JMP Clinical Basics | Frequently Asked Questions

Frequently Asked Questions
How do I access the Help system in JMP Clinical?
The JMP Clinical Help system can be accesses from several paths.
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Click any of the “?” links in the analysis dialogs to access the relevant Help page for a particular term or specification.
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Click the Process Description link at the top of any analysis dialog to see a description of the analysis, including requirements.
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Click the Output Description link at the top of any output dashboard to see a detailed description of tabs, drill downs, output data sets, follow-up processes, general action buttons, or any other feature on the dashboard.
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Open the Help system from the JMP Clinical Starter window. Click Documentation and Help and then click User Guide.
To find specific information within the Help system, use either the Table of Contents, the Index, or the Search options, as shown below:
Finally, you can access the JMP Clinical Help system from either the JMP website or from the local version that was included with your JMP Clinical software. By default, JMP Clinical accesses the Online version of the Help system. This version is frequently updated and you can be assured of having the latest information when you access this version. However, if your computer is isolated from the Internet, you can access the local version of the Help system by completing the following steps:
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Click File > Configure Life Sciences Settings to open the Configure Life Sciences Settings dialog.
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Check the Local version of the User Guide radio button (circled below) and click Run.
A Results window appears when the configuration is complete. You can repeat this process, clicking the Online version of the User Guide radio button, to access the Online version of the Help system.
Where do I find the Trouble Shooting section of the JMP Clinical Help system?
The Trouble Shooting section of the Help is found in the Appendixes.
How does JMP Clinical handle date and time information?
Times and dates are an integral part of the data generated in all clinical trials. At least one timing variable must be included in all SDTM subject-level domain data sets. Time and date variables are numerically formatted according to the following ISO 8601 standard: YYYY-MM-DDThh:mm:ss, where
YYYY is the four-digit year,
MM is the two-digit month (values rage from 01-12),
DD is the two-digit day (values range from 01-31),
hh is the two-digit hour (values range from 00-23)
mm is the two-digit minutes (values range from 00-59), and
ss is the two-digit seconds (values range from 00-59).
Additional, allowable characters include
T, which indicates that time information is included (omitted if no time component is included),
-, which either separates the date elements or can be used to indicate missing date components
:, which separates time elements,
/, which can be used to separate the date components from the time components, and
P, which serves as a duration indicator and precedes the date/time components representing the duration of an event or intervention.
Note: Spaces are never allowed in any ISO 8601-formatted representations of dates/times.
Dates and times can be and are expressed as complete dates/times, partial date/times, or incomplete date/times. JMP Clinical recognizes each of these elements and handles partial or incomplete dates/times as described in the separate FAQ: How does JMP Clinical Handle partial or incomplete date and time information?
How does JMP Clinical Handle partial or incomplete date and time information?
When date/time values are either partial or incomplete, JMP Clinical invokes a “first moment” rule. In these cases, when a date/time component is not included in the ISO 8601 value, that value is assumed to be the first possible value. For example, if the value for an event is listed as “2013-12”, JMP Clinical assumes that the event occurred on the first day of December 2013. and assigns a day value of “01”.The resulting sort order of partial dates using the first-moment rule is the same as that of the ISO 8601 strings themselves.
Narrative findings are reported as follows:
When a partial date identified (xxDTC for LB, EG or VS), an asterisk (*) is appended to the end of the finding name or test code. You should review the findings for the appropriately reported set of observations.
When the reference date (RFSTDTC) is partial, an asterisk is appended to the AETERM. You should review all reported dates, study days, and contents for correctness.
When the AE start date (AESTDTC) is partial, an asterisk is appended to the date in the narrative. You should review all contents of the narrative.
When the AE end date (AEENDTC) is partial, an asterisk is appended to the date in the narrative. You should review the final outcome and narrative header information for correctness.
When any of the dosing records have partial dates for exstdtc or exendtc, an asterisk is placed in the drug header that explains dose at time of the event, or the pre- or post-dose status. All text related to the drug should be reviewed.
When the date of completion or discontinuation (DSSTDTC) is partial, an asterisk is appended to the date in the narrative. You should review these dates for correctness.
When either or both of the start or stop dates (CMSTDTC or CMENDTC) for Concomitant medications are partial, an asterisk is appended to the end of CMTERM or CMDECOD (based on the selected analysis option). You should review the data for this medication for correctness.
How does JMP Clinical perform Crossover Analysis?
Refer to Crossover Analyses.
How does JMP Clinical define various terms for risk-based monitoring?1
Subjects are considered RANDOMIZED if there is at least one record from DS where the index ((DS.DSDECOD2), RANDOMIZED) is true
Depending on the available information, subjects are considered SCREEN FAILURES if:
the value in either DM.ARM or DM.ACTARM is SCREEN FAILURE, or
the values in DS.EPOCH is SCREENING, the value in DS.DSCAT is DISPOSITION EVENT, and value in DS.DECOD is COMPLETED, or
the value in DS.DSEPOCH is SCREENING and the value in DS.DSDECOD is COMPLETED, or
To determine whether the subjects have COMPLETED the trial, a The SAS WHERE Expression can be included on the analysis dialog to select the appropriate DS records (this statement should also select the records that indicate whether a subject has alternatively DISCONTINUED or WITHDRAWN). If this The SAS WHERE Expression is supplied and the value in DS.DSDECOD is COMPLETED, the subject is considered to have completed the trial. Otherwise, based on the available variables, the subject is considered to have completed the trial only if
the value in DS.EPOCH is TREATMENT and the value in DS.DSCAT is DISPOSITION EVENT and the value in DS.DSDECOD is COMPLETED, or
the value in DS.EPOCH is TREATMENT and the value in DS.DSDECOD is COMPLETED, or
the value in DS.DSCAT is DISPOSITION EVENT and the value in DS.DSDECOD is COMPLETED.
Subjects are considered to have DISCONTINUED or WITHDRAWN when a The SAS WHERE Expression is supplied and DS.DSDECOD is COMPLETED. Otherwise, based on the available variables the subject is considered to have discontinued the trial if
the value in DS.EPOCH is TREATMENT and the value in DS.DSCAT is DISPOSITION EVENT and the value in DS.DSDECOD is COMPLETED, or
the value in DS.EPOCH is TREATMENT and the value in DS.DSDECOD is COMPLETED, or
the value in DS.DSCAT is DISPOSITION EVENT and the value in DS.DSDECOD is COMPLETED.
Randomized subjects who have neither completed nor discontinued the trial are considered ONGOING.
Depending on the available information, subjects are considered TREATED if
Date/Time of First Study Treatment (DM.RFXSTDTC) is nonmissing, or
value for DM.ACTARM is neither SCREEN FAILURE, NOT TREATED, nor NOT ASSIGNED, or
value for DM.ARM is neither SCREEN FAILURE, NOT TREATED, nor NOT ASSIGNED, or
An adverse event (AE) is considered serious (an SAE) if the value in AE.AESER is either Y or YES.
An AE is considered fatal if the value in either AE.AEOUT or is either FATAL or DEATH, or if the value in AESDTH is either Y or YES.
A subject is considered to have signed informed consent if there is a value for Date/Time of Informed Consent (DM.RFICDTC).
A subject is considered to have died if
the value in Date/Time of Death (DM.DTHDTC) is nonmissing, or
the value in DM.DTHFL is either Y or YES, or
the subject discontinued the trial with and the value in DS.DSDECOD is either DEATH or DIED or DEAD.
Subject discontinuations or withdrawals are separated into various reasons for discontinuation:
If the value in DS.DSDECOD is either DEATH, DIED, or DEAD, then the subject is considered to have Discontinued Due to Death, or
If the value in DS.DSDECOD is either LOST TO FOLLOW-UP, LOST TO FOLLOWUP, LOST TO FOLLOW UP, or LTFU, then the subject is considered to be Lost to Followup, or
If the value in DS.DSDECOD is either ADVERSE EVENT or AE, then the subject is considered to have Discontinued Due to Adverse Event, or
If the value in DS.DSDECOD is either WITHDRAWAL BY SUBJECT, SUBJECT WITHDRAWAL, WITHDREW CONSENT, or SUBJECT WITHDREW CONSENT, then the Patient Withdrew from Study, or
How are risk thresholds defined?
A risk threshold data set is used to 1) define the risk levels for individual variables for RBM analyses 2) specify the contribution of each variable to overall indicators of site risk.
In general, risk thresholds work the same for individual indicators as they do for Overall Indicators and can be defined as described below:
For the ith site or country and the jth risk indicator,
where is the mean, median or user-supplied center value. The quantity equals , , and , for Direction of Risk Signals equal to B, U, and L, respectively, and is the value for the it h site or country and the jth risk indicator.
It is acceptable to specify both yellow and red risk thresholds, one or no risk thresholds. When specifying only a moderate threshold, the Red Percent of Center is left missing in the risk threshold data set so that moderate risk is considered. In instances where values do not meet the criteria for moderate or severe risk, the risk is considered mild (green). Note that for risk thresholds defined using the above criteria, no threshold colors are determined in instances where the mean, median or center value is calculated or set to zero.
Risk thresholds can also be defined based solely only the magnitudes of the values observed. In this case,
where the quantity is defined as described above.
In this case, it is acceptable to specify both thresholds, one threshold, or no risk thresholds at all. When specifying only a moderate threshold, the Red Magnitude is left missing in the risk threshold data set so that moderate risk is . In cases where neither moderate nor severe risk applies, the risk is considered mild (green).
There are five overall risk indicators. These are either weighted averages or combinations of the individual risk indicators for which at least one risk threshold is defined, where both the Weight for Overall Risk Indicator and the standard deviation of the indicator > 0.
The first, or Overall Risk Indicator, incorporates all of the variables meeting these criteria into a single measure that signifies the overall risk and performance of a clinical site. This indicator is generated only when the Weight for Overall Risk Indicator exceeds 0 for at least one of the available risk indicators exhibiting variability. If none of the individual indicators have a Weight for Overall Risk Indicator > 0, then the corresponding Overall Risk Indicator is not generated.
Each of the other four overall indicators - Enrollment Metrics, Disposition, Adverse Events, and Manually Entered - combines subsets of the risk indicators based on Category in the risk weight data set. By default, Category matches how variables are grouped in Risk-Based Monitoring, with Manually Entered applied to all user-supplied risk indicators from Update Study Risk Data Set. If no indicators have a Weight for Overall Risk Indicator > 0 for a given category, then the corresponding overall indicator is not provided.
The Weight for Overall Risk Indicator (wj) can either be missing (in this case, it is assumed to be zero) or greater than or equal to zero. The weights are self-normalizing in that each weight is divided by the sum of all weights for variables contributing to the particular overall indicator. The contribution of each indicator to an overall indicator is based on its weight, center value (either mean, median or user-provided center value, ), standard deviation (), and direction. In general, the value for an overall indicator for the ith site or country and the jth risk indicator is defined as , where , , or when Direction equals B,U, or L, respectively. This can be interpreted as larger values imply greater risk. By default, all weights are assumed equal to one in the Default Risk Threshold data set, meaning that each variable contributes equally to each overall indicator.

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To avoid confusion in this FAQ, variables are written as domain.domain-variable. For example, USUBJID from the DM domain is written as DM.USUBJID. When a term can be applied to multiple domains, "xx" is used to imply a two-letter domain code.

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Note: Although variables are listed in uppercase in this document, JMP Clinical is case insensitive.