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Before You Get Started

System Requirements

Working with JMP

The Example Data

Frequently Asked Questions

Report Analyses and Calculations

System Operations, Configurations, and Preferences

Navigating the Help System

System Operations

Using JMP Clinical

JMP Clinical Main Window

Using the Review Builder

Available Reports

Using the Review Viewer

The JMP Clinical Main Window Changes Depending on the Assigned User Role.

Performing Clinical Analyses

Clinical Data Science

Distribution Reports

Adverse Events Narratives

Findings Analyses

Crossover Analyses

Risk-Based Monitoring - External Standard - Version 2

How Supplemental Data Sets are Used by JMP Clinical.

Data Management

Cluster Subjects across Study Sites

Cluster Subjects within Study Sites

Create Cross Domain Data

Multivariate Inliers and Outliers

Birthdays and Initials

DM Distribution

Enrollment Patterns

Perfect Scheduled Attendance

Weekdays and Holidays

Adverse Events Report

AE Bayesian Hierarchical Model

AE Distribution

AE Incidence Screen

AE Resolution Screen

AE Severity ANOVA

AE Time to Event

Discontinuation Time to Event

Events Distribution

Events Incidence Screen

Mortality Time to Event

Standardized MedDRA Queries Distribution

Standardized MedDRA Queries Incidence Screen

Treatment Emergent AE Summary

Constant Findings

Correlated Findings

Digit Preference

Duplicate Records

Findings Box Plots

Findings Bubble Plot

Findings Distribution

Findings Shift Plots

Findings Time to Event

Findings Time Trends

Findings Waterfall Plots

Hy’s Law Screening

Missing Findings

Summary Statistics

Exposure Summary

Interventions Distribution

Interventions Incidence Screen

Disease Response Swimmer Plot

Progression Free Survival

Patient Recruitment

Risk Based Monitoring

Standard Safety Reports

Study Visit Report

Notes Distribution

Required Domain Report

Review Status Distribution

Variable Report

Findings Incidence Report

Missing Value Imputation

Import SAS Transport Files

Generate Clinical Dialogs

Configure Life Sciences Settings

Set Clinical Preferences

Customize Clinical Starter

Convert Character Date

List-Style Specification

The SAS WHERE Expression

Rules for Study Names

Rules for SAS Data Set Names

Rules for Paths

Rules for Review Package Names

JMP Clinical Files Are Identified by Suffixes

JMP Clinical Reports Call SAS PROCS

Trouble Shooting

Contingency Plot

Contingency Table

Geographical Map

Hazard Ratio Event Plot

Heat Map and Dendrogram

Hy’s Law Time Course Plot

Mahalanobis Distances

Matched Pairs Analysis

Principal Components Analysis Plot

Reliability Diagram

Survival Curves

Time Series Graph

Add Notes (Disproportionality Analysis)

Add Record-Level Notes

Apply Subject Filter

Change Significance Criterion

Check Variable Requirement and Usage

Cluster Subjects

Column Switcher for TreeMap Tabs

Construct One-way Plots

Contingency Analysis

Create Animal Filter

Create Narratives

Create Static Report

Create Static Report for Review...

Demographic Counts

Enter New -log10(p) Cutoff

Fit Incidence Density Model

Fit Model and Plot LS Means

Forest Plots of Credible Intervals

Generate Report

Graph Time Profiles

Graph Time Trends

Graph Trellis Plot

Hierarchical for Drug

Hierarchical for Event

JMP Clinical Variable Report

K-Means for Drug

K-Means for Event

Kaplan-Meier and Hazard Plots

Liver Lab Shift Plots

Manage Data Templates

Manage Display Templates

Manage Holiday and Event Data Set...

Add Holiday or Event

Manage Risk Threshold Data Sets...

Manage Subject Filters

Missing Bar Charts

Odds Ratio Plot

Overall Bubble across Time

Plot Survival Curves for Stratified Data

Profile Subjects

Relative Risk Plot

Remove Stable Records

Report Navigator

Revert Clustering

Show All Records

Show Domain Keys

Show Dropped Records

Show Duplicates

Show Events Leading to SMQs

Show New or Modified Records

Show Patients at Risk

Show Records with Missing Test Results

Show Rows in Heat Map

Study Variable Report

Subset Clustering

Unique Occurrence Subject Counts

View Domain Notes

View Record-Level Notes

Visits Standard Report

Import SAS Transport Files

Generate Clinical Dialogs

Convert Character Date

Define Risk Threshold Data Set

Update Risk Threshold Data Sets

Add Holiday or Event

Edit Holiday and Event Data Set

Create Subject Filter

Combine Studies

Refresh Study Metadata

Rename Study...

Change Study Folder Locations

Snapshot History

Update Study with New Snapshot

Update Study Risk Data Set

Subject Explorer

Update Study Risk Data Set

Set Value Ordering in Studies

Manage Profile Data

Variable Contributions to Distance

Select Percentage of Subjects Exceeding Threshold

Report Option Descriptions

A 0 dose for placebo or vehicle indicates a dose interruption

Add treatment group difference threshold to select significant tests

Additional Class Variables

Additional Filter to include Adverse Events

Additional Filter to Include Animals

Additional Filter to Include Disease Response Records

Additional Filter to include Events

Additional Filter to Include Findings Records

Additional Filter to Include Findings Tests

Additional Filter to Include Subjects

Additional Filter to include tumor results records

Additional Fixed Effects

AE Narrative Template

All study treatments are to be taken at least once per day

Amount of Increment in the Remaining Enrollment (How Often to Simulate)

Analyze all tests from all findings domains

Analyze findings using:

Analyze Selected Site Categories

Analyze Selected Sites

Analyze sites with at least this many subjects:

Analyze these digits:

Annotate Plots with Selected Disposition Events

Annotate disposition events and new lesions that occur between tumor results visits:

Attempt study combinations when study variables don’t match

Baseline Time Window

Binary Variables in ADSL

Body System Sorted Alphabetically

Body System Sorted by p-Value

By variables for table transpose

Calculate baseline as:

Calculate exact Mantel-Haenszel p-values

Calculate Overall Response Rate as

Calculate Relative Risks to compare incidence in treatment groups versus a control

Calculate Visit-matched baseline measurements

Character Findings

Class Variables

Cluster subjects

Combine Supplemental Domain

Combined New Study Name

Compute Time Trends

Consider BY variables in the analysis

Consider Group Level to identify unique event terms

Concomitant Medications

Concomitant medications are reported using:

Conditions Summary

Count multiple occurrences of an event per subject

Count multiple occurrences of an intervention per subject

Create additional distributions for selected variables

Create Age Group Table

Create Counts by Severity

Create Hy’s Law 3D Plot

Create summary statistic variables for numeric findings

Category for Response Assessment Criteria Identification

Death Age Analysis

Death Age Group

Default value for lesions marked TOO SMALL TO MEASURE

Derive visits from:

Determine Resolved / Not Resolved Status using:

Direction of the Treatment Group Difference

Disease Response Test for Analysis

Display cross-tabulation tables of Baseline versus Trial laboratory measurement elevations

Display shift tables of Baseline versus Trial laboratory measurement elevations

Display shift tables by Treatment Variable values

Display subject count bar charts on average time trend plots

Display Subject Identifiers on swimmer plot y-axis

Display Subject Identifiers on Waterfall Plot x-Axis

Display symmetrical axes for Shift Plots

Display Visit summary statistic tables for each findings test

Divisor for Lower Normal Limit

Dropout Group and Reason

Dropout Listing

Drug Body System

Duration Time Scale

Duration Time Scale to Plot on X-Axis

Duration Time Window Method

Duration Time Windows

Enable Future Snapshot Comparisons

End Date Variable to Use for Censoring

End Date Variable to Use for Subject Duration

Ending Time Value

Event Definition

Exclude comparisons of treatment variables

Exclude findings after the last day of study treatment

Exclude subjects who experience the event at baseline

Filter to Choose Adverse Events for RBM

Filter to Choose Appropriate Disposition Event for Completion Status

Filter to choose Appropriate Supplemental AE Records for Multiple Causalities or Actions

Filter to Choose Deviations for RBM

Filter to Choose Disposition Event for Completion or Discontinuation Status

Filter to Choose Healthcare Encounters for RBM

Filter to Choose Inclusion or Exclusion Criteria for RBM

Filter to Include Adverse Events

Filter to Include Events

Filter to Include Exposure Records

Filter to Include Findings Tests

Filter to Include Healthcare Encounters

Filter to Include Interventions

Filter to Include Specific Finding

Filter to Include Visits

Filter to only include Target Lesions in numeric result summaries

Findings domains

Findings Domain to Analyze

Findings Domain Tests for Analysis

Findings domain tests to include

Findings domain to include

Gradient Convergence Criterion

Generate summary statistics by visit

Groups Subjects by Treatment Variable

Healthcare encounters are reported using:

Hepatotoxicity Patient Listing

Hierarchical Clustering Method

High and Low Labs

High Baseline Lab Tests

Ignore available treatment emergent flags

Ignore duplicate records when covariates don’t match

Ignore duplicate records within subject

Import SAS Transport Files

Use SAS Transport Files

Include a findings domain in the narrative

Include adverse event reports

Include aggregate subject count and percentages for shift table categories

Include closest on-study findings test dates:

Include concomitant medication indication in narrative text

Include a summary table of concomitant medications

Include demographic reports

Include disposition reports

Include event domains

Include events with overall percent occurrence greater than

Include events or interventions experienced by at least this percent of patients:

Include Exponentiated Estimates and Differences

Include exposure (EX) in the narrative

Include findings domains

Include healthcare encounters (HO) in the narrative

Include intervention domains

Include interventions with overall percent occurrence greater than

Include lab reports

Include medical history reports

Include on-study lab tests where reference range indicator is:

Include p-values in addition to -log10(p-values)

Include Progressive Disease responses on swimmer plot

Include serious adverse events only

Include Stable Disease responses on swimmer plot

Include subject-level table of contents

Include summary for subjects with severe TEAE

Include summary of baseline findings

Include T-statistics

Include the following adverse events:

Include the following events:

Include the following exposure

Include the following findings records:

Include the following interventions:

Include the reported event term in the header only when different than the coded term

Incorporate Findings Time Points in plots

Initial Number of Additional Centers

Intervention domains

Intervention Type

JMP Script Output File Name

Label Hy’s Law quadrants

Lab Test Short Name for Alanine Aminotransferase

Lab Test Short Name for Alkaline Phosphatase

Lab Test Short Name for Aspartate Aminotransferase

Lab Test Short Name for Bilirubin

Limit reported related events to those that are serious

Linearly interpolate values

List every model fit

Location of MedDRA ASCII Files

-log10(p-Value) Cutoff

log Transformation of Lab Measurements

Low Baseline Lab Tests

Lower or Higher Outcome Better

LSMeans Difference Set for Volcano Plots

LSMeans Treatment Control Level

Mark subjects with selected disposition events in the waterfall plot

Match subjects based on:

Maximum Probability of Meeting the Target Date to Initiate Adaptive Adjustment

Mean Change from Baseline

Mean Chemistry Values for Visit

Mean Values Baseline Worst

Medical History

Medical history terms are reported using:

Medical history terms are summarized as a

Merge supplemental domain

Minimum Probability of Meeting the Target Date to Stop Adding New Centers

Model baseline as:

Mortality Treatment Group

Multiple Testing Method

Multiplier for Upper Normal Limit

Multiplier of Abnormal High Lab Test at Baseline

Multiplier of Abnormal Low Lab Test at Baseline

New Combined ADaM Folder

New Combined SDTM or SEND Folder

New SDTM Folder

Normalization of Lab Measurements

Normalize laboratory values by:

Number of Bins for Dose Group

Number of Burn In Samples to Discard per Markov Chain

Number of days around Adverse Event start date for reported related events

Number of Days around Birthday

Number of Days Delayed at New Centers

Number of days prior to Adverse Event start date for reporting concomitant medications

Number of decimals for numeric findings

Number of decimals to display for event percentages in tables

Number of decimals to display for summary statistics in tables

Number of Duration Time Windows

Number of Monte-Carlo Samples

Number of Posterior Samples per Markov Chain

Number of Simulations

Number of Time Windows

Offset for Censor End Date (in Study Days)

Offset for End of Dosing

Only include BY variables if they are domain keys

Only include on-trial measurements

Only mark the first occurrence of a new lesion for each subject

Output Data Set

Output report as

Overall Summary Statistic to Display in Plots

Overlay treatment groups in plots

Overlay visits when treatment crossover is detected

Patient Population by Age

Patient Population by Race

Patient Population by Sex

Patient Population by Treatment

Patient Visit Count

Percent Body System

Percent Drug Body System

Percent Occurrence Threshold

Perform Double FDR Adjustment

Perform incidence analysis using the following SMQs:

Perform Matched-Pairs analysis of Baseline versus Trial measurements for each treatment group

Perform Oneway or Contingency Analysis

Perform treatment comparison analysis for demographic variables

Plot average time trends across treatment groups

Plot findings measurements as:

Plot standardized residuals

Plot tumor results measurements as:

Pool subjects in average time trend plots when treatment crossover is detected

Preserve trailing zero in decimals for result in original units

Prompt when exiting unsaved Review Template

Random seed for simulation

Refer to findings tests using:

Reference Treatment Level

Reference Value or Day

Relationship to Drug

Remove all variables with missing values

Remove Follow-up Records

Remove tests when percentage of subjects expected for a test is equal to or below:

Remove unscheduled visits

Remove variables from analysis with a missing data percentage of at least:

Report healthcare encounters this many days around Adverse Event start date:

Report the following healthcare encounters:

Restrict plots to measurements within a starting time and ending time

Risk Threshold Data Set

Round numeric findings results

SDTM or SEND Folder

Select the color to represent Complete Response

Select the color to represent Partial Response

Select the color to represent Progressive Disease

Select the color to represent Stable Disease

Select the analysis population

Select the population to include in the analysis

Selected ADaM Domains

Selected SDTM Domains

Selected Studies

Set custom reference lines for bubble plot

Set custom reference lines for Hy’s Law plots

Set reference line for transaminase tests

Set reference line for bilirubin

Set reference line for x-Axis

Set reference line for y-Axis

Show lines connecting the responses

Show markers only when response changes

Show Shaded Confidence Intervals on Survival Plot

Show ULN and LLN reference lines for lab tests

Show standard error bars for treatment group time trends

Significant Changes

Size of Time Window in Days

Special visits to exclude

Specify Target Enrollment

Specify the Number of Independent Markov Chains

Specify the Rate of Thinning

Specify the Seed Value

Starting Number for Tables

Starting Time Value

Stratification Variables

Select saved subject Filter

Subsequent visits

Subset of Visits to Analyze

Subset of Domains to Analyze for Events

Subset of Domains to Analyze for Interventions

Subset of Visits to Analyze for Findings

Summarize multiple records per day using:

Summarize subgroups with at least this many subjects

Summarize sites with this many levels or fewer:

Summarize sites with at least this many subjects:

Summarize tumor lesion measurement results by:

Summary Statistic for Findings Data

Summary Statistic for Trial Data

Summary Statistic to Compute Within Time Windows or Visits

Summary Statistics to Display in Tables

Supplemental SAS data set for AE Narrative

Supplemental SAS data set for RBM

Target Enrollment

Target Enrollment of Subjects per Week per Site

Test Treatment Level

Define events as:

Time Lag (in Days) for Classifying Hy’s Law Cases

Time Scale for trend plot x-Axis

Time Windows for Start of AE

Time Window Method

Transpose so that columns are

Treatment Control Level

Treatment end date is equivalent to the start date

Treatment Group Difference Cutoff

Treatment Variable

Treatment or Comparison Variable

Treatment or Comparison Variable to Use

Trial Time Windows

Truncate Early Recruitment Data

Truncation Date

Tumor Result Summary to Display in Waterfall Plot

Tumor Results Test for Analysis

Use Grey Scale for Bar Color

Use log scaling to display findings test measurements

Use Related Records (RELREC) data set to identify concomitant medications that were given due to the event

Use result or finding in:

Use Review Subject Filter for subject-level reports

Use site active date from the Risk Data Set, if available

Use site active date from the Study Risk Data Set, if available

Use subject identifier for study in lieu of unique subject identifier, if available

Use the following time scale for exposure time

Use the Last Randomization Date as Current Date

Variables to include in Report Filter

Visit Number to Compare to Visit 1

x-Axis Findings Test

X-Axis for Volcano Plot

Y-Axis Findings Test

Combine this Study with Study from Update Tab

Combined Study Name

Dependent Variable

Input SAS Data Set

List-Style Specification of Lock-In Class Predictor Variables

List-Style Specification of Lock-In Continuous Predictor Variables

List-Style Specification of Predictor Class Variables

List-Style Specification of Predictor Continuous Variables

Lock-In Class Predictor Variables

Lock-In Continuous Predictor Variables

Predictor Class Variables

Predictor Continuous Variables

Weight Variable

Configuring JMP Clinical 7