Findings Shift Plots

This report displays shift plots to compare test measurements for a specified findings domain at baseline versus on-therapy values and performs a matched pairs analysis on average score during baseline and a summary score during the trial. A separate analysis is done for each findings measurement.

Note: JMP Clinical uses a special protocol for data including non-unique Findings test names. Refer to How does JMP Clinical handle non-unique Findings test names? for more information.

Methodology

No testing is performed. Analysis is restricted to calculating simple statistics of post-baseline findings results or their log transformed and/or normalized values against baseline values.

Usage and Interpretation

The Findings Box Plots report was run with Nicardipine sample data set under several scenarios to demonstrate usage and interpretation of results.

Example 1:

It contains the following elements:

• One set of Shift Plots for each finding observed in the study.

These plots show how findings levels change from baseline values as a result of treatment. Blue points represent patients treated with nicardipine. Gray points represent patients receiving the placebo. The approximately square spread of points (with a diagonal line splitting approximately even across it) indicates similar variability of measurements before and after treatment.

Note: You may notice a difference in baseline vital signs results between JMP Clinical v8.1 and v19. This can happen when the baseline calculation is for the mean of recorded predose measurements for findings that have "Y" as a value for VSBLF if some of those rows are missing a value for VSDY. v8.1 computes the mean for all rows that have a value of "Y" as a value for VSBLF, regardless of the value of VSDY. v19 ignores any rows lacking a value for VSDy and computes baseline means using just the rows that both have a value of "Y" as a value for VSBLF, and some value for VSDY.

Options

Data

Domain

Use this widget to specify whether to plot the distribution of measurements from either the Electrocardiogram (EG), Laboratory (LB), or Vital Signs (VS) findings domains.

LB is selected by default.

Findings Tests

Use this widget to select specific Findings tests. If you leave this field blank, all tests are run.

8 Click to open the Add window (shown below) that lists available test names (shown below).

8 Select the desired test(s) and click to add them to the text box.

Summary Statistic for Trial Data

Use the drop down to specify whether to display the mean (specified by default), median, maximum, minimum, or last values to summarize the results of the trial period.

 

 

Options are defined in the following table:

Summary Statistic

Definition

Min

• Reports the minimum value observed across the trial period.

Mean

• Reports the mean of all measurements observed across the trial period.
• This value is always used to summarize data from the baseline period.

Median

• Reports the median of all measurements observed across the trial period.

Max

• Reports the maximum value observed across the trial period.

Last

• Reports the last value observed across the trial period.

Normalization of Lab Measurements

By default, JMP Clinical reports unaltered laboratory measurement values (None). In any cases, simply examining the raw numbers can make interpretation somewhat confusing. Normalization of Lab Measurements to accepted values can often ease these difficulties. JMP Clinical offers several methods for normalizing your data.

Note: This option is not available for domains lacking upper or lower limits of normal variables.

Use the drop-down menu to select a normalization to be applied to the baseline and on-therapy measurements.

Available normalizations are described in the following table:

Normalization

Definition

None

Choose this option to apply no normalization to the laboratory measurements.

LLN

Select this option to divide the measured lab values by the value considered to be the lower limit of the normal range (LLN) of values. This measure normalizes the labs relative to the LLN.

Selecting this method is best used when you expect the values to fall below the normal. Normalized values less than one are considered to be lower than normal.

ULN

Select this option to divide the measured lab values by the value considered to be the upper limit of the normal range (ULN) of values. This measure normalizes the labs relative to the ULN.

Selecting this option is best used when you expect the values to exceed the normal range. Normalized values greater than one are considered to be higher than normal.

Geometric

Select this option to normalize the data using the formula: normalized value = (log(x) - log(GM))/log(GSD), where x is the raw value, GM is the geometric mean of the upper limit of the normal range (ULN) of values and the lower limit of the normal range (LLN) of values, and GSD is the geometric standard deviation of the ULN and LLN. The geometric normalized data are measured on a scale (centered on 0) based on the number of GSD units the observations are from GM.

On this scale the GM is the midpoint between the log transformed upper and lower limits (ULN and LLN) and each GSD is equal to half the range between the log(ULN) and log(LLN). With this normalization, values -1 and 1 are set to equal the LLN and ULN respectively and behave similar to a z-score. Clinically, values greater than 1 (or less than -1) can be interpreted as a measure of how far away the finding was from the ULN (or LLN) with respect to the normal range of values (ULN - LLN). Values less than 1 or greater than -1 would indicate that the finding was within the normal range of values.

Note: This option is available only in select reports.

log Transformation of Findings Measurements

Log transformations can make certain response distributions closer to Gaussian with constant variance and can enable you to draw more accurate statistical conclusions under standard modeling assumptions. They are especially useful for ratio-type measurements or measurements that are always positive and skewed to the right.

Use the drop-down menu to select the transformation to be applied to the baseline and experimental measurements. None is selected by default.

Options are listed in the following table:

Summary Statistic

Definition

None

• Applies no transformation to the observed values.

Log2

• Calculates and reports the log2 value for each of the observations.

Log10

• Calculates and reports the log10 value for each of the observations.

Remove unscheduled visits

You might or might not want to include unscheduled visits when you are analyzing findings by visit.

By default, this box is checked. When it is checked, records are excluded from the analysis if the VISIT variable exists and contains the text "unscheduled" for those records. If the box is not checked all records are included regardless of the VISIT status.

For some reports, you may have to specify Visits as the Time Scale to enable this field.

Calculate baseline as:

Use this widget to use the flagged baseline record, last recorded pre-dose measurement or the mean of all the measurements taken during the baseline time window as the baseline measurement.

By default, the flagged baseline record is used.

The following test measurements are considered when forming the baseline measurement:

• those flagged as baseline, and
• those taken prior to Study Day 1

Choose Last recorded pre-dose measurement to use the last recorded pre-dose test measurement (out of the test measurement pool generated from the above list) as the baseline measurement.

Choose Mean of recorded pre-dose measurements to average these pre-dose test measurements to form the baseline measurement.

Note: When the selected option to calculate baseline is to use the baseline flag and there are two records flagged as baseline, JMP Clinical uses the last record. This differs from JMP Clinical version 8.1, wherein the mean of the flagged baseline values was used.

Snapshot Records to Include

Use this widget to specify which updated snapshot records to include in your analysis. This option is surfaced only in studies where the number of snapshots is greater than 0.

The default state of this option is to show new, modified and stable - effectively all - snapshot records. To see specific records you must remove undesired records from the analysis. For example, to surface only the new records, select both Modified and Stable and click . Click to restore deleted records.

Note: JMP Clinical now relies on the JMP Compare Data Tables platform to detect new records. When duplicate rows appear, the platform evaluates them based on their row order. As a result, records are no longer labeled as Non‑Unique or Previously Non‑Unique, and the corresponding options to include those records have been removed.

Additional Filters - Findings

This filter lets you restrict your analysis to only those subjects that meet specific criteria at the level of the specified Findings domain (EG, LB, or VS) .

This filters uses JMP WHERE clauses to Select Rows that meet the specified criteria. To use this filter, you must enter the JSL (JMP Scripting Language) expressions that constitute the WHERE clause in the appropriate text box for specific filtering of findings. Note: This is an advanced concept that not only requires some basic knowledge of the JSL where clause syntax (similar to, but different from, SQL), but also an understanding of the exact variables in the tables in the study.

Risk indicators are calculated using this subset only.

To specify a Findings filter:

8 Click to open the Where Clause Builder to construct the desired filter.
8 Click to clear the filter.

Note: To filter subjects with a specific event or finding, one could also use the Subpopulation Builder on any domain of interest. For example, filter to all subjects that exhibit cardiac failure ( :Customized Query 01 Name == "Cardiac failure" ) and run all reports on those.

Display

Test Results/Vital Signs

This option lists all of the tests performed over the course of the study. The list is specific to the selected Findings domain and changes when you change the selected domain.

8 Select one or more tests to display only the results for the selected domain(s).

Action Buttons

Action buttons provide you with an easy way to drill down into your data. The following action buttons are generated by this report:

• Click to rerun the report using default settings.
• Click to view the associated data tables. Refer to Show Tables for more information.
• Click to generate a standardized PDF- or RTF-formatted report containing the plots and charts of selected sections.
• Click to generate a JMP Live report. Refer to Create Live Report for more information.
• Click to take notes, and store them in a central location. Refer to Add Notes for more information.
• Click to read user-generated notes. Refer to View Notes for more information.
• Select one or more subjects, then click to apply the Review Subject Filter and filter all reports in the review builder on the selected subjects.
• Select a group of subjects and click to specify Derived Population Flags that enable you to distinguish the selected group of subjects from the general population.

Default Settings

Refer to Set Study Preferences for default Subject Level settings.