Package index • aNCA

All functions

PKNCA_build_units_table(): Build Units Table for PKNCA
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
add_exclusion_reasons(): Add Exclusion Reasons to PKNCAdata Object
add_f_to_pknca_results(): Add bioavailability results to PKNCA results
add_label_attribute(): Helper function to add "label" attribute to columns based on parameter names.
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
adjust_class_and_length(): Helper: adjust class and length (optional) for a data.frame based on metadata_nca_variables
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_ratio_app(): Links the table ratio of the App with the ratio calculations via PKNCA results
calculate_ratios(): Calculate Ratios from PKNCA Results
calculate_summary_stats(): Calculate Summary Statistics
calculate_table_ratios(): Apply Ratio Calculations to PKNCAresult Object
check_slope_rule_overlap(): Check overlap between existing and new slope rulesets
check_valid_pknca_data(): Checks Before Running NCA
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
.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.
.create_filter_expr(): Helper function create text used to filter data frame
.eval_range(): Evaluates range notation. If provided notation is invalid, returns NA.
.handle_tooltips(): Tooltip construction helper
.plotly_empty_plot(): Generate an Empty Plotly Object
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
g_lineplot(): Generate a Unified Line Plot for PK Data
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.
g_pkcg03_lin(): Wrapper around aNCA::pkcg03() function. Calls the function with LIN scale argument.
g_pkcg03_log(): Wrapper around aNCA::pkcg03() function. Calls the function with LOG scale argument.
generate_tooltip_text(): Generate HTML Tooltip Text
get_conversion_factor(): Transform Units
get_halflife_plots(): Create a Plotly Half-life Plot
get_label(): Get the Label of a Heading
get_session_code(): Generate a session script code in R that can replicate the App outputs
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.
keep_blq_timepoints(): Helper function for BLQ processing
l_pkcl01(): Create PK Concentration Listing
lambda_slope_plot(): Generate a Lambda Slope Plot
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.ermax(): Calculate the maximum excretion rate
pk.calc.ertlst(): Calculate the midpoint collection time of the last measurable excretion rate
pk.calc.ertmax(): Calculate the midpoint collection time of the maximum excretion rate
pk.calc.volpk(): Calculate the total urine volume
pk_dose_qc_plot(): Create a PK Dose Quality Control (QC) Plot
pkcg01(): Generate PK Concentration-Time Profile Plots
pkcg02(): Generate Combined PK Concentration-Time Profile Plot by Cohort
pkcg03(): Generate PK Concentration-Time Profile Plots
pknca_calculate_f(): Calculate bioavailability for intravascular vs extravascular aucs
prepare_plot_data(): Prepare Data for PK Dose QC Plotting
process_data_individual(): Process data for individual line plot
process_data_mean(): Create a Mean PK Line Plot
read_pk(): Reads PK datasets from various file formats.
read_settings(): Helper Logic to parse and structure settings YAML
remove_pp_not_requested(): Filter Out Parameters Not Requested in PKNCA Results (Pivot Version)
rm_impute_obs_params(): Apply Imputation for PKNCA Data
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
update_main_intervals(): Update an intervals data frame with user-selected parameters by study type
validate_pk(): Validates data table with raw pk data.