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JMP Clinical Basics

General Information

System Requirements

Text Conventions

SAS Variable Names and Labels

Localization-Specific Value Specification

Data Sets Generated by the AE Narrative Report

Sample Case Studies

Crossover Analyses

Using JMP Clinical for Crossover Analysis

Findings Time Trends

Adverse Events Distribution

Other JMP Clinical Cross-over Analyses

Distribution Reports

AE/Events/Interventions Distributions Workflows and Computations

Distribution Workflow Summary

Distribution Report Results

Understanding Count and Percent Calculations

Distribution Results When Counting Multiple Occurrences of an Event or Intervention

Other Distribution Results

Determining If an Event Is a Treatment Emergent Adverse Event

Frequently Asked Questions

System Operations

JMP Clinical Main Window

Adding and Manipulating Studies

Generating a New Review

Using a Prior Template for a New Study

Opening an Existing Review

Available Reports

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 Animals

Additional Filter to Include Findings Tests

Additional Filter to Include Subjects

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:

Baseline Time Window

Binary Variables in ADSL

Body System Sorted Alphabetically

Body System Sorted by p-Value

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

Duration Time Window Method

Class Variables

Cluster subjects

Combine Supplemental Domain

Combined New Study Name

Compute Time Trends

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

Death Age Analysis

Death Age Group

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

For Intervention and Disposition reports:

For AE Time to Event:

Divisor for Lower Normal Limit

Dropout Group and Reason

Dropout Listing

Drug Body System

Duration Time Scale

Duration Time Windows

Enable Future Snapshot Comparisons

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 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 to include

Gradient Convergence Criterion

Generate summary statistics by visit

Healthcare encounters are reported using:

Hepatotoxicity Patient Listing

Hierarchical Clustering Method

High and Low Labs

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 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:

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

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 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 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 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:

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 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 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 visit numbers

Specify Target Enrollment

Specify the Number of Independent Markov Chains

Specify the Rate of Thinning

Specify the Seed Value

Starting Time Value

Stratification Variables

Subsequent visits

Summarize multiple records per day using:

Summarize sites with at least this many subjects:

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 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 Windows 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 to Compare to Visit 1

x-Axis Findings Test Short Name Value

x-Axis for Volcano Plot

y-Axis Findings Test Short Name Value

Annotation Data Sets

Combine this Study with Study from Update Tab

Combined Study Name

Default Annotation Data Set

Default Experimental Design Data Set

Default Tall Input Data Set

Default Wide Input Data Set

Dependent Variable

Experimental Design Data Sets

Folder of Annotation Study Data Sets

Folder of Experimental Design Study Data Sets

Folder of Tall Study Data Sets

Folder of Wide Study Data Sets

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

Server Output Directory

Weight Variable

Output Graphics and Action Buttons

Autocorrelation Plot

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

Receiver Operating Characteristics (ROC) Curves

Reliability Diagram

Segmentation Summary Plot

Standardized Residual Plots

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 Domains

Cluster Subjects

Column Switcher for TreeMap Tabs

Construct One-way Plots

Contingency Analysis

Create Animal Filter

Create Narratives

Create Static Report

All Other Reports:

Create static report for Review...

Create Subject Filter

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

Missing Bar Charts

Odds Ratio Plot

Overall Bubble Across Time

Plot Survival Curves for Stratified Data

Profile Subjects

Relative Risk Plot

Remove Stable Records

Revert Clustering

Show All Records

Show Domain Keys

Show Dropped Records

Show Duplicates

Show Events Leading to SMQs

Show New or Modified Records

Show Records with Missing Test Results

Show Rows in Heat Map

Study Variable Report

Subset Clustering

Uniques Occurrence Subject Counts

View Domain Notes

View Notes (Disproportionality Analysis)

View Record-Level Notes

Visits Standard Report

Import SAS Transport Files

Generate Clinical Dialogs

Convert Character Date

Output Overview Descriptions

Clinical Reports

Combine Studies

Required Domain Report

Snapshot History

Subject Explorer

Assign Default Data Sets

Assign Wide Variable Roles

Workflow Builder

DM Distribution

Enrollment Patterns

Weekdays and Holidays

Exposure Summary

Interventions Distribution

Interventions Incidence Screen

Mortality Time to Event

Mortality Cause Comparison

Discontinuation Time to Event

AE Distribution

AE Incidence Screen

AE Bayesian Hierarchical Model

Treatment Emergent AE Summary

AE Time to Event

AE Time to Event (One ARM)

AE Severity ANOVA

AE Resolution Screen

Adverse Events Report

Standardized MedDRA Queries Distribution

Standardized MedDRA Queries Incidence Screen

Events Distribution

Events Incidence Screen

Findings Distribution

Findings Shift Plots

Findings Box Plots

Findings Time Trends

Findings Waterfall Plots

Findings Bubble Plot

Findings Time to Event

Findings Subgroup Forest Plot

Missing Findings

Hy’s Law Screening

Summary Statistics

Study Visit Report

Standard Safety Reports

Adverse Events Report

Findings Incidence Report

Profile Subjects

Profile Selected Subjects

Profile All Subjects

Cluster Subjects

Create Subject Filter

Manage Subject Filters

Create Cross Domain Data

Patient Recruitment

Risk Based Monitoring

Update Study Risk Data Set

Define Risk Threshold Data Set

Birthdays and Initials

Cluster Subjects Across Study Sites

Edit Holiday and Event Data Set

Perfect Scheduled Attendance

Constant Findings

Correlated Findings

Duplicate Records

Digit Preference

Multivariate Inliers and Outliers

Cluster Subjects within Study Sites

Disproportionality Analysis

Review Status Distribution

Variable Report

Map Geocoding Help

Output Tab Descriptions

Adaptive Adjustment

Adverse Event Distribution

Between-Subject Distance Summary

Between-Subject Distance Summary (Cluster Subjects Across Study Sites)

Body System or Organ Class Exploding Volcano

Body System or Organ Class Results

Body System or Organ Class TreeMap

Bubble Plot of LB

Case Distribution

Cause of Death Contingency Analysis

Concomitant Medications

Country-Level Distributions

Country-Level Map

Country-Level Data

Define Risk Threshold Data Set

Demographic (Mortality Time to Event)

Demographic Tables

Dictionary-Derived Term Exploding Volcano

Dictionary-Derived Term Results

Distribution Details

Distribution Details (AE Distribution)

Distribution Details (SMQ Distribution)

Distribution Details (Weekdays and Holidays)

Distributions (AE Distribution)

Distributions (Hy’s Law Screening)

Duration Distribution

ECG Test Results

ECG Test Results (Frequencies)

ECG Test Results (Missing Findings)

ECG Test Results (Outliers)

Enrollment by Planned/Actual Arm

Exposure Summary

Findings Details

Frequencies Volcano Plot

Hierarchical SMQ’s

High Baseline Lab Test

Hyperparameters

Hy’s Law Screening

LB Matched Pairs

LB Shift Tables

Laboratory Test Results

Laboratory Test Results (Frequencies)

Laboratory Test Results (Outliers)

List of Subjects with Duplicates for Birthday

Low Baseline Lab Test

Mahalanobis Distance

MCMC Diagnostics

Medical History

Missing Findings Volcano Plot

Missing Lab Test Summary

Missing Test Details

Name of Standardized MedDRA Queries Results

Outliers Volcano Plot

Overall Enrollment

Patient Recruitment

Record Distribution

Results (Discontinuation Time to Event)

Overall Survival

Screening Bias Volcano Plot

Site-Level Distributions

Site-Level Maps

Site-Level Data

Site XX Distance Matrix

Subgroup Clustering

Subject Time Trends

Summary Statistics Volcano Plot

Tables (Patient Profiler)

Test Results (Digit Preference)

Tests by Study Day

Treatment Comparisons

Treatment Time Trends

Tree Map for BCPNN

Tree Map for MGPS

Tree Map for PRR

Tree Map for ROR

TreeMap Results

Update Study Risk Data Set

Usage Components

Variable Summary

Variability Estimates

Variability Estimates (AE Severity ANOVA)

Visit Day Distributions

Vital Signs (Frequencies)

Vital Signs (Missing Findings)

Vital Signs (Outliers)

Volcano Plot for Difference in Proportions

Volcano Plot for Odds Ratio

Waterfall Plots

Weekdays and Holidays Volcano Plot

Using JMP Graphics in Presentations and Publications

Server Profiles

Delete SAS Server Profile

Select SAS Server Profile

Specifying Folders, Files, and Data Sets

Specifying Files or Data Sets

Examining Folders, Files, and Data Sets

Examining Folders, Files, and Data Sets When JMP Is Connected to SAS on Your Local Machine

Examining Folders, Files, and Data Sets When JMP Is Connected to SAS on a Server

List-Style Specification

The SAS WHERE Expression

Estimate Statements and the Estimate Builder

Rules for Study Names

Rules for Paths

Rules for Review Package Names

JMP Life Sciences Files are Identified by Suffixes

JMP Life Sciences Processes Call SAS PROCS

Trouble Shooting