{ "_id": "6ace89e8f6f39cd7e29a11f9", "Package": "aNCA", "Title": "(Pre-)Clinical NCA in a Dynamic Shiny App", "Version": "0.1.0.9208", "Authors@R": "c(\nperson(\"Ercan\", \"Suekuer\", email = \"ercan.suekuer@roche.com\", role = \"aut\",\ncomment = c(ORCID = \"0009-0001-1626-1526\")),\nperson(\"Gerardo Jose\", \"Rodriguez\", email = \"gerardo.jrac@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1413-0060\")),\nperson(\"Pascal\", \"Baertschi\", email = \"paesce.26@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6533-0399\")),\nperson(\"Jana\", \"Spinner\", email = \"spinnerjana@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0009-0009-2197-9530\")),\nperson(\"Mateusz\", \"Kolomanski\", email = \"mateusz.kolomanski@appsilon.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7424-3919\")),\nperson(\"Lucy\", \"Aspridis\", email = \"lucy.aspridis@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0009-0003-1300-3622\")),\nperson(\"Valentin\", \"Legras\", email = \"anca.pharmaverse@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\"))\n)", "Description": "An interactive 'shiny' application for performing\nnon-compartmental analysis (NCA) on pre-clinical and clinical\npharmacokinetic data. The package builds on 'PKNCA' for core\nestimators and provides interactive visualizations, CDISC\noutputs ('ADNCA', 'PP', 'ADPP'), configurable TLGs (tables,\nlistings, and graphs) and draft slide decks. Typical use cases\ninclude exploratory analysis, validation, reporting or\nteaching/demonstration of NCA methods. Methods and core\nestimators are described in Denney, Duvvuri, and Buckeridge\n(2015) \"Simple, Automatic Noncompartmental Analysis: The PKNCA\nR Package\" .", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Language": "en-US", "URL": "https://pharmaverse.github.io/aNCA/,\nhttps://github.com/pharmaverse/aNCA", "BugReports": "https://github.com/pharmaverse/aNCA/issues", "LazyData": "true", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibudunits2-dev zlib1g-dev", "Repository": "https://pharmaverse.r-universe.dev", "Date/Publication": "2026-10-13 15:48:33 UTC", "RemoteUrl": "https://github.com/pharmaverse/anca", "RemoteRef": "HEAD", "RemoteSha": "f8d921bfc8abc0b8ab0cbac6fe65cba58efdefed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-13 19:32:27 UTC", "User": "root" }, "Author": "Ercan Suekuer [aut] (ORCID: ),\nGerardo Jose Rodriguez [aut] (ORCID:\n),\nPascal Baertschi [aut] (ORCID: ),\nJana Spinner [aut] (ORCID: ),\nMateusz Kolomanski [aut] (ORCID:\n),\nLucy Aspridis [aut] (ORCID: ),\nValentin Legras [aut, cre],\nF. 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from their data-derived default", "topics": [ "changed_units" ] }, { "page": "convert_volume_units", "title": "Convert Volume Units to Match Concentration Denominator Units", "topics": [ "convert_volume_units" ] }, { "page": "create_metabfl", "title": "Create METABFL Column Based on Selected Metabolites", "topics": [ "create_metabfl" ] }, { "page": "create_pptx_dose_slides", "title": "Create a PowerPoint presentation with dose escalation results, including main and extra figures Adds slides for summary tables, mean plots, line plots, and individual subject results", "topics": [ "create_pptx_dose_slides" ] }, { "page": "create_qmd_doc", "title": "Create a new Quarto presentation file with YAML header and setup chunk", "topics": [ "create_qmd_doc" ] }, { "page": "create_qmd_dose_slides", "title": "Create all slides for dose escalation results in a Quarto document", "topics": [ "create_qmd_dose_slides" ] }, { "page": "create_settings_version", "title": "Create a versioned settings entry", "topics": [ "create_settings_version" ] }, { "page": "create_start_impute", "title": "Create C0 Impute Column", "topics": [ "create_start_impute" ] }, { "page": "delete_settings_version", "title": "Delete a version from a versioned settings list", "topics": [ "delete_settings_version" ] }, { "page": "detect_study_types", "title": "Detect study types", "topics": [ "detect_study_types" ] }, { "page": "dm_example", "title": "dm_example", "topics": [ "dm_example" ] }, { "page": "dose_profile_duplicates", "title": "Create duplicates in concentration data with Pre-dose and Last Values for Dosing Cycles", "topics": [ "dose_profile_duplicates" ] }, { "page": "ex_example", "title": "ex_example", "topics": [ "ex_example" ] }, { "page": "exploration_individualplot", "title": "Create an Individual PK Line Plot", "topics": [ "exploration_individualplot" ] }, { "page": "exploration_meanplot", "title": "Create a Mean PK Line Plot", "topics": [ "exploration_meanplot" ] }, { "page": "export_cdisc", "title": "Export CDISC Data", "topics": [ "export_cdisc" ] }, { "page": "export_validation_blocks_save", "title": "Do export findings block saving?", "topics": [ "export_validation_blocks_save" ] }, { "page": "filter_breaks", "title": "Filter Breaks for X-Axis", "topics": [ "filter_breaks" ] }, { "page": "flexible_violinboxplot", "title": "Flexible Violin/Box Plot", "topics": [ "flexible_violinboxplot" ] }, { "page": "format_pkncaconc_data", "title": "Create PK Concentration Dataset", "topics": [ "format_pkncaconc_data" ] }, { "page": "format_pkncadata_intervals", "title": "Create Dose Intervals Dataset", "topics": [ "format_pkncadata_intervals" ] }, { "page": "format_pkncadose_data", "title": "Create PK Dose Dataset", "topics": [ "format_pkncadose_data" ] }, { "page": "format_unit_string", "title": "Formats a unit string if a unique unit exists", "topics": [ "format_unit_string" ] }, { "page": "g_lineplot", "title": "Generate a Unified Line Plot for PK Data", "topics": [ "g_lineplot" ] }, { "page": "g_pkcg01_lin", "title": "Wrapper around aNCA::pkcg01() function. Calls the function with 'LIN' scale argument.", "topics": [ "g_pkcg01_lin" ] }, { "page": "g_pkcg01_log", "title": "Wrapper around aNCA::pkcg01() function. Calls the function with 'LOG' scale argument.", "topics": [ "g_pkcg01_log" ] }, { "page": "g_pkcg01_sbs", "title": "Wrapper around aNCA::pkcg01() function. Calls the function with 'SBS' scale argument.", "topics": [ "g_pkcg01_sbs" ] }, { "page": "g_pkcg02_lin", "title": "Wrapper around aNCA::pkcg02() function. Calls the function with 'LIN' scale argument.", "topics": [ "g_pkcg02_lin" ] }, { "page": "g_pkcg02_log", "title": "Wrapper around aNCA::pkcg02() function. Calls the function with 'LOG' scale argument.", "topics": [ "g_pkcg02_log" ] }, { "page": "g_pkcg02_sbs", "title": "Wrapper around aNCA::pkcg02() function. Calls the function with 'SBS' scale argument.", "topics": [ "g_pkcg02_sbs" ] }, { "page": "g_pkcg03_lin", "title": "Wrapper around aNCA::pkcg03() function. Calls the function with 'LIN' scale argument.", "topics": [ "g_pkcg03_lin" ] }, { "page": "g_pkcg03_log", "title": "Wrapper around aNCA::pkcg03() function. Calls the function with 'LOG' scale argument.", "topics": [ "g_pkcg03_log" ] }, { "page": "g_pkcg03_sbs", "title": "Wrapper around aNCA::pkcg03() function. Calls the function with 'SBS' scale argument.", "topics": [ "g_pkcg03_sbs" ] }, { "page": "generate_pre_specs", "title": "Generate Pre-Specifications for CDISC Datasets", "topics": [ "generate_pre_specs" ] }, { "page": "generate_tooltip_text", "title": "Generate HTML Tooltip Text", "topics": [ "generate_tooltip_text" ] }, { "page": "get_conversion_factor", "title": "Transform Units", "topics": [ "get_conversion_factor" ] }, { "page": "get_halflife_plots", "title": "Create a Plotly Half-life Plot", "topics": [ "get_halflife_plots" ] }, { "page": "get_label", "title": "Get the Label of a Heading", "topics": [ "get_label" ] }, { "page": "get_settings_code", "title": "Generate a session script from a settings YAML file", "topics": [ "get_settings_code" ] }, { "page": "interval_add_impute", "title": "Add specified imputation methods to the intervals in a PKNCAdata or data.frame object.", "topics": [ "interval_add_impute" ] }, { "page": "interval_remove_impute", "title": "Remove specified imputation from the intervals in a PKNCAdata or data.frame (intervals) object.", "topics": [ "interval_remove_impute" ] }, { "page": "keep_blq_timepoints", "title": "Helper function for BLQ processing", "topics": [ "keep_blq_timepoints" ] }, { "page": "l_pkcl01", "title": "Create PK Concentration Listing", "topics": [ "l_pkcl01" ] }, { "page": "l_pkcl01_tad", "title": "Wrapper around aNCA::l_pkcl01() for TAD-based concentration listings.", "topics": [ "l_pkcl01_tad" ] }, { "page": "l_pkcl02_uri", "title": "Urine Concentration and Volume Listing (pkcl02)", "topics": [ "l_pkcl02_uri" ] }, { "page": "l_pkpl01", "title": "Individual PK Parameters Listing (pkpl01)", "topics": [ "l_pkpl01", "l_pkpl01_mp" ] }, { "page": "l_pkpl04_mp", "title": "Individual Treatment Comparison Listing (pkpl04)", "topics": [ "l_pkpl04_mp" ] }, { "page": "metadata_nca_parameters", "title": "metadata_nca_parameters", "topics": [ "metadata_nca_parameters" ] }, { "page": "metadata_nca_variables", "title": "metadata_nca_variables", "topics": [ "metadata_nca_variables" ] }, { "page": "multiple_matrix_ratios", "title": "Calculate Matrix Ratios This function calculates the ratios for a given data set, based on the shared time points for each matrix concentration sample. The user can input multiple tissues for which ratios should be calculated.", "topics": [ "multiple_matrix_ratios" ] }, { "page": "p_pkcg03_lin_dose", "title": "Wrapper around aNCA::pkcg03() function. Mean linear plot grouped by dose.", "topics": [ "p_pkcg03_lin_dose" ] }, { "page": "p_pkcg03_log_dose", "title": "Wrapper around aNCA::pkcg03() function. Mean log plot grouped by dose.", "topics": [ "p_pkcg03_log_dose" ] }, { "page": "p_pkcg03_sbs_dose", "title": "Wrapper around aNCA::pkcg03() function. Mean side-by-side plot grouped by dose.", "topics": [ "p_pkcg03_sbs_dose" ] }, { "page": "p_pkpg01_cum", "title": "Mean Urine PK Parameter Profile Plot (pkpg01)", "topics": [ "p_pkpg01_cum", "p_pkpg01_per" ] }, { "page": "p_pkpg02_doseprop", "title": "Dose-Proportionality Scatter Plot with Power-Model Regression (pkpg02)", "topics": [ "p_pkpg02_doseprop" ] }, { "page": "p_pkpg03_boxp", "title": "Boxplot of Primary PK Parameters (pkpg03)", "topics": [ "p_pkpg03_boxp", "p_pkpg04_boxp" ] }, { "page": "p_pkpg06_mp", "title": "Boxplot of Metabolite/Parent PK Parameter Ratios (pkpg06)", "topics": [ "p_pkpg06_mp" ] }, { "page": "parse_annotation", "title": "Generate an Empty Plotly Object", "topics": [ "parse_annotation" ] }, { "page": "pc_example", "title": "pc_example", "topics": [ "pc_example" ] }, { "page": "pivot_wider_pknca_results", "title": "Reshape PKNCA Results", "topics": [ "pivot_wider_pknca_results" ] }, { "page": "pk_dose_qc_plot", "title": "Create a PK Dose Quality Control (QC) Plot", "topics": [ "pk_dose_qc_plot" ] }, { "page": "pk.calc.ermax", "title": "Calculate the maximum excretion rate", "topics": [ "pk.calc.ermax" ] }, { "page": "pk.calc.ertlst", "title": "Calculate the midpoint collection time of the last measurable excretion rate", "topics": [ "pk.calc.ertlst" ] }, { "page": "pk.calc.ertmax", "title": "Calculate the midpoint collection time of the maximum excretion rate", "topics": [ "pk.calc.ertmax" ] }, { "page": "pk.calc.volpk", "title": "Calculate the total urine volume", "topics": [ "pk.calc.volpk" ] }, { "page": "pkcg01", "title": "Generate PK Concentration-Time Profile Plots", "topics": [ "pkcg01" ] }, { "page": "pkcg02", "title": "Generate Combined PK Concentration-Time Profile Plot by Cohort", "topics": [ "pkcg02" ] }, { "page": "pkcg03", "title": "Generate PK Concentration-Time Profile Plots", "topics": [ "pkcg03" ] }, { "page": "PKNCA_build_units_table", "title": "Build Units Table for PKNCA", "topics": [ "PKNCA_build_units_table" ] }, { "page": "PKNCA_calculate_nca", "title": "Calculates results for PKNCA analysis.", "topics": [ "PKNCA_calculate_nca" ] }, { "page": "PKNCA_create_data_object", "title": "Creates a 'PKNCA::PKNCAdata' object.", "topics": [ "PKNCA_create_data_object" ] }, { "page": "PKNCA_hl_rules_exclusion", "title": "Exclude NCA results based on user-defined rules over the half-life related parameters This function applies exclusion rules to the NCA results based on user-defined parameters.", "topics": [ "PKNCA_hl_rules_exclusion" ] }, { "page": "PKNCA_impute_method_start_c1", "title": "This function imputes the start concentration using the first concentration after dose", "topics": [ "PKNCA_impute_method_start_c1" ] }, { "page": "PKNCA_impute_method_start_logslope", "title": "This function imputes the start concentration using the log slope method.", "topics": [ "PKNCA_impute_method_start_logslope" ] }, { "page": "PKNCA_update_data_object", "title": "Create a PKNCAdata Object for NCA or Slope Analysis", "topics": [ "PKNCA_update_data_object" ] }, { "page": "prepare_plot_data", "title": "Prepare Data for PK Dose QC Plotting", "topics": [ "prepare_plot_data" ] }, { "page": "read_pk", "title": "Reads datasets from various file formats.", "topics": [ "read_pk" ] }, { "page": "read_settings", "title": "Helper Logic to parse and structure settings YAML", "topics": [ "read_settings" ] }, { "page": "read_versioned_settings", "title": "Read a versioned settings YAML file", "topics": [ "read_versioned_settings" ] }, { "page": "remove_pp_not_requested", "title": "Filter Out Parameters Not Requested in PKNCA Results (Pivot Version)", "topics": [ "remove_pp_not_requested" ] }, { "page": "rm_impute_obs_params", "title": "Apply Imputation for PKNCA Data", "topics": [ "rm_impute_obs_params" ] }, { "page": "run_app", "title": "Run the Shiny app", "topics": [ "run_app" ] }, { "page": "settings_version_summary", "title": "Build a summary table of version entries", "topics": [ "settings_version_summary" ] }, { "page": "simplify_unit", "title": "Simplify compound unit expressions", "topics": [ "simplify_unit" ] }, { "page": "t_pkct01", "title": "Summary Concentration Table (pkct01)", "topics": [ "t_pkct01", "t_pkct01_dose", "t_pkct01_dose_tad", "t_pkct01_tad" ] }, { "page": "t_pkpt03_col", "title": "Summary PK Parameters Table - statistics in columns (pkpt03)", "topics": [ "t_pkpt03_col", "t_pkpt03_MP_col" ] }, { "page": "t_pkpt07_norm", "title": "Mean Dose-Normalized PK Parameters Table (pkpt07)", "topics": [ "t_pkpt07_norm" ] }, { "page": "t_pkpt08_uri", "title": "Mean Urine Amount and Percent Recovered Table (pkpt08)", "topics": [ "t_pkpt08_uri" ] }, { "page": "t_pkpt11_gmr", "title": "GMR Table with Confidence Intervals (pkpt11)", "topics": [ "t_pkpt11_gmr" ] }, { "page": "translate_terms", "title": "Translate Terms from One Nomenclature to Another", "topics": [ "translate_terms" ] }, { "page": "update_main_intervals", "title": "Update an intervals data frame with user-selected parameters by study type", "topics": [ "update_main_intervals" ] }, { "page": "update_pknca_with_rules", "title": "Apply Slope Rules to Update Data", "topics": [ "update_pknca_with_rules" ] }, { "page": "validate_cdisc_types", "title": "Validate CDISC datasets against metadata-declared data types", "topics": [ "validate_cdisc_types" ] }, { "page": "validate_export_outputs", "title": "Validate exported outputs before saving", "topics": [ "validate_export_outputs" ] }, { "page": "validate_pk", "title": "Validates data table with raw pk data.", "topics": [ "validate_pk" ] }, { "page": "write_versioned_settings", "title": "Write a versioned settings YAML file", "topics": [ "write_versioned_settings" ] } ], "_readme": "https://github.com/pharmaverse/anca/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "bslib", "cachem", "checkmate", "cli", "commonmark", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "formatters", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "logger", "magrittr", "memoise", "mime", "nlme", "openssl", "otel", "pillar", "pkgconfig", "PKNCA", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reactable", "reactable.extras", "reactR", "rjson", "rlang", "rmarkdown", "S7", "sass", "scales", "shiny", "shinycssloaders", "shinyjqui", "shinyjs", "shinyWidgets", "sourcetools", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "units", "utf8", "vctrs", "viridisLite", "withr", "writexl", "xfun", "xtable", "yaml", "zip" ], "_score": 7.445267845067624, "_indexed": true, "_nocasepkg": "anca", "_universes": [ "pharmaverse" ], "_previous": "0.1.0.9206", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0.9208", "date": 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