| Compresses a numeric vector into the simplest possible character string that, when evaluated, will create the same numeric vector. | .compress_range |
| Helper function create text used to filter data frame | .create_filter_expr |
| Evaluates range notation. If provided notation is invalid, returns NA. | .eval_range |
| Tooltip construction helper | .handle_tooltips |
| Add Exclusion Reasons to PKNCAdata Object | add_exclusion_reasons |
| Helper function to add "label" attribute to columns based on parameter names. | add_label_attribute |
| Add a slide with a plot only | add_pptx_sl_plot |
| Add a slide with both a plot and a table | add_pptx_sl_plottable |
| Add a slide with a table only | add_pptx_sl_table |
| Helper to create a Quarto code chunk for a plot | add_qmd_plot |
| Add a slide to the Quarto document with a single plot | add_qmd_sl_plot |
| Add a slide to the Quarto document with a plot and two tables (side by side) | add_qmd_sl_plottabletable |
| Helper to create a Quarto code chunk for a table | add_qmd_table |
| Add a new version to an existing versioned settings list | add_settings_version |
| Helper: adjust class and length (optional) for a data.frame based on metadata_nca_variables | adjust_class_and_length |
| adnca_example | adnca_example |
| Apply Filters to a Dataset | apply_filters |
| Apply Labels to a dataset | apply_labels |
| Apply UI-Based Column Mapping to a Dataset | apply_mapping |
| Apply default target units onto a data-derived units table | apply_unit_defaults |
| Links the table ratio of the App with the ratio calculations via PKNCA results | calculate_ratio_app |
| Calculate Ratios from PKNCA Results | calculate_ratios |
| Calculate Summary Statistics | calculate_summary_stats |
| Apply Ratio Calculations to PKNCAresult Object | calculate_table_ratios |
| Does a set of validation findings block saving? | cdisc_validation_blocks_save |
| Keep only units that differ from their data-derived default | changed_units |
| Convert Volume Units to Match Concentration Denominator Units | convert_volume_units |
| Create METABFL Column Based on Selected Metabolites | create_metabfl |
| 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 | create_pptx_dose_slides |
| Create a new Quarto presentation file with YAML header and setup chunk | create_qmd_doc |
| Create all slides for dose escalation results in a Quarto document | create_qmd_dose_slides |
| Create a versioned settings entry | create_settings_version |
| Create C0 Impute Column | create_start_impute |
| Delete a version from a versioned settings list | delete_settings_version |
| Detect study types | detect_study_types |
| dm_example | dm_example |
| Create duplicates in concentration data with Pre-dose and Last Values for Dosing Cycles | dose_profile_duplicates |
| ex_example | ex_example |
| Create an Individual PK Line Plot | exploration_individualplot |
| Create a Mean PK Line Plot | exploration_meanplot |
| Export CDISC Data | export_cdisc |
| Do export findings block saving? | export_validation_blocks_save |
| Filter Breaks for X-Axis | filter_breaks |
| Flexible Violin/Box Plot | flexible_violinboxplot |
| Create PK Concentration Dataset | format_pkncaconc_data |
| Create Dose Intervals Dataset | format_pkncadata_intervals |
| Create PK Dose Dataset | format_pkncadose_data |
| Formats a unit string if a unique unit exists | format_unit_string |
| Generate a Unified Line Plot for PK Data | g_lineplot |
| Wrapper around aNCA::pkcg01() function. Calls the function with 'LIN' scale argument. | g_pkcg01_lin |
| Wrapper around aNCA::pkcg01() function. Calls the function with 'LOG' scale argument. | g_pkcg01_log |
| Wrapper around aNCA::pkcg01() function. Calls the function with 'SBS' scale argument. | g_pkcg01_sbs |
| Wrapper around aNCA::pkcg02() function. Calls the function with 'LIN' scale argument. | g_pkcg02_lin |
| Wrapper around aNCA::pkcg02() function. Calls the function with 'LOG' scale argument. | g_pkcg02_log |
| Wrapper around aNCA::pkcg02() function. Calls the function with 'SBS' scale argument. | g_pkcg02_sbs |
| Wrapper around aNCA::pkcg03() function. Calls the function with 'LIN' scale argument. | g_pkcg03_lin |
| Wrapper around aNCA::pkcg03() function. Calls the function with 'LOG' scale argument. | g_pkcg03_log |
| Wrapper around aNCA::pkcg03() function. Calls the function with 'SBS' scale argument. | g_pkcg03_sbs |
| Generate Pre-Specifications for CDISC Datasets | generate_pre_specs |
| Generate HTML Tooltip Text | generate_tooltip_text |
| Transform Units | get_conversion_factor |
| Create a Plotly Half-life Plot | get_halflife_plots |
| Get the Label of a Heading | get_label |
| Generate a session script from a settings YAML file | get_settings_code |
| Add specified imputation methods to the intervals in a PKNCAdata or data.frame object. | interval_add_impute |
| Remove specified imputation from the intervals in a PKNCAdata or data.frame (intervals) object. | interval_remove_impute |
| Helper function for BLQ processing | keep_blq_timepoints |
| Create PK Concentration Listing | l_pkcl01 |
| Wrapper around aNCA::l_pkcl01() for TAD-based concentration listings. | l_pkcl01_tad |
| Urine Concentration and Volume Listing (pkcl02) | l_pkcl02_uri |
| Individual PK Parameters Listing (pkpl01) | l_pkpl01 l_pkpl01_mp |
| Individual Treatment Comparison Listing (pkpl04) | l_pkpl04_mp |
| metadata_nca_parameters | metadata_nca_parameters |
| metadata_nca_variables | metadata_nca_variables |
| 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. | multiple_matrix_ratios |
| Wrapper around aNCA::pkcg03() function. Mean linear plot grouped by dose. | p_pkcg03_lin_dose |
| Wrapper around aNCA::pkcg03() function. Mean log plot grouped by dose. | p_pkcg03_log_dose |
| Wrapper around aNCA::pkcg03() function. Mean side-by-side plot grouped by dose. | p_pkcg03_sbs_dose |
| Mean Urine PK Parameter Profile Plot (pkpg01) | p_pkpg01_cum p_pkpg01_per |
| Dose-Proportionality Scatter Plot with Power-Model Regression (pkpg02) | p_pkpg02_doseprop |
| Boxplot of Primary PK Parameters (pkpg03) | p_pkpg03_boxp p_pkpg04_boxp |
| Boxplot of Metabolite/Parent PK Parameter Ratios (pkpg06) | p_pkpg06_mp |
| Generate an Empty Plotly Object | parse_annotation |
| pc_example | pc_example |
| Reshape PKNCA Results | pivot_wider_pknca_results |
| Create a PK Dose Quality Control (QC) Plot | pk_dose_qc_plot |
| Calculate the maximum excretion rate | pk.calc.ermax |
| Calculate the midpoint collection time of the last measurable excretion rate | pk.calc.ertlst |
| Calculate the midpoint collection time of the maximum excretion rate | pk.calc.ertmax |
| Calculate the total urine volume | pk.calc.volpk |
| Generate PK Concentration-Time Profile Plots | pkcg01 |
| Generate Combined PK Concentration-Time Profile Plot by Cohort | pkcg02 |
| Generate PK Concentration-Time Profile Plots | pkcg03 |
| Build Units Table for PKNCA | PKNCA_build_units_table |
| Calculates results for PKNCA analysis. | PKNCA_calculate_nca |
| Creates a 'PKNCA::PKNCAdata' object. | PKNCA_create_data_object |
| 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. | PKNCA_hl_rules_exclusion |
| This function imputes the start concentration using the first concentration after dose | PKNCA_impute_method_start_c1 |
| This function imputes the start concentration using the log slope method. | PKNCA_impute_method_start_logslope |
| Create a PKNCAdata Object for NCA or Slope Analysis | PKNCA_update_data_object |
| Prepare Data for PK Dose QC Plotting | prepare_plot_data |
| Reads datasets from various file formats. | read_pk |
| Helper Logic to parse and structure settings YAML | read_settings |
| Read a versioned settings YAML file | read_versioned_settings |
| Filter Out Parameters Not Requested in PKNCA Results (Pivot Version) | remove_pp_not_requested |
| Apply Imputation for PKNCA Data | rm_impute_obs_params |
| Run the Shiny app | run_app |
| Build a summary table of version entries | settings_version_summary |
| Simplify compound unit expressions | simplify_unit |
| Summary Concentration Table (pkct01) | t_pkct01 t_pkct01_dose t_pkct01_dose_tad t_pkct01_tad |
| Summary PK Parameters Table - statistics in columns (pkpt03) | t_pkpt03_col t_pkpt03_MP_col |
| Mean Dose-Normalized PK Parameters Table (pkpt07) | t_pkpt07_norm |
| Mean Urine Amount and Percent Recovered Table (pkpt08) | t_pkpt08_uri |
| GMR Table with Confidence Intervals (pkpt11) | t_pkpt11_gmr |
| Translate Terms from One Nomenclature to Another | translate_terms |
| Update an intervals data frame with user-selected parameters by study type | update_main_intervals |
| Apply Slope Rules to Update Data | update_pknca_with_rules |
| Validate CDISC datasets against metadata-declared data types | validate_cdisc_types |
| Validate exported outputs before saving | validate_export_outputs |
| Validates data table with raw pk data. | validate_pk |
| Write a versioned settings YAML file | write_versioned_settings |
