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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
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
Data Integrity
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
Study Visits
Visit Order
Weekdays and Holidays
Adverse Events Report
AE Bayesian Hierarchical Model
AE Distribution
AE Incidence Screen
AE Narrative
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 ANOVA
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
Screening Bias
Summary Statistics
Exposure Summary
Interventions Distribution
Interventions Incidence Screen
Patient Recruitment
Risk Based Monitoring
Standard Safety Reports
Study Visit Report
Domain Viewer
Notes Viewer
Required Domain Report
Review Status Distribution
Variable Report
Statistical Methods Used by JMP Clinical
SAS Rules
List-Style Specification
The SAS WHERE Expression
Rules for Study Names
Rules for Paths
Rules for Review Package Names
JMP Clinical Files Are Identified by Suffixes
JMP Clinical Reports Call SAS PROCS
Trouble Shooting
Autocorrelation Plot
Bar Chart
Box Plot
Bubble Plot
Cell Plot
Contingency Plot
Contingency Table
Contour Plot
Distance Graph
Forest Plot
Geographical Map
Hazard Ratio Event Plot
Heat Map and Dendrogram
Hy’s Law Time Course Plot
Mahalanobis Distances
Manhattan Plot
Matched Pairs Analysis
Mosaic Plot
One-way Plot
Overlay Plot
Parallel Plot
Principal Components Analysis Plot
Q-Q Plot
Receiver Operating Characteristics (ROC) Curves
Reliability Diagram
Scree Plot
Segmentation Summary Plot
Shift Plot
Shift Plot
Standardized Residual Plots
Survival Curves
Survival Plot
Time Series Graph
Trace Plot
Tree Map
Trellis Plot
Volcano Plot
Waterfall Plot
Action Buttons
Add Notes
Add Notes (Disproportionality Analysis)
Add Record-Level Notes
Apply Subject Filter
Box Plots
Change Significance Criterion
Check Variable Requirement and Usage
Close All
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
Dot Plot
Enter New -log10(p) Cutoff
Fit Incidence Density Model
Fit Model and Plot LS Means
Forest Plot
Forest Plots of Credible Intervals
Generate Report
Geocode Sites
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 Tabs...
Missing Bar Charts
Odds Ratio Plot
Overall Bubble
Overall Bubble across Time
Plot Survival Curves for Stratified Data
Profile Subjects
Related AE
Related CM
Related Labs
Related Vitals
Relative Risk Plot
Remove Stable Records
Reopen Dialog
Report Actions
Report Navigator
Revert Clustering
Shift Plots
Show All Records
Show Domain Keys
Show Dropped Records
Show Duplicates
Show Events
Show Events Leading to SMQs
Show Map
Show New or Modified Records
Show Records with Missing Test Results
Show Rows in Heat Map
Show SMQs
Show Subjects
Strata Bubble
Study Variable Report
Subset Clustering
Time Trend
Trend Plots
Unique Occurrence Subject Counts
View Comments
View Data
View Domain
View Domain Notes
View 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
Add Study...
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
Delete Study
Report Option Descriptions
A 0 dose for placebo or vehicle indicates a dose interruption
ADaM Folder
Add treatment group difference threshold to select significant tests
Additional Class Variables
Additional Filter to Include Animals
Additional Filter to Include Findings Tests
Additional Filter to Include Subjects
Additional Fixed Effects
AE Narrative Template
Age and Sex
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 for:
Analyze Selected Site Categories
Analyze Selected Sites
Analyze sites with at least this many subjects:
Analyze these digits:
Animal Filter
Attempt study combinations when study variables don’t match
Baseline Time Window
Begin Time
Binary Variables in ADSL
Body System Sorted Alphabetically
Body System Sorted by p-Value
By Age Group
By Race
By Sex
By Variables
Calculate baseline as:
Calculate exact Mantel-Haenszel p-values
Calculate Relative Risks to compare incidence in treatment groups versus a control
Calculate Visit-matched baseline measurements
Character Findings
Class Variables
Cluster subjects
Color Theme
Combine Supplemental Domain
Combined New Study Name
Compute Time Trends
Consider BY variables in the analysis
Concomitant medications are reported using:
Conditions Summary
Count multiple occurrences of an event per subject
Count multiple occurrences of an intervention per subject
Create Counts by Severity
Create Hy’s Law 3D Plot
Create summary statistic variables for numeric findings
Current Date
Death Age Analysis
Death Age Group
Death Days
Death Gender
Death Listing
Death Race
Derive visits from:
Determine Resolved / Not Resolved Status using:
Direction of the Treatment Group Difference
Display cross-tabulation tables of Baseline versus Trial laboratory measurement elevations
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 Window Method
Duration Time Windows
Enable Future Snapshot Comparisons
End Date
End Date Variable to Use for Censoring
End Time
Ending Time Value
Event Definition
Event domains
Event Name
Event Type
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 Findings Tests
Filter to Include Healthcare Encounters
Filter to Include Interventions
Filter to Include Specific Finding
Filter to Include Visits
Findings domains
Findings Domain to Analyze
Findings Domain Tests for Analysis
Findings domain tests to include
Findings domain to include
Findings Tests
Fit model type
Fixed Effects
Gradient Convergence Criterion
Generate summary statistics by visit
Group 1
Group 2
Group 3
Group 4
Group 5
Group Level
Healthcare encounters are reported using:
Hepatotoxicity Patient Listing
Hierarchical Clustering Method
High and Low Labs
Ignore available treatment emergent flags
Ignore duplicate records when covariates don’t match
Ignore duplicate records within subject
Import SAS Transport Files
Import SAS Transport Files (If Available)
Include a findings domain in the narrative
Include adverse event reports
Include closest on-study findings test dates:
Include concomitant medication indication in narrative
Include demographic reports
Include disposition reports
Include events or interventions experienced by at least this percent of patients:
Include Exponentiated Estimates and Differences
Include exposure (EX) in the narrative
Include healthcare encounters (HO) in the narrative
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 serious adverse events only
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 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
Linearly interpolate values
List every model fit
Location of MedDRA ASCII Files
-log10(p-Value) Cutoff
log Transformation of Lab Measurements
Lower or Higher Outcome Better
LSMeans Difference Set for Volcano Plots
LSMeans Treatment Control Level
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 terms are reported using:
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
New Study Name
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 End of Dosing
Output as PDF
Output as RTF
Output Data Set
Output Folder
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 treatment comparison analysis for demographic variables
Plot average time trends across treatment groups
Plot findings measurements as:
Plot standardized residuals
Pool subjects in average time trend plots when treatment crossover is detected
Random Effects
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 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:
Response Type
Restrict plots to measurements within a starting time and ending time
Risk Threshold Data Set
Round numeric findings results
SAE Listing
SDTM or SEND Folder
Seed Number
Select a task
Select the population to include in the analysis
Selected ADaM Domains
Selected SDTM Domains
Selected Studies
Set Age Groups
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 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
SMQ Folder
Special visit numbers
Specify Target Enrollment
Specify the Number of Independent Markov Chains
Specify the Rate of Thinning
Specify the Seed Value
Start Date
Starting Time Value
Stratification Variables
Study Name
Subject Filter
Subsequent visits
Summarize multiple records per day using:
Summarize subgroups with at least this many subjects
Summarize sites with at least this many subjects:
Summary Report
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 Date
Target Enrollment
Target Enrollment of Subjects per Week per Site
Term Level
Test Treatment Level
Define events as:
Time Lag (in Days) for Classifying Hy’s Law Cases
Time Scale
Time Unit
Time s for Start of AE
Time Window Method
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
Use log scaling to display findings test measurements
Use result or finding in:
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
Visit Number 1
Visit Number 2
Visit Number to Compare to Visit 1
x-Axis Findings Test Short Name Value
X-Axis for Volcano Plot
Y-Axis Findings Test Short Name Value
Combine this Study with Study from Update Tab
Combine with:
Combined Study Name
Delete Study
Dependent Variable
Input SAS Data Set
Label Variable
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
New Study Name
Output Folder
Predictor Class Variables
Predictor Continuous Variables
Study Name
Weight Variable
Configuring JMP Clinical