aNCA Shiny App User Guide

This guide will provide users with information on how to get started with the aNCA app.

Step 1: Prepare Dataset

Uploading a dataset

Click Upload File and select the dataset you would like to use. The data must be in .csv or .rds format. The best input for the app is data that follows the ADNCA format. Other formats of data will also work.

Data format

	Variable	Description	Format
	STUDYID	Study Identifier	character
Grouping Identifiers	USUBJID	Unique Subject Identifier	character/numeric
	TRT01A	Treatment Group Identifier (Actual)	character
	TRT01P	Treatment Group Identifier (Planned)	character
	AGE	Age of Subject	numeric
	RACE	Race of Subject	character
	SEX	Sex of Subject	character
Sample variables	ANALYTE	Analyte	character
	PCSPEC	Specimen Material Type	character
	AVAL	Analysis Value	numeric
Dose Variables	DOSNO	Dose Number	numeric
	ROUTE	Route of Administration, either {intravascular} or {extravascular}	character
	DOSEA	Actual Treatment Dose	numeric
	ADOSEDUR	Actual Treatment Dose	numeric
Time Variables	AFRLT	Actual Relative Time from Analyte First Dose	numeric
	ARRLT	Actual Relative Time from Reference Dose	numeric
	NFRLT	Nominal Relative Time from Analyte First Dose	numeric
	NRRLT	Nominal Relative Time from Reference Dose	numeric
	AVALU	Analysis Value Unit	character
	DOSEU	Treatment Dose Units	character
	RRLTU	Relative Time from Reference Dose Unit	character

Data mapping

Once the dataset has been uploaded, you can verify that the data is as expected, and click on the Mapping and Filters tab. - Map the correct columns in your dataset to the corresponding label. For more information on what the column requires, hover over the input boxes. - For Unit Variables, if your dataset has a defined column for units, select it. Otherwise manually input the units for the corresponding columns. - Click Submit Mapping. You will be automatically directed to the next tab.

Verifying adding filters

Check that the data contains all the information you were expecting and is mapped correctly. If you want to change the data by adding filters, return to the Mapping and Filters page, then scroll down to add filters.

Don’t forget to scroll down and click submit!

Step 2: Run NCA

Click on the NCA tab at the top of the screen to switch to the next section.

Data selection

1. Choose the analytes you would like to run the NCA on.

2. Click Submit and check that the data is as expected.

3. Move to Settings in the menu on the left hand side. Choose the Dose Number(s) you would like to run the NCA on and the extrapolation method. Select additional options including partial AUCs, or rule sets to flag the data.

4. Click Run NCA. You will automatically be redirected to the Results tab.

Step 3: NCA Results

Main Results

The NCA results tab shows the individual results of the NCA. You can select which parameters you would like to view. Results in red have been flagged as False for the rule sets selected, results in purple are flagged as Missing, and results in white are not flagged.

Click on the Slopes tab to view more detailed information about the slopes selected in the NCA.

In Parameter datasets you can see and export the ADPP and PP datasets.

Exclusions and Manual Slopes

To add exclusions or manual slope selections, redirect to the Slope Selector tab in the Setup page.

There are two different ways to add exclusions/selections to the slopes.

Via the Buttons.

1. Click + Exclusion/Selection
2. Input required information: Type, Patient, Profile, Range, Reason. IXrange is the Data Point number in the slope, which can be seen by hovering over the points in the plots below.

3. To remove, select the sample row and click -Remove selected rows

Via the Plots

For in-app guidance, you can click the ? button.

1. For selection, click the first point and then the last point you want included in the slope. The plot should then update and a row should be added to the table. There you can add your reason for selection.
2. For exclusion, double click the point you want to exclude. The plot should update along with the table.
3. To remove, either remove via the table selection, or repeat the same action (i.e. select a new slope, double click the same point).

Applying the exclusions

Once the exclusions/selections have been added, click Apply.

You can check if they have been applied in the Results -> Exclusions tab.

If you do not click Apply, the manual slopes will not be added!

Saving and uploading settings

After completing an NCA and creating manual slopes, you may want to save these for next time.

Saving

Click Results -> NCA Results -> Save Project Settings. This will download a .csv file.

Uploading

To upload settings next time, after column mapping, Setup -> Data Selection -> Upload settings. The inclusions and exclusions will be automatically added to the data.

Step 4: Visualization

In the Visualization tab, you will find the different visualization options, including individual plots, mean plots, descriptive statistics, and boxplots.

Currently work in progress

Step 5: TLG

Currently work in progress