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| XML_COMPARE |
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MEANING: XML_COMPARE program
CONTEXT: NONMEM run
The utility program xml_compare compares the contents of two NONMEM
report XML files that are produced by NONMEM.
USAGE:
xml_compare myresult1.xml myresult2.xml myprecision.xtl >mydifferences.txt
where delimiter is {, t s} for {comma tab space}, and myprecision.xtl
is a precision specification or control file. Default delimiter is
space and default control file is xml_compare.xtl. It is useful to
redirect difference results to a file, in this example mydiffer-
ences.txt.
The control file can be quite elaborate, but it allows specification
of various precision values for the many different types of values in
the NONMEM report XML file, and to ignore certain entries as well. An
example xml_compare.xtl file is in the util directory, and has the
following contents:
$IGNORE
monitor
elapsed_time
datetime
covariance_status
termination_status
nonmem(version)
$PRECISION
GENERAL=0.2,0.2 OBJ_BAYES=2.0,0.0 OBJ_SAEM=0,100.0
OBJ_ITS=0,5.0 OBJ_IMP=0,10.0 OBJ_F=0,5.0
DIAG=0.3,0 OFFDIAG=0,0.5 COR=0.0,0.3 VAR=0.3,0.1 COV=-1.0
EIGENVALUES=2.0,0 OBJ_DIRECT=0,100.0
correlation_o=-1.0 INVCOVARIANCE_O=-1 INVCOVARIANCE_D=-1
etashrink=0,20 epsshrink=0,10
METHOD=DIRECT ALL=-1
METHOD=SAEM epsshrink=0,20
The $IGNORE record will ignore all elements that are listed, or just a
specific attribute of an element, such as nonmem(version).
Under the $PRECISION record, a
GENERAL=R,A
can be given for most items, where relative is the relative tolerance,
and absolute is the absolute tolerance. Following the GENERAL speci-
fication, tolerances may be specified for other items.
Two items of identical element and attributes are compared between the
two files, where the equation for comparison is, between value X of
xml file 1 and value Y of xml file 2,
ABS(X-Y)>R*MAX(ABS(X),ABS(Y))+A
The OBJ_BAYES is given a special test, as it has a standard deviation
with it:
STD(X,Y)=SQRT(STD(X)2+ STD(Y)2)
ABS(X-Y)>R*STD(X,Y)+A
In the above example OBJ_BAYES=(2,0) means that if the Bayes objective
functions in the two files differ by more than 2 standard deviations,
then the difference is noted.
To ignore an item for comparison, specify -1. To specify an exact
comparison, use 0,0. To refer to a particular optimization method,
then enter METHOD=SAEM for example, and thereafter, all entries of
items pertain to that estimation method, until METHOD is changed.
The METHOD attribute may have one of the following settings:
FOCE, ITS, IMP, SAEM, DIRECT, BAYES
For the total list of items, and their scope:
See INTRODUCTION TO NONMEM 7, xml_compare Utility Program and its Use
for Installation Qualification
Because of the versatility of selecting which items are to be compared
and with what precision, the xml_compare program can be used for batch
processing installation qualification procedures, in comparing NONMEM
results of a test run against a reference run. All results given in
the standard NONMEM output file are also reported in the XML file.
REFERENCES: Guide Introduction_7
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