(Pre-)Clinical NCA in a Dynamic Shiny App

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Documentation for package ‘aNCA’ version 0.1.0

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.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