Review NCA Results

The Results Review page in PumasCP presents a streamlined summary of the completed analysis type, in this case a non-compartmental analysis (NCA). It provides key details about the analysis, subjects, and groups, along with access to the raw and transformed results.

NCA Analysis Summary

Upon successful completion of an NCA PumasCP provides a concise overview:

• Analysis Type: Indicates that the analysis performed is NCA.
• Subjects: Displays the total number of subjects included in the analysis, allowing for a quick headcount to ensure all relevant data has been considered.
• Groups Created: Shows the number of distinct groups that have been analyzed, aiding in understanding the stratification of the data.
• Grouped by: Details the criteria used to group subjects, which could be by dose, treatment arm, or any other relevant stratification factor.

Result Sources

Below the summary, you will find two types of result sources:

• Raw Result: This section contains the original results generated by the analysis. You can download the raw data or open it in a detailed view. Note that this file is non-editable.

  • Last Updated: Provides the timestamp of the last update to the raw results, ensuring you're looking at the most recent data.

• Transformed Result: This is a copy of the Raw Results file that allows a user to perform any post-analysis transformations.

  • Last Updated: Similarly, this timestamp indicates when the transformed results were last modified.

User Interaction

Each result source comes with options for further actions:

• Download: This function allows you to download the raw results of your NCA analysis. The process is straightforward and can be completed with a few simple steps

  1. File Name: The default file name for the raw results is pre-filled. You can edit this name to something more descriptive for better file management.

  2. Select File Format: Choose the format in which you would like to download the results. The available options are:

     • CSV (Comma-Separated Values): A versatile file format that can be opened with many software applications, including spreadsheet programs like Microsoft Excel.
     • Arrow: A binary file format that is efficient for storing and transferring large datasets.
     • XPT (SAS Transport File): A format commonly used for sharing files between different versions of SAS and other software.

  3. PP Domain: If you need the results in the pharmacokinetics domain format, check the "PP Domain" box. This option formats the downloaded data according to the pharmacokinetics (PP) domain standards, which may be required for regulatory submissions or further statistical analysis.

After configuring your download preferences, click the "Cancel" button to abort the download or the "Confirm" button to save the file to your device.

• Expand/View: The expand icon allows users to open the results in a more detailed format in a new tab that allows for in-depth review or discussion. Note that changes cannot be made to the raw results in this view. Further, if the tab remains open, any changes in the results on the main tab will not be reflected here.
• Edit: Accessible for the transformed results, the edit icon enables users to make adjustments to the post-analysis data if needed. Please refer to the data wrangling section for more information on the transformations that can be applied.

Tables

The tables can be expanded by clicking on the respective rectangular boxes enclosing them. The existing tables can be previewed, edited, deleted, expanded/minimised by clicking on the Icons situated on the right side within the rectangular box. Additional tables can be added by clicking on + symbol on the top right of the rectangular box. At present two kinds of tables are available in the NCA results review page:

1. Summary Tables
2. Ratio Tables

Parameter Summary Table

The Parameter Table, which is a Summary Table of the NCA parameters is a key component in the results section of the NCA analysis in PumasCP. This table provides a summary of the calculated pharmacokinetic parameters for each subject or group within the study.

Interface Components

• Add Parameter Table: By clicking this button, you can introduce a new parameter table to your results section. This is useful if you have multiple sets of parameters or groupings that you wish to compare side-by-side.

• Parameter Table Box: This box contains the title 'NCA parameter summary', indicating that it will display a summary of all the NCA parameters calculated during the analysis. By default, the information in this section is collapsed to streamline the results page view.

User Interaction

• Expanding the Table: You can expand the table to view the detailed NCA parameters by clicking on the accordion toggle, or anywhere in the box. This allows for a comprehensive review of the results without navigating away from the summary page.

• Editing the Table: If you need to make changes to the parameter table, such as adjusting the displayed parameters or changing the statistics, you can do so by clicking the edit button (represented by a pencil icon). This opens the table in an editable format.

• Expand/View: The expand icon allows users to open the results in a more detailed format in a new tab that allows for in-depth review or discussion. Note that changes cannot be made in this view. Further, if the view tab remains open, any changes in the results on the main tab will not be reflected here.

Editing the Table

Upon clicking the pencil icon on the Parameter Summary Table, the editing window opens, allowing the user to modify various aspects of the table:

• Table Type: Verify that the table type is set to Summary Table which indicates the kind of data presentation. The other option for Ratio Table will be discussed later.

• Result Source: Choose 'Raw Results' to base the table on the initial output of the analysis. If the user has made any transformations to the raw results in the Transformed Raw Results, they can select 'Transformed Results' to reflect these changes in the table. Note that if no transformations have been made, the two sources will be identical and hence the user will not be presented with the dropdown option to change the source.

• Table Caption: Confirm or edit the caption of the table, which currently reads 'NCA parameter summary', for clarity and context. The caption entered here will be carried forward to the final report.

• Parameters to Summarize: Here, you can see which parameters are currently included in the summary. They typically include key pharmacokinetic metrics such as tmax, cmax, auclast, half_life, and aucinf_obs. You can select or deselect parameters as needed for your analysis.

• Groups: Define the grouping variable for the analysis, such as 'dose', to categorize the results accordingly.

• Select Summary Statistics: Choose which summary statistics to display in the table, like the number of non-missing observations (nonmissing), geometric mean (geomean), and geometric coefficient of variation (geocov).

The following statistics are available for selection:

Formatting Options

Additional formatting settings are available to fine-tune how the data appears:

• Rounding Mode: Determine how the numbers in the table should be rounded. Options include:

  • Auto: The software automatically decides the best rounding based on the data (default is 3 digits).
  • Significant Digits: Round the numbers to a specific number of significant digits (default is 3 significant digits) .
  • Digits: Specify the exact number of digits after the decimal point (default is 3 digits).

• Show Trailing Zeros: Tick this option if you want the table to display zeros at the end of a number, which can be important for maintaining consistent decimal places across all values.

After making all the necessary adjustments, you can save the changes by clicking the 'Done' button. This will update the Parameter Summary Table with the new settings, ensuring that the table reflects the most relevant and accurately formatted data for your NCA analysis.

Ratio Table

Users can add a new parameter table by clicking the + symbol on the top right of the rectangular box. The Ratio Table is a specialized table type that allows for the comparison of pharmacokinetic parameters across different groups. This feature is particularly useful for assessing the relative effects of different treatments or conditions on key NCA metrics.

User Interaction

1. Table Type: Ensure that the table type is set to 'Ratio Table.' This type of table is designed to display the ratios of selected pharmacokinetic parameters across different groups.

2. Table Caption: Enter a descriptive caption for the new table. This should be succinct but clear enough to convey the essence of the data it contains and is useful for reference in the final report.

3. Parameter Selection:

   • Parameter: Choose the pharmacokinetic parameter for which you want to calculate ratios.
   • Groups: Select the grouping factors that define the subsets of data within your analysis. This could be based on different doses, treatment arms, or study days.
   • Reference Group: Specify the reference group against which all other groups' parameters will be compared. The ratios will be calculated as the parameter value in each group divided by the parameter value in this reference group.

4. Rounding Mode: If necessary, set the rounding mode to define how numeric values should be displayed, which can be left as 'Auto' for the software to determine the best format.

After setting up the required fields, you can preview the table to verify the settings. Once satisfied, click 'Done' to add the new Ratio Table to your analysis results. This table will enable you to easily compare the effects of different study conditions on pharmacokinetic outcomes, providing a clear visual and quantitative assessment of the data.

Listings

Parameter Listings Table

The Parameter Listings Table is a critical feature in PumasCP for NCA analysis that lists the pharmacokinetic parameters for each study subject per group. This table is customizable to fit the specific requirements of your study.

Interface Components

• Add Parameter Listing: To accommodate various datasets or comparison needs, use this button to introduce a new parameter listings table to the results section.

• Parameter Listings Box: This section, labeled 'NCA parameter listing,' will display a list of all NCA parameters calculated during the analysis. The list is initially collapsed to simplify the view but can be expanded for detailed examination.

User Interaction

• Expanding the Listing: Click on the box or the accordion toggle to expand and review detailed NCA parameters.

• Editing the Listing: Changes to the parameter listings, such as modifications to displayed parameters or statistical information, are made by clicking the edit icon.

Editing Process

Refer to the Parameter Summary Tables section for in-depth guidance on editing processes, including arranging parameters, grouping, and selecting statistics. For details on adjusting these elements in the Parameter Listings Table, the same instructions apply. However, the listing tables have additional features to enhance the presentation of raw data that is discussed below.

Additional Formatting Options in Listing Tables

• Summarize on: Select the key variable, such as 'dose', on which to base the summarization of your data. This will organize the table by the chosen variable, making it easier to compare results across different levels or groups. Even if you have multiple grouping variables, users can choose only one primary variable for summarization.

• Column Sections per Page: Adjust the number of column sections displayed on each page of your table. Use the plus and minus buttons to increase or decrease the number, allowing you to customize the breadth of data shown on a single page for clarity and conciseness. This allows the customization of the table view in the final word or PDF report. If the number of columns is too wide, the table will be split into multiple pages.

• Row Sections per Page: Similarly, define the number of row sections per page using the plus and minus buttons. This helps manage the length of the table on each page, ensuring that each section is digestible and aligns with the desired layout for reporting or reviewing. This allows the customization of the table view in the final word or PDF report. If the number of columns is too long, the table will be split into multiple pages, as can be seen in the paginated view of the table.

Applying the Settings

Once you've adjusted these settings, along with those common to the Parameter Summary Table, your Parameter Listings Table will be formatted to provide a clear and structured presentation of your NCA data. For detailed guidance on initial table settings, refer to the earlier section on the Parameter Summary Table. Remember to click 'Done' to save your configurations and update the table in your analysis results.

Formatting Options

Control the presentation of numerical data in your listings with the following settings:

• Rounding Mode: Choose 'Auto' for automatic rounding, or specify the number of significant digits or fixed digits after the decimal.

• Show Trailing Zeros: Enable this to display numbers with consistent decimal places, retaining zeros at the end.

Once configured, select 'Done' to apply your changes, ensuring the Parameter Listings Table accurately represents the critical data for your analysis.

Figures

Figures are an integral part of presenting and reviewing NCA results in PumasCP, allowing for visual comparison of pharmacokinetic parameters across different groups within the study.

Adding and Customizing Figures

• Add Figure: Click this button to create a new graphical representation of your data. This feature is useful for visualizing the distribution and trends of parameters such as tmax, cmax, auclast, half_life, and aucinf_obs across different groups. The plots represented by default are the ones selected in the Parameters to Summarize section of the Set NCA Preferences in step 5.

• Figures Box: Each listed figure represents a specific parameter comparison against a group. You can expand each accordion to customize or review the figures.

User Interaction

• Expanding the Figure: Expand a figure to see a full-size plot in a new browser tab. Changes are not allowed in the view tab, and any modifications made in the main tab will not be reflected here when the view tab remains open.

• Editing the Figure: Use the edit button to adjust figure settings such as the parameter to plot, the grouping variable, and the figure type.

Editing the Figure

In the edit window:

• Figure Type: Choose from 'Parameters vs. Group', 'Parameter Distributions', or 'Dose vs. Dose Normalized' to determine the structure of the figure.

• Settings:

  • Result Source: Select 'Raw Results' to base the figure on the initial output or 'Transformed Results' if any post-processing has been applied to the data.
  • Figure Caption: Provide a clear title that reflects the content of the figure.
  • Parameter: Specify which pharmacokinetic parameter the figure should display.

• Format:

  • Color: Choose a color to differentiate groups or parameters within the figure.
  • Plot Type: Select 'Violin' or 'Boxplot' to represent the data distribution. Violin plots are useful for showing the probability density of the data, while boxplots provide a summary of the distribution.

Conclusion

After configuring the figure settings, ensure that you save your changes.