# (Pre-)Clinical NCA in a Dynamic Shiny App

## Documentation for package ‘aNCA’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.apply_slope_rules | Apply Slope Rules to Update Data
.compress_range | Compresses a numeric vector into the simplest possible character string that, when evaluated, will create the same numeric vector.
.eval_range | Evaluates range notation. If provided notation is invalid, returns NA.
.plotly_empty_plot | Generate an Empty Plotly Object
add_f_to_pknca_results | Add bioavailability results to PKNCA results
add_optional_layers | Helper function to handle optional layers
add_pptx_sl_plot | Add a slide with a plot only
add_pptx_sl_plottable | Add a slide with both a plot and a table
add_pptx_sl_table | Add a slide with a table only
add_qmd_plot | Helper to create a Quarto code chunk for a plot
add_qmd_sl_plot | Add a slide to the Quarto document with a single plot
add_qmd_sl_plottabletable | Add a slide to the Quarto document with a plot and two tables (side by side)
add_qmd_table | Helper to create a Quarto code chunk for a table
apply_filters | Apply Filters to a Dataset
apply_labels | Apply Labels to a dataset
apply_mapping | Apply UI-Based Column Mapping to a Dataset
calculate_f | Calculate bioavailability with pivoted output
calculate_ratios | Calculate Ratios from PKNCA Results
calculate_summary_stats | Calculate Summary Statistics
check_slope_rule_overlap | Check overlap between existing and new slope rulesets
convert_volume_units | Convert Volume Units to Match Concentration Denominator Units
create_html_dose_slides | Render dose escalation results to HTML via Quarto
create_metabfl | Create METABFL Column Based on Selected Metabolites
create_pptx_doc | Create a new PowerPoint document from a template and add a title slide
create_pptx_dose_slides | 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_qmd_doc | Create a new Quarto presentation file with YAML header and setup chunk
create_qmd_dose_slides | Create all slides for dose escalation results in a Quarto document
create_start_impute | Create C0 Impute Column
detect_study_types | Detect study types
dose_profile_duplicates | Create duplicates in concentration data with Pre-dose and Last Values for Dosing Cycles
ensure_column_unit_exists | Ensure Unit Columns Exist in PKNCA Object
export_cdisc | Export CDISC Data
filter_breaks | Filter Breaks for X-Axis
filter_slopes | Filter dataset based on slope selections and exclusions
flexible_violinboxplot | Flexible Violin/Box Plot
format_pkncaconc_data | Create PK Concentration Dataset
format_pkncadata_intervals | Create Dose Intervals Dataset
format_pkncadose_data | Create PK Dose Dataset
format_unit_string | Formats a unit string if a unique unit exists
general_lineplot | Generate a General Line Plot for ADNCA Dataset
general_meanplot | Generate a Mean Concentration Plot for ADNCA Dataset
generate_tooltip_text | Generate HTML Tooltip Text
get_conversion_factor | Transform Units
get_label | Get the Label of a Heading
g_pkcg01_lin | Wrapper around aNCA::pkcg01() function. Calls the function with 'LIN' scale argument.
g_pkcg01_log | Wrapper around aNCA::pkcg01() function. Calls the function with 'LOG' scale argument.
g_pkcg02_lin | Wrapper around aNCA::pkcg02() function. Calls the function with 'LIN' scale argument.
g_pkcg02_log | Wrapper around aNCA::pkcg02() function. Calls the function with 'LOG' scale argument.
interval_add_impute | Add specified imputation methods to the intervals in a PKNCAdata or data.frame object.
interval_remove_impute | Remove specified imputation from the intervals in a PKNCAdata or data.frame (intervals) object.
lambda_slope_plot | Generate a Lambda Slope Plot
l_pkcl01 | Create PK Concentration Listing
metadata_nca_parameters | metadata_nca_parameters
metadata_nca_variables | metadata_nca_variables
multiple_matrix_ratios | 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.
parse_annotation | Parses annotations in the context of data. Special characters and syntax are substituted by actual data and/or substituted for format that is better parsed via rendering functions (e.g. plotly).
pivot_wider_pknca_results | Reshape PKNCA Results
pk.calc.volpk | Calculate the total urine volume
pkcg01 | Generate PK Concentration-Time Profile Plots
pkcg02 | Generate Combined PK Concentration-Time Profile Plot by Cohort
PKNCA_build_units_table | Build Units Table for PKNCA
pknca_calculate_f | Calculate bioavailability for intravascular vs extravascular aucs
PKNCA_calculate_nca | Calculates results for PKNCA analysis.
PKNCA_create_data_object | Creates a 'PKNCA::PKNCAdata' object.
PKNCA_hl_rules_exclusion | 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_impute_method_start_c1 | This function imputes the start concentration using the first concentration after dose
PKNCA_impute_method_start_logslope | This function imputes the start concentration using the log slope method.
PKNCA_update_data_object | Create a PKNCAdata Object for NCA or Slope Analysis
pk_dose_qc_plot | Create a PK Dose Quality Control (QC) Plot
prepare_plot_data | Prepare Data for PK Dose QC Plotting
preprocess_data_for_plot | Prepare Data for PK Lineplot
read_pk | Reads PK datasets from various file formats.
run_app | Run the Shiny app
select_minimal_grouping_cols | Find Minimal Grouping Columns for Strata Reconstruction
simplify_unit | Simplify compound unit expressions
translate_terms | Translate Terms from One Nomenclature to Another
validate_pk | Validates data table with raw pk data.
verify_parameters | Conditionally Verify and Override PK Parameters Based on Sample Type