+--------------------------------------------------------------------+
| |
| $DATA |
| |
+--------------------------------------------------------------------+
MEANING: Describes the NM-TRAN data set
CONTEXT: NM-TRAN Control Record
USAGE:
$DATA [filename|*] [(format)] [IGNORE=c1] [NULL=c2]
[IGNORE=(list)...|ACCEPT=(list)...]
[PRED_IGNORE_DATA]
[NOWIDE|WIDE] [CHECKOUT]
[RECORDS=n1|RECORDS=label]
[LRECL=n2] [NOREWIND|REWIND]
[NOOPEN] [LAST20=n3] [TRANSLATE=(list)]
[BLANKOK]
[MISDAT=r...]
[REPL=n...]
SAMPLE:
$DATA DATAFILE
DISCUSSION:
This record specifies the data set to be used. It is required with
the first problem specification. It must precede any other NM-TRAN
control record that refers to specific data item types. May also be
coded $INFILE.
Optional with the second or subsequent problem specifications. If
omitted, NONMEM re-uses the data set from the previous problem (which
will include any modifications made via transgeneration, e.g., via use
of NONMEM's PASS, or via simulation).
OPTIONS:
filename
Name of the file containing the data set. Must be the first
option. If it contains commas, semicolons, or parentheses, then
it must be surrounded by single quotes ' or double quotes ".
Filename may also contain equal signs if it is enclosed in
quotes. If the file is opened by NM-TRAN, filename may contain
embedded spaces if it is enclosed in quotes, and may contain at
most 80 characters. If the file is opened by NONMEM, the file-
name may not contain embedded spaces, and may contain at most 71
characters. If filename is the same as any option of the $DATA
record, it must be enclosed in quotes.
* may be coded in a problem subsequent to the first. This has
the same effect as omitting the $DATA record (NONMEM is told to
re-use the previous data set), but allows the CHECKOUT option to
be included. With *, no other option may be included.
(format)
FORTRAN format specification to be used to read the data. Format
codes F, E, and X may be used, but not I. When a format is pro-
vided, the label DROP cannot be used on the $INPUT record and
options WIDE and NULL may not be coded. If omitted, NM-TRAN will
generate a suitable FORMAT specification.
RECORDS=n1
The number of records to be read from the NM-TRAN data set. Com-
ment records are not counted. If NM-TRAN does not drop any
records from its data set (see IGNORE list and ACCEPT list), then
n1 is also the number of records written to the NONMEM data set.
If NM-TRAN drops records, then the total number of records writ-
ten to the NONMEM data set is n1 minus the number of dropped
records.
With NONMEM 7.5, records may also be dropped using the
PRED_IGNORE_DATA block of abbreviated code. The same total
applies to these dropped record. See PRED_IGNORE_DATA, below.
If omitted, the records written to the NONMEM data set are all
the records in the NM-TRAN data set up to the end-of-file (or up
to a NONMEM FINISH record) minus the number of comment and
dropped records. May also be coded NRECORDS, RECS, or NRECS.
If the option is coded as RECORDS=label, where label is a data
item label, NM-TRAN understands the data records for the problem
to start with the first data record of the NM-TRAN data set (at
the place where the file is positioned before data records are
read; see the NOREWIND option), and to include as well, those and
only those subsequent contiguous data records having the same
value of the data item as does the first record. It counts the
total number of these data records, minus any comment or dropped
records, and puts this number in the NONMEM control file.
In particular, the ID label may be used (or alternatively, the
option may be coded RECORDS=IR, RECORDS=INDREC, or RECORDS=INDI-
VIDUALRECORD). If a label other than ID is used, the $INPUT
record must precede the $DATA record. If the data are single-
subject data, the ID data items used to determine the data
records for the problem are those labeled ID (not .ID.).
If there is more than one problem specification with a $DATA
record that includes an option of the form RECORDS=label, then
either none of these $DATA records may also include a format
specification, or all of them must include the same format speci-
fication. (See records=id).
LRECL=n2
The number of characters in a logical record. Needed for certain
operating systems (e.g., IBM/CMS).
IGNORE=c1
[Note: The following two options, IGNORE and ACCEPT allow the
user to drop records from the NM-TRAN data set prior to the run.
With NONMEM 7.5, it is also possible to drop records from the
NONMEM data set using abbreviated code, which is more flexible
than the criteria that can be specified in the $DATA record.
See PRED_IGNORE_DATA, below.]
Specifies that any data record having the character c1 in column
1 should be ignored, i.e., these records are not included in the
NONMEM data set. This allows comment records to be included in
the NM-TRAN data set. In general, records having the character
c1 in column 1 will be called "comment records".
Also permitted: IGNORE='c' or IGNORE="c", where c may be any
character except space. IGNORE=# is the default. That is, in
the absence of IGNORE option, any record whose first character is
# is treated as a comment record.
IGNORE=@ signifies that any data record having an alphabetic
character or @ as its first non-blank character (not just in col-
umn 1) should be ignored. Alphabetic characters are the letters
A-Z and a-z. This permits a table file having header lines to be
used as an NM-TRAN data set.
IGNORE=(list)
"List" is a list of one or more data item labels, with logical
operators and values, of the form "label=value",
"label.EQ.value", "label.NE.value", "label.GT.value",
"label.GE.value", "label.LT.value", and "label.LE.value". (For-
tran 90 logical operators such as '==' '/=' '<' '<=' '>' '>=' "
may also be used.) Thus, the following are identical:
"label=value","label==value","label.EQ.value". With NONMEM 7.3,
"label.NEN.value" and "label.EQN.value" are permitted. (There is
no Fortran 90 operator for this comparison.) If the logical
operator is omitted, the default is "=". With each data record,
the value of the data item with the given label and the value in
the list are compared according to the logical operator, and if
result is "true", the record is ignored, i.e. it is not included
in the NONMEM data set (see example below). Such records are
called "dropped records". With "=", "==", "/=', ".EQ." and
".NE.", the value in the data record and the value in the list
are compared as character strings. Otherwise, they are converted
to numeric and compared numerically. (This is the case with |
.NEN. and .EQN.) This comparison is made prior to time transla-
tion. Hence, the TIME item cannot be compared numerically if it
contains non-numeric characters such as ":".
Note: if the data file is a table file from a previous NONMEM |
run, values that had been integers (0,1,..) in the original data |
file will be real values (0.0000E+00, 1.0000E+00, ...) in the ta- |
ble file. A comparison for equality or inequality should now be |
for the real value. E.g. |
IGNORE=(OCC==1.0000E+00). |
With NONMEM 7 the default format for the table file is PE11.4, as |
in the examples above. The FORMAT option of $TABLE may be used |
to change this and the values used in a subsequent IGNORE will |
have to be changed accordingly. |
The .NEN. and .EQN. operators that are described above will |
always work.
A data item label along with a logical operator and value is
called a condition. A list may contain several conditions; these
should be separated by commas, and the list should be enclosed in
parentheses. Up to 100 different conditions altogether can be
specified. IGNORE=(list) may be used with IGNORE=c, where c is a
character. Multiple IGNORE options with different lists may be
used. A list may span one or more NM-TRAN records. The use of
"=" after IGNORE is optional, but parentheses are required with
this form of IGNORE. Values may be alphabetic or numeric, and
may optionally be surrounded by single quotes ' or double quotes
". Quotes are required if a value contains special characters
such as =. However, a value may not contain spaces or commas.
No format specification is permitted with this form of IGNORE.
A data item type may be dropped from the NONMEM data set by means
of the DROP or SKIP synonym on the $INPUT record, after records
are dropped due to a condition based on the data item type.
E.g.,
$INPUT ... GEN=SKIP ...
$DATA file IGNORE=(GEN='M')
Records having GEN equal to 'M' will be dropped, and the GEN data
item type will then be omitted from the NONMEM data set. A
dropped data item may be any alphanumeric string (without a data
item delimiter - a blank or a comma).
If there is more than one condition, then records satisfying at
least one of these conditions will be dropped. In effect, the
conditions for dropping a record are connected by the implied
conjunction ".OR.". E.g.
IGNORE=(GEN.EQ.1,AGE.GT.60).
Records having GEN equal to 1 or AGE greater than 60 are dropped.
All others are accepted.
ACCEPT=(list)
The ACCEPT list option is identical to the IGNORE list option,
except that it specifies conditions for acceptance of records.
An ACCEPT list cannot be used together with an IGNORE list. How-
ever, it may be used with IGNORE=c, where c is a character.
E.g.
ACCEPT=(GEN.EQ.1,AGE.GT.60).
Records having GEN equal to 1 or AGE greater than 60 are
accepted. All others are dropped.
Suppose it is desired that records be dropped that satisfy the
logical ".AND." of several conditions. This can be implemented
by using an ACCEPT list with the negations of the conditions.
For example, suppose that records to be ignored are those having
GEN=1 .AND. AGE > 60. This may be done as follows:
ACCEPT=(GEN.NE.1,AGE.LE.60)
PRED_IGNORE_DATA (NM75)
Informs NONMEM that a PRED_IGNORE_DATA pass through the data set
is required. If the abbreviated code uses variables
PRED_IGNORE_DATA or PRED_IGNORE_DATA_TEST, this option is sup-
plied. The explicit option is needed if the use of the
PRED_IGNORE_DATA variables occurs in user-written or verbatim
code, so that NMTRAN is unaware of it.
(See Guide Introduction_7 "Extension to $DATA IGNORE=st filter-
ing")
NULL=c2
Specifies that null data items in the NM-TRAN data set are to be
replaced in the NONMEM data set by the character c2. E.g.,
NULL=0 or NULL=..
Null data items consist of a single dot (.) or consecutive commas |
or consecutive tab characters. c2 may be any character except
space (" ") or semicolon (";").
Also permitted: NULL='c' or NULL="c", where c may be any charac-
ter.
If this option is omitted, NM-TRAN replaces each null with a
space.
NOWIDE
Requests that NM-TRAN attempt to limit FDATA to 80-character
records. Space between adjacent columns may be suppressed and
multi-line records may be generated. This is the default.
WIDE Requests that FDATA contain single-line records, and that at
least one space separate columns. (Records in FDATA will never
be wider than 300 characters.) With this option, there will be
no FINISH (FIN) record in the NONMEM data set.
NOREWIND|REWIND
With the first problem specification in a control stream, the
file is positioned at its initial point so that the first NM-TRAN
data set in the file is used. The options REWIND and NOREWIND
apply only with a $DATA record in a subsequent problem specifica-
tion, and only when the file named on the record is the same as
that specified for the previous problem. When the file named on
the record is different from that specified for the previous
problem, the file is (re)positioned at its initial point so that
the first NM-TRAN data set in the file is used.
REWIND: Reposition the file at its intial point so that the first
NM-TRAN data set in the file is re-used.
(Whether the file input to NONMEM itself will be repositioned
depends on whether this file is FDATA or is one named in the
$DATA record; see NONMEM Users Guide, Part IV for a complete
explanation.)
NOREWIND: Leave the file at its current position so that the next
NM-TRAN data set in the file is used. The $DATA record with the
previous problem specification must have included the RECORDS
option (or a FINISH record must have terminated the data set used
in the previous problem), so that NM-TRAN did not read to a phys-
ical end-of-file. This is the default.
CHECKOUT
Requests that NONMEM implement the data checkout mode, in which
the PRED routine is not called and predictions, residuals,
weighted residuals and the objective function are not computed.
May also be coded CHECKDATA. No tasks other than $TABLE or $SCAT
can be specified.
With NONMEM 7.5, an additional file, FDATA.csv is produced that
outputs the contents of its input data file (typically FDATA) in
a comma delimited file format, so you can check how NONMEM inter-
prets the input data. If the REPL option of $DATA or the REPL_
data item is used, the replicated form of the data will appear in
FDATA.csv.
NOOPEN
NM-TRAN will not open the named data file. This permits the data
file to be created by one problem and used in a subsequent prob-
lem of the same run. May not be used with options IGNORE, DROP,
or when data items ID, MDV, or EVID must be generated by NM-TRAN.
With NOOPEN, a format specification is required. No day-time
translation takes place.
LAST20=n3
Override the LAST20 constant in resource/TRGLOBAL.f90 (default: |
50).
One or two digit years > LAST20 are assumed to be in the 1900's,
One or two digit years <= LAST20 are assumed to be in the 2000's.
E.g,. suppose LAST20=50. Then two digit years are interpreted as
follows:
00-50 = 2000-2050
51-99 = 1951-1999
LAST20=-1 can be used when two digit years span the year 2051.
All two digit years will be assumed to be in the same century.
If year is recorded with four digits, it is always processed cor-
rectly and the value of LAST20 is of no consequence.
TRANSLATE=(list)
"list" describes modifications to be made to the contents of the
data file. It may contain one of:
TIME/F, TIME/F/D
and/or one of
II/F, II/F/D
F ("factor") may be an integer or a real value. If F is a real
number, the translated value in FDATA will have the same number
of digits after the decimal point. If F is an integer and D is
omitted, there will be 2 digits. Alternately, the number of dig-
its may be specified explicitly by D ("digits"). If D is a real
number, it is truncated to integer. If D is specified as 0, it
defaults to 2. The maximum value of D is 12. The number of dig-
its that may be requested in F is limited by the precision of the
computer.
For example, either of the following can be used to request val-
ues of TIME in FDATA that have 4 digits to the right of the deci-
mal point:
TIME/1.0000
TIME/1/4
Another example is
II/0.01/6
which divides II values by 0.01, and writes 6 digits to the right
of the decimal point.
If F is specified as "24" (or 24.0..), the options involving TIME
(II) can be used to convert the units of time (of the steady-
state interval) from hours to days. The TIME (II) data item is
first processed as if the option were not present. Then the
resulting value is divided by F.
Note: The value of TIME is divided by F, whether or not day-time
translation occurs (i.e., whether or not relative times are being
computed by NM-TRAN). Similarly, the value of II is divided by F
whether or not ":" appears in any II data value.
BLANKOK
Specifies that blank lines are permitted in the NM-TRAN data set.
With all versions prior to NONMEM VI 2.0 a blank line was permit-
ted, and was copied to the NONMEM data set. A warning message was
issued. With later versions, NM-TRAN stops with an error message
when there is a blank line in the NM-TRAN data set. Option
BLANKOK restores the previous behavior. There is no
abbreviation. BLANKOK must be coded in full.
MISDAT=r (NM74)
A numerical value indicating a missing data value in the data
set, which is displayed on $TABLE table outputs, but is safely
interpreted as 0 by other steps of NONMEM. May be used up to 20
times.
Example: $DATA mydatafile MISDAT=1.0E-99 MISDAT=1.0E-102.
REPL=n (NM75)
When the REPL=n option of $DATA is coded, the NONMEM data set is
considered to be a template data set. NONMEM itself replicates
the template data set n times at the start of the problem to cre-
ate an expanded NONMEM data set.
(Note that the NONMEM data set is typically the file FDATA gener-
ated by NM-TRAN. If there is nothing for NM-TRAN to change and
the format is supplied on the $DATA record, the file named on the
$DATA record is the NONMEM data set. See NONMEM Users Guide,
Part IV.)
The REPL option may be used with the REPL_ data item. If both
are used the REPL_ data item applies first, and the REPL option
applies second.
See REPL_ data item.
The REPL option and REPL_ data item are meant to be used with
$SIMULATION or $DESIGN.
For important information, see Guide Introduction_7 Section
"$DATA REPL".
(See Guide Introduction_7 "Extension to $DATA IGNORE=st filter-
ing")
Another change in NONMEM VI 2.0 is that tab characters (and other
characters that are smaller than blank in the computer's collating
sequence, such as carriage return ^M) are permitted in NM-TRAN input
files. In the NM-TRAN data set they are treated like commas, i.e., as
field delimiters. In the NM-TRAN control stream they are converted to
spaces. They are left unchanged in verbatim code. With NONMEM 7, the |
last non-blank character on the line is replaced by a space if it is a |
low-value character.
Note: The character ":" in TIME or II data items requests day-time
translation of TIME or II values. These values must have the form
hh:mm (i.e., hours:minutes). With NONMEM 7.3, values may also have |
the form hh:mm:ss (i.e., hours:minutes:seconds). |
(See Guide IV, section II.C.2)
REFERENCES: Guide IV Section III.B.5
REFERENCES: Guide V Section 6.4
REFERENCES: Guide Section Introduction_7
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