { "page": "get_data", "title": "Get controller data set", "concept": [ "pmxclass" ], "topics": [ "get_data" ] }, { "page": "get_occ", "title": "Get controller occasional covariates", "concept": [ "pmxclass" ], "topics": [ "get_occ" ] }, { "page": "get_plot", "title": "Get plot object", "concept": [ "pmxclass" ], "topics": [ "get_plot" ] }, { "page": "get_plot_config", "title": "Get the plot config by name", "concept": [ "pmxclass" ], "topics": [ "get_plot_config" ] }, { "page": "get_strats", "title": "Get extra stratification variables", "concept": [ "pmxclass" ], "topics": [ "get_strats" ] }, { "page": "getPmxOption", "title": "Get ggPMX Option", "topics": [ "getPmxOption" ] }, { "page": "gtable_remove_grobs", "title": "Remove named elements from gtable", "topics": [ "gtable_remove_grobs" ] }, { "page": "individual", "title": "This function can be used to obtain individual prediction and compare with observed data and population prediction for each individual separately", "concept": [ "plot_pmx" ], "topics": [ "individual" ] }, { "page": "input_finegrid", "title": "Merge input and fingrid data sets", "topics": [ "input_finegrid" ] }, { "page": "is.pmx_gpar", "title": "Check if an object is a pmx_gpar class", "topics": [ "is.pmx_gpar" ] }, { "page": "l_left_join", "title": "Merge 2 lists", "topics": [ "l_left_join" ] }, { "page": "load_config", "title": "Obtain the data source config", "topics": [ "load_config" ] }, { "page": "load_data_set", "title": "Load data set", "topics": [ "load_data_set" ] }, { "page": "load_source", "title": "Load all/or some source data set", "topics": [ "load_source" ] }, { "page": "n_pages", "title": "Determine the number of pages in a paginated facet plot", "topics": [ "n_pages" ] }, { "page": "param_table", "title": "Creates parameter kable", "topics": [ "param_table" ] }, { "page": "parse_mlxtran", "title": "Parse MONOLIX mlxtran file", "topics": [ "parse_mlxtran" ] }, { "page": "pk_occ", "title": "Creates pmx controller using monlix data having Occasional variable", "topics": [ "pk_occ" ] }, { "page": "pk_pd", "title": "Creates pkpd pmx controller using package internal data", "topics": [ "pk_pd" ] }, { "page": "plot_names", "title": "Get plot names", "concept": [ "pmxclass" ], "topics": [ "plot_names" ] }, { "page": "plot_pmx", "title": "This is a generic plot method that produces all plots by default described in pmx model evaluation guidance.", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx", "plot_pmx.pmx_vpc" ] }, { "page": "plot_pmx.distrib", "title": "Plot EBE distribution", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.distrib" ] }, { "page": "plot_pmx.eta_cov", "title": "This plots an ETA covariance matrix which can be used to define the co-relation between the parameters and its shrinkage", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.eta_cov" ] }, { "page": "plot_pmx.eta_pairs", "title": "Plot random effect correlation plot", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.eta_pairs" ] }, { "page": "plot_pmx.individual", "title": "This function can be used to plot individual prediction and compare with observed data and population prediction for each individual separately", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.individual" ] }, { "page": "plot_pmx.pmx_dens", "title": "This function plots EBE versus covariates using qq plots", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.pmx_dens" ] }, { "page": "plot_pmx.pmx_gpar", "title": "The ggPMX base plot function", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.pmx_gpar" ] }, { "page": "plot_pmx.pmx_param_history", "title": "S3 method for plots of class pmx_param_history", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.pmx_param_history" ] }, { "page": "plot_pmx.pmx_qq", "title": "This function plot EBE versus covariates using qq plots", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.pmx_qq" ] }, { "page": "plot_pmx.residual", "title": "This function plots residual for each observed value by finding the difference between observed and predicted points. It also fits a distribution to the residual value.", "concept": [ "plot_pmx" ], "topics": [ "plot_pmx.residual" ] }, { "page": "plot_shrink", "title": "Plot shrink in eta matric", "topics": [ "plot_shrink" ] }, { "page": "plots", "title": "Get plots description", "concept": [ "pmxclass" ], "topics": [ "plots" ] }, { "page": "pmx", "title": "Create a pmx object", "topics": [ "pmx", "pmx_mlx", "pmx_mlxtran" ] }, { "page": "pmx_bloq", "title": "Creates BLOQ object attributes", "topics": [ "pmx_bloq" ] }, { "page": "pmx_comp_shrink", "title": "Compute Shrinkage", "topics": [ "pmx_comp_shrink" ] }, { "page": "pmx_config", "title": "This function can be used to define the pmx configuration used in plots. e.g. Monolix/Nonmem", "topics": [ "pmx_config" ] }, { "page": "pmx_copy", "title": "Creates a deep copy of the controller", "topics": [ "pmx_copy" ] }, { "page": "pmx_cov", "title": "Select/Map covariates using human labels", "topics": [ "pmx_cov" ] }, { "page": "pmx_dens", "title": "Creates a density plot object", "topics": [ "pmx_dens" ] }, { "page": "pmx_endpoint", "title": "Creates pmx endpoint object", "topics": [ "pmx_endpoint" ] }, { "page": "pmx_filter", "title": "filter data in a pmx controller", "topics": [ "pmx_filter" ] }, { "page": "pmx_get_configs", "title": "Get List of built-in configurations", "topics": [ "pmx_get_configs" ] }, { "page": "pmx_gpar", "title": "Handling pmx Graphical parameters", "topics": [ "pmx_gpar" ] }, { "page": "pmx_list_nm_tables", "title": "List NONMEM output tables", "topics": [ "pmx_list_nm_tables" ] }, { "page": "pmx_manual_nm_import", "title": "Manually define nonmem tables to be imported", "topics": [ "pmx_manual_nm_import" ] }, { "page": "pmx_nlmixr", "title": "Creates pmx controller from an nlimxr fit object", "topics": [ "pmx_nlmixr" ] }, { "page": "pmx_nm", "title": "Creates pmx controller from NONMEM model outputs", "topics": [ "pmx_nm" ] }, { "page": "pmx_plot", "title": "Generic pmx plot", "topics": [ "pmx_plot" ] }, { "page": "pmx_plot_cats", "title": "Generic pmx stratified plot", "topics": [ "pmx_plot_cats" ] }, { "page": "pmx_plot_eta_matrix", "title": "Eta matrix plot", "topics": [ "pmx_plot_eta_matrix" ] }, { "page": "pmx_plot_individual", "title": "Individual plot", "topics": [ "pmx_plot_individual" ] }, { "page": "pmx_plot_iwres_dens", "title": "IWRES density plot", "topics": [ "pmx_plot_iwres_dens" ] }, { "page": "pmx_plot_saem_convergence", "title": "SAEM Convergence Plot", "topics": [ "pmx_plot_saem_convergence" ] }, { "page": "pmx_plot_vpc", "title": "VPC plot", "concept": [ "vpc" ], "topics": [ "pmx_plot_vpc" ] }, { "page": "pmx_qq", "title": "This function creates a qq plot object", "concept": [ "qq_plot" ], "topics": [ "pmx_qq" ] }, { "page": "pmx_qq_plot", "title": "Quantile-quantile plots", "concept": [ "qqq" ], "topics": [ "pmx_plot_cwres_qq", "pmx_plot_eta_qq", "pmx_plot_iwres_qq", "pmx_plot_npde_qq", "pmx_plot_npd_qq", "pmx_qq_plot" ] }, { "page": "pmx_read_nm_files", "title": "NONMEM output file import function", "topics": [ "pmx_read_nm_files" ] }, { "page": "pmx_read_nm_model", "title": "NONMEM model file parser", "topics": [ "pmx_read_nm_model" ] }, { "page": "pmx_read_nm_tables", "title": "NONMEM output table import function", "topics": [ "pmx_read_nm_tables" ] }, { "page": "pmx_register_plot", "title": "Register plot (Jun2025, Alex: I believe it doesn't work at all)", "topics": [ "pmx_register_plot" ] }, { "page": "pmx_report", "title": "Generates ggpmX report from a pre-defined template", "topics": [ "pmx_report" ] }, { "page": "pmx_report_template", "title": "Gets build-in report templates", "topics": [ "pmx_report_template" ] }, { "page": "pmx_settings", "title": "Create controller global settings", "topics": [ "pmx_settings" ] }, { "page": "pmx_shrink", "title": "Create shrinkage parameter object", "topics": [ "pmx_shrink" ] }, { "page": "pmx_sim", "title": "Create simulation object", "topics": [ "pmx_sim" ] }, { "page": "pmx_theme", "title": "Define ggPMX theme", "topics": [ "pmx_theme" ] }, { "page": "pmx_update", "title": "Update plot object", "concept": [ "pmxclass" ], "topics": [ "pmx_update" ] }, { "page": "pmx_vpc", "title": "Creates vpc object", "concept": [ "vpc" ], "topics": [ "pmx_vpc" ] }, { "page": "pmx_vpc_bin", "title": "Creates vpc bins", "concept": [ "vpc" ], "topics": [ "pmx_vpc_bin" ] }, { "page": "pmx_vpc_ci", "title": "Sets vpc confidence interval layer", "concept": [ "vpc" ], "topics": [ "pmx_vpc_ci" ] }, { "page": "pmx_vpc_obs", "title": "Sets vpc observation layer", "concept": [ "vpc" ], "topics": [ "pmx_vpc_obs" ] }, { "page": "pmx_vpc_pi", "title": "Sets vpc percentile layer", "concept": [ "vpc" ], "topics": [ "pmx_vpc_pi" ] }, { "page": "pmx_vpc_rug", "title": "Sets vpc rug layer", "concept": [ "vpc" ], "topics": [ "pmx_vpc_rug" ] }, { "page": "pmxOptions", "title": "This function can be used to set ggPMX options", "topics": [ "pmxOptions" ] }, { "page": "print.abbreviation", "title": "S3 print abbreviation", "topics": [ "print.abbreviation" ] }, { "page": "print.configs", "title": "This function can be used to print configuration of the defined object using S3 method.", "topics": [ "print.configs" ] }, { "page": "print.pmx_gpar", "title": "Print pmx_gpar object", "topics": [ "print.pmx_gpar" ] }, { "page": "print.pmxClass", "title": "Print pmxClass object", "concept": [ "pmxclass functions" ], "topics": [ "print.pmxClass" ] }, { "page": "print.pmxConfig", "title": "S3 method print pmxConfig object", "topics": [ "print.pmxConfig" ] }, { "page": "read_extfile", "title": "Reads .ext files generated by NONMEM", "topics": [ "read_extfile" ] }, { "page": "read_input", "title": "Read Modelling input data", "topics": [ "read_input" ] }, { "page": "read_mlx_ind_est", "title": "Read MONOLIX individual parameters", "topics": [ "read_mlx_ind_est" ] }, { "page": "read_mlx_par_est", "title": "Read MONOLIX parameter estimation file", "topics": [ "read_mlx_par_est" ] }, { "page": "read_mlx_pred", "title": "Read MONOLIX model predictions", "topics": [ "read_mlx_pred" ] }, { "page": "read_mlx_saem_conv", "title": "Read MONOLIX SAEM convergence file", "topics": [ "read_mlx_saem_conv" ] }, { "page": "residual", "title": "This function create a residual for each observed value and also generates a residual distribution", "topics": [ "residual" ] }, { "page": "residual_scatter", "title": "Scatter residual plots", "concept": [ "residual" ], "topics": [ "pmx_plot_abs_iwres_ipred", "pmx_plot_abs_iwres_time", "pmx_plot_cwres_cpred", "pmx_plot_cwres_pred", "pmx_plot_cwres_time", "pmx_plot_dv_ipred", "pmx_plot_dv_pred", "pmx_plot_iwres_ipred", "pmx_plot_iwres_time", "pmx_plot_npde_pred", "pmx_plot_npde_time", "pmx_plot_npd_epred", "pmx_plot_npd_pred", "pmx_plot_npd_time", "residual_scatter" ] }, { "page": "set_abbrev", "title": "update or add a new abbreviation", "topics": [ "set_abbrev" ] }, { "page": "set_data", "title": "Set a controller data set", "concept": [ "pmxclass" ], "topics": [ "set_data" ] }, { "page": "set_plot", "title": "Create a new plot of the desired type", "concept": [ "pmxclass" ], "topics": [ "set_plot" ] }, { "page": "theophylline", "title": "Creates pmx controller using theophylline data", "topics": [ "theophylline" ] }, { "page": "wrap_formula", "title": "merge facets formula with new formula", "topics": [ "wrap_formula" ] } ], "_readme": "https://github.com/ggpmxdevelopment/ggpmx/raw/HEAD/README.md", "_rundeps": [ "assertthat", "backports", "base64enc", "bit", "bit64", "bslib", "cachem", "checkmate", "cli", "clipr", "cpp11", "crayon", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "fs", "generics", "GGally", "ggforce", "ggplot2", "ggstats", "glue", "gtable", "highr", "hms", "htmltools", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "memoise", "mime", "patchwork", "pillar", "pkgconfig", "polyclip", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "readr", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidyr", "tidyselect", "tinytex", "tweenr", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "ggPMX-guide.Rmd", "filename": "ggPMX-guide.html", "title": "ggPMX - User Guide", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Architecture", "Workflow overview", "Modeling datasets", "Controller", "Single-endpoint models", "Controller creation", "Models fitted with Monolix (versions 2016 and later)", "Models fitted with NONMEM (versions 7.2 and later)", "Models fitted with nlmixr", "Optional arguments for controller creation", "Multiple-endpoint models", "Using pmx_endpoint() (only for Monolix)", "A simplified syntax for endpoints (for Monolix, NONMEM and nlmixr)", "Controller with covariates", "Controller content", "Plot names", "Plot types", "Default diagnostic plots", "Visual Predictive Checks (VPC)", "Initialization", "VPC plot", "Default", "Scatter/Percentile", "Binning", "Stratification", "Monolix-like customisation", "Diagnostics report", "Customizing plots", "Visualization of BLQs (Monolix and NONMEM)", "Simulated BLOQ (Monolix 2018 and later)", "Customizing global settings - pmx_settings()", "Remove DRAFT label globally", "Use abbreviation definitions", "Use finegrid.txt file for individual plots", "Set stratification color legend", "Define labels of categorical variables", "Appendix", "Generic Controller creation with pmx()", "Software requirements", "Monolix", "NONMEM", "nlmixr", "Plots table", "ggPMX main functions", "ggPMX graphical parameters", "Pre-defined configurations", "Shrinkage", "Default call", "Var function", "Shrinkage and stratification" ], "created": "2019-04-25 05:48:29", "modified": "2025-09-02 11:58:04", "commits": 21 } ], "_score": 8.125481265700595, "_indexed": true, "_nocasepkg": "ggpmx", "_universes": [ 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