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Title: Cumulative Incidence for Alanine Aminotransferase (ALT): Elevations > 3 Times the Upper Limit of Normal

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Title Cumulative Incidence for Alanine Aminotransferase (ALT): Elevations > 3 Times the Upper Limit of Normal
Graph_Subgroup Labs Liver
Labs_Liver_Clinical_Question
Baseline: 2. Is there a temporal relationship between treatment and lab value?
Description This is a cumulative incidence plot. The cumulative incidence of those subjects with > 3 times the upper limit of normal for the liver function test alanine aminotransferase (ALT) is plotted for treatment versus placebo over time. Standard error bars are added to the graph and are calculated using the following formula:

Lower Bound = P 1.96*SQRT(P(1-P)/n) where P is the proportion of subjects with an elevation (i.e. number o f subjects with an elevation > 3xULN divided by the total number at risk) and n is the total number at risk.
Upper Bound = P + 1.96*SQRT(P(1-P)/n) where P is the proportion of subjects with an elevation (i.e. number o f subjects with an elevation > 3xULN divided by the total number at risk) and n is the total number at risk.


Another formula that gives similar results that is used in the literature for the crude standard error of cumulative incidence is as follows:

Lower Bound = P 1.96*P/SQRT(n) where P is the proportion of subjects with an elevation (i.e. number o f subjects with an elevation > 3xULN divided by the total number at risk) and n is the total number at risk.
Upper Bound = P + 1.96*P/SQRT(n) where P is the proportion of subjects with an elevation (i.e. number o f subjects with an elevation > 3xULN divided by the total number at risk) and n is the total number at risk.


The standard error calculation can be modified as necessary within the code.

Upper limit of normal is calculated by dividing the standard result ( SDTM data set variable lbstresn) in numeric units by the standard high range limit (SDTM dataset variable lbstnrhi). Original units can be substituted if needed as the upper limit of normal is normalized (has no units).

Below the graphic are both a legend indicating the treatment groups depicted on the graph and a legend indicating the at risk subject population by treatment group at each specific visit. Note that due to the uniform axis separation, and the visit schedule of the study, there may be blanks in the at risk population legend if there is no data for a specific visit. Note that the placement of the treatment group legend can be adjusted within the code based upon end user preferences. It is important to consider that if a color graphic is not presented, the line styles will allow for distinction between treatment groups.
In addition, the amount of white space (y-axis range) can be adjusted within the programming. The current graph depicts the y-axis range from 0 to 0.6 and the line separation between treatment groups is adequate so that the viewer can easily discern the two groups. However, if the lines were closer it may be advantageous to lessen the y-axis range and therefore broaden the separation between close lines.

There is also the possibility of adding another analysis group (i.e. >5 times the upper limit of normal for example). In this instance, it is possible that there would be two lines for each treatment group and the programmer would need to choose line styles/colors appropriately.

*Note: The actual data had very few measurements that were >3 xULN. Therefore, for the graph to offer a beneficial representation, the ULN values were quadrupled (multiplied by 4). This allows for a good separation and representation of the effectiveness of the graph in such situations. This multiplication factor is NOT included in the attached code. It is mentioned here purely in an effort to explain why running the attached code produces almost a flat line graphic with no separation and not the one depicted on this page.
Contributor/Email Robert Gordon (rgordon2@its.jnj.com)
Additional_Contributor_Info

Background This graphic was inspired from a GSK cumulative incidence graphic supplied by Susan Duke.
Keywords Cumulative, Incidence, Step
References

Datasets

CDISC_Data

Data_Format Dataset(s) necessary for the graphic are created within the code.
CLASSIFICATIONS

Graph_Type

Variable_Relationship Continuous versus Continuous
Data_Types Continuous
Special_Considerations Depending on the lab parameter and the level of concern, clinically meaningful values (e.g. > 3 times upper limit of normal) and interpretation will differ. It is important to specify these values and properly incorporate them into the code before producing a graphic for interpretation.
Code_Available Yes
Software Program SAS
Software SAS v9.2
R-Code - Attachment

R-Code

SAS-Code - Attachment Gordon - Cumulative Incidence - SAS -Doc
SAS-Code - v9.2 - Attachment

Stata-Code - Attachment

Stata-Code

Other Code - Attachment

Other Code

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Permission Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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Reference Image GordonCumulIncidencePlot_200.png
Topic revision: r7 - 27 Nov 2012 - 10:05:53 - RobertGordon
 

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