NMSEE(local)
MISC. REFERENCE MANUAL PAGES
NMSEE(local)
NAME
NMSEE - Display NONMEM Output
SYNOPSIS
nmsee [option ... ] filename ...
DESCRIPTION
Nmsee displays to standard output a summary of a NONMEM output report. It strips off blank lines, the initial portion
of NONMEM output (which consists of the repetition of the
input), tables, scatters, and other extraneous lines. It
displays problem header lines, initial and final parameter
estimates,
initial and final gradients, final (scaled
transformed) parameters, messages describing the outcome of
the search, minimum value of the objective function, standard errors, covariance step output, etc.
If there are
error messages, it displays those.
Initial estimates of theta are displayed in the same format
as are the final estimates: exponential, with 1 leading significant digit before the decimal point. Initial estimates
of theta that are blank (and are consequently supplied later
by NONMEM's Initial Estimates step) are displayed as zeroes,
not blanks.
This is different than the display of initial
estimates of omega and sigma; see BUGS.
The minimum value of the objective function is displayed in
both the above exponential format and its original format.
Nmsee can be used in a pipe or with redirection. The
filename can also be supplied as a command-line argument, in
which case 1) there can be more than one filename, and 2)
they are echoed in the summary itself.
E.g.,
nmsee < filename
cat filename | nmsee
nmsee filename1 filename2 ...
Command line options may be used with all the above. They
must be specified immediately following "nmsee". They may
be upper case or lower case. A character string that is not
recognized as an option is assumed to be a filename. When
the command line contains more than one filename, options
may intervene between the filenames. The new options are
appended to the previous set of defaults and options, and
may override them. See examples below.
OPTIONS
text Requests that NONMEM's text lines describing
the
numeric values be retained in the output (the default).
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notext
Requests that NONMEM's text lines be omitted.
covar
Requests that the following matrices be displayed:
COVARIANCE MATRIX OF ESTIMATE
CORRELATION MATRIX OF ESTIMATE
INVERSE COVARIANCE MATRIX OF ESTIMATE
(the default).
nocovar
Requests that these matrices not be displayed.
dots Requests that those positions in the above matrices
which NONMEM prints as dots (.......) because they are
not estimated remain as printed (the default).
When the matrices are printed by NONMEM in compressed
format,
the "dots" option requests that they be
displayed as-is, including the header lines
that
describe the values.
nodots
Requests that these positions be displayed as zeros,
e.g., when the output of nmsee is going to be processed
by some other program which cannot read dots correctly.
When the matrices are printed by NONMEM in compressed
format, the "nodots" option requests that the header
lines that describe the values be suppressed, and that
the values be reformated to fit an 80-character line.
"ncov" option may also be used.
nth k
Number of theta values to be displayed on a single line
of output. Default is 11, the same as in NONMEM's output.
"nth 7" might be specified to prevent the terminal from
wrapping the lines of output.
"nth 20" causes all theta values to be displayed in one
line of output, e.g., when the output of nmsee is going
to be processed by some other program which cannot
easily be instructed to read values of theta from multiple lines.
The value of nth also applies to the number of gradient
and parameter values displayed per line. Thus, the
default is effectively changed from 10 (in NONMEM's
output) to 11, and lines are joined as necessary.
ncov j
Number of elements of the covariance matrices to be
displayed on a single line of output. Default is 12,
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the same as in NONMEM's output.
"ncov 7" might be
specified to prevent wrapping, as with nth. However,
unlike nth, a large value does not cause nmsee to join
existing lines of output.
mmfix
Requests that the minimum value of the objective function be displayed exactly as printed in NONMEM output,
i.e., in fixed format (F10.3). This is the default.
mmexp
Requests that the minimum value of the objective function be displayed in exponential format (1P,E10.2).
mmboth
Requests that the minimum value of the objective function be displayed in both exponential and fixed formats
(1P,E10.2,F10.3).
exp
Requests that numeric values be displayed in
tial format (1P,E10.2). This is the default.
exponen-
fix
Requests that numeric values be displayed in fixed format (F10.3).
This affects all numeric values EXCEPT:
the minimum value of the objective function, gradients,
scaled transformed parameters, and matrices affected by
"dots" when that option is present.
fixw.d
Same as "fix", but supplies alternate values for w
(width of field) and d (number of decimal digits).
E.g., with "fix12.2" the value 123456789.12 is printed
as "123456789.12", whereas with "fix" it is printed as
stars (**********). There should be no space between
"fix" and w.d. Nmsee does not check that the characters following "fix" are a valid FORTRAN editing
specification. If they are not, run time errors will
occur or nmsee's output will be incorrect.
prefix
Requests that 2 line prefixes be appended to each line.
Prefixes are designed to facilitate the use of grep to
extract only certain values. See examples below. Prefixes are:
ti theta initial
tu theta upper bound
tl
oi
si
tj
oj
sj
theta
omega
sigma
theta
omega
sigma
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lower bound
initial
initial
from initial estimates step
from initial estimates step
from initial estimates step
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gi
gf
pf
mm
tf
of
sf
te
oe
se
cx
cr
cv
cy
ne
nc
xx
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gradients initial
gradients final
scaled transformed parameters final
minimum value of objective function
theta final
omega final
sigma final
theta standard errors
omega standard errors
sigma standard errors
covariance matrix of estimate
correlation matrix of estimate
inverse covariance matrix of estimate
T matrix
(nonparametric) expected value of eta
(nonparametric) covariance matrix of eta
text lines
noprefix
Requests no prefixes (the default).
Note: nmsee is similar to nmsmy, but imposes no restrictions
on file names and creates no output files. Nmsee is implemented locally as a Unix shell script and an exportable FORTRAN program.
EXAMPLES
nmsee nth 7 nocovar run1.lst run2.lst
Displays each of two output file, with theta displayed 7 per
line, no covariance matrices.
cat run1.lst run2.lst | nmsee nth 7 nocovar
Same as the above, except that the names of the files are
not displayed, and no blank line separates the display from
the two files.
nmsee prefix reportfile | grep t
Displays only those lines having to do with theta.
nmsee prefix file1 nocovar file2
Displays file1 with prefixs and covariance
default),
and
file2 with prefixes and
matrices.
matrices (the
no covariance
nmsee prefix nth 20 *.lst | grep tf | sed 's/tf//' > finalth
Extracts the final estimates of theta from a group of files.
Presumably, the user has already checked the output to be
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sure the runs were successful. File "finalth" contains only
numeric values and is ready for input to a statistical
analysis package.
FILES
The nmsee program reads its options from a file called
"nmsee.opt".
If no such file exists, it reads the report
file from standard input and applies all the defaults.
The nmsee shell script always attempts to remove nmsee.opt,
whether or not there are any command line options. When
command line options are present, the nmsee shell script
then echoes them to "nmsee.opt".
If the user does not have write permission in the current
directory, the only way to use nmsee is with defaults and
redirection:
nmsee < filename
Note that in this case an existing nmsee.opt file will persist, because it cannot be removed by the non-owner.
OTHER ENVIRONMENTS
When used in Microsoft Windows/DOS environment, this
is suggested:
change
Locate these lines of the source code:
C FOR MICROSOFT WINDOWS AND OTHER ENVIRONMENTS THAT DO NOT
PRECONNECT
C UNIT 6, ACTIVATE THE FOLLOWING STATEMENT
C
OPEN (OU,FILE='nmsee.lst')
Change the "C" to blank in the OPEN statement to activate it.
Use MS-DOS command "start nmsee.lst" to display nmsee.lst.
Use MS-DOS command "find" to select lines from nmsee.lst.
AUTHOR
Alison Boeckmann
BUGS
Initial estimates of omega and sigma are displayed exactly
as in NONMEM's output. This means that, when omega or sigma
has block structure, the initial estimates are not printed
in the same triangular form as the final estimates. In particular, initial estimates of omega and sigma that are blank
(and are consequently supplied later by NONMEM's Initial
Estimates step) are not displayed at all.
Nmsee reads the first 999 characters from nmsee.opt.
Characters beyond the 999th. are truncated and no warning is
given.
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