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  • [NMusers] question re: % time spent modeling
    2005 9 28 am Colleagues About what percentage of time does your team spend on compartmental versus non compartmental analysis Do you consider clinical trial simulation to be so important that almost every compound is modeled I ve been hearing

    Original URL path: http://nonmem.org/nonmem/nm/99jan222005.html (2016-04-25)
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  • [NMusers] Update for NONMEM bug XII
    would actually prefer that the TABLE record be treated as though the FORWARD option appears on it see the discussion point below But this is not what is suppose to happen and if indeed it is desired that the NOFORWARD option be recognized then after the last TABLE record insert an additional TABLE record using a FILE option with a different file name This file name can be that of the system junk file so that no table is really seen by the user Discussion The following helpful fact is undocumented There is an exception as to when the NOFORWARD option is the default option With a series of contiguous TABLE records in a given problem specification each having a FILE option that uses the same file name the second and subsequent TABLE records in the series are always treated as though the FORWARD option appears on these records because otherwise the presence of these records makes no sense It also really makes no sense to use the NOFORWARD option with any TABLE record regardless of the file name used by the FILE option in a problem specification with an NSUBS value of 2 or more So with NONMEM Version VI this will constitute another exception as to when the NOFORWARD option is the default option VI When each of two different problems within the scope of a superproblem use the same file as either a NONMEM data file Model Specification Input file or Model Specification Output file or table file an abnormal operating system termination may arise If these circumstances do not lead to such a termination the user should not be concerned Fix Before each of the two instances of the statement I2 0 in routine SUPER insert the statement IF I2 EQ 1 CLOSE UN 2 Before each of the two instances of the statement I3 0 in routine SUPER insert the statement IF I3 EQ 1 CLOSE UN 3 Before each of the two instances of the statement I4 0 in routine SUPER insert the statement IF I4 EQ 1 CLOSE UN 4 Work around Avoid such circumstances An example of where these circumstances arise may be found in the Help Guide Superproblem Example 1 For this example the file simulation is used as a table file in problem 2 and as a NONMEM data file in problem 3 This can be avoided by taking the data set of problem 3 to be the internal data set created with problem 2 remove both the TABLE record of problem 2 and the DATA record of problem 3 VII When a mixture model is used estimates of etas available to the PRED routine during problem finalization i e when ICALL 3 are always those for the first submodel With each individual they should be those for the submodel to which the individual is classified VIII The statistic ETABAR and results from the Centering First Order Conditional Estimation method are incorrect when 1 a mixture model is used 2

    Original URL path: http://nonmem.org/nonmem/nm/99jan192005.html (2016-04-25)
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  • [NMusers] Number of subject and population PK/PD modeling
    or WinNonlin is superior to a mixed effect modeling approach I am not concerned with population models being more complicated or take longer time I am more interested to know whether the former produces better and more reliable estimates than the latter Best regards Toufigh Gordi From Serge Guzy GUZY xoma com Subject RE NMusers Number of subject and population PK PD modeling Date Fri January 14 2005 12 40 pm My experience with both Winnonlin and the population approach is that the mixed effect approach always gave me better estimates of at least the population means Using Winnonlin and averaging the PK estimates never gave me superior average values of the main PK parameters On the other hand sometimes I saw problems with the estimates of the covariance components of the population variance covariance matrix when dealing with small number of patients and in a rich data environment Correlation sometimes would be drifted to 1 with the log likelihood being flat across a big range of correlation values In that case rich data analysis using Winnonlin would give me better estimates of the true correlation between the PK parameters My experience was also that population variances were estimated equally in a rich data environment and better of course in a semi rich data environment some patients did not have enough information to be analyzed with Winnonlin My conclusion was that a mixed effect approach is always as good as and most of the time better than a Winnonlin approach expect for very rich data environment where we are interested to estimate the population covariance Serge Guzy President POP PHARM From Mats Karlsson mats karlsson farmbio uu se Subject RE NMusers Number of subject and population PK PD modeling Date Mon January 17 2005 4 33 am Dear Toufigh We

    Original URL path: http://nonmem.org/nonmem/nm/99jan132005.html (2016-04-25)
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  • [NMusers] R scripts for NM output tables
    6 2005 9 06 am Dear NM users This is to inform the NM users that a set of R scripts is available for analysing the output tables produced by NM Briefly the scripts allow to readily analyse PRED OBS WRES etc or to observe relationships between PK params and covariates or to produce graphs for publication Splitting of data according to a factor or categorical variable in tables can

    Original URL path: http://nonmem.org/nonmem/nm/99jan062005.html (2016-04-25)
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  • [NMusers] MSFI issue - apparent state: unit 3 named
    a suggestion Thanks Paul control streams follow first PROBLEM THEOPHYLLINE SINGLE SUBJECT DATA INPUT DOSE AMT TIME CP DV DATA DATA3 SUBROUTINES ADVAN2 PK CALLFL 1 KA THETA 1 K THETA 2 SC THETA 3 ERROR Y F ERR 1 THETA 0 1 7 0 102 0 29 ESTIMATION MAXEVAL 2 PRINT 2 MSFO MSF1 COVR then PROBLEM THEOPHYLLINE SINGLE SUBJECT DATA INPUT DOSE AMT TIME CP DV DATA DATA3 MSFI MSF1 SUBROUTINES ADVAN2 PK CALLFL 1 KA THETA 1 K THETA 2 SC THETA 3 ERROR Y F ERR 1 THETA 0 1 7 0 102 0 29 ESTIMATION MAXEVAL 999 PRINT 2 MSFO MSF2 COVR Paul Hutson Pharm D Associate Professor CHS UW School of Pharmacy 777 Highland Avenue Madison WI 53705 2222 Tel 608 263 2496 FAX 608 265 5421 Pager 608 265 7000 7856 From Bachman William MYD bachmanw iconus com Subject RE NMusers MSFI issue apparent state unit 3 named Date Tue January 4 2005 11 16 am Paul Your control3 example ran without error on my system gcc version 3 2 mingw special 20020817 1 and O optimization Bill From Nick Holford n holford auckland ac nz Subject Re NMusers MSFI issue apparent state unit 3 named Date Tue January 4 2005 4 19 pm Paul I suspect the error message is caused because NONMEM cannot find the MSF file It is important under WFN that you take care with the path needed to find the MSFI file Because WFN uses a sub directory for the NONMEM run it needs to have an explicit path to the sub directory containing the MSFO output file Assuming you do a run with name run1 using WFN and it produces an MSF file run1 msf in the directory run1 g77 the default directory name used by WFN

    Original URL path: http://nonmem.org/nonmem/nm/99dec282004.html (2016-04-25)
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  • [NMusers] How does NONMEM $DES work?
    What if WT IS a time dependent covariate Has anyone used the covariate model this way or in a closed form equation pattern Thanks a lot for any comment Yaning Wang PhD Pharmacometrician OCPB FDA From Nick Holford n holford auckland ac nz Subject Re NMusers How does NONMEM DES work Date Tue December 21 2004 8 58 pm Yaning NONMEM uses the value of the data item e g C specified in the record for which a solution is sought e g ID TIME C DV 1 1 0 10 1 2 1 8 When NONMEM solves the DE system for the second record TIME 2 it will assume that C is 1 throughout the interval from TIME 1 to TIME 2 If you are unable to find a model for C then you can interpolate a value using the T variable in DES There are several ways to do this but the most efficient might be to pre compute the slope connecting each two values of C and use this to predict C at T Add this slope to the data set and use it in DES e g ID TIME C DV SLOP 1 1 0 10 0 1 2 1 8 1 DES CNOW C SLOP T Nick Nick Holford Dept Pharmacology Clinical Pharmacology University of Auckland 85 Park Rd Private Bag 92019 Auckland New Zealand email n holford auckland ac nz tel 64 9 373 7599x86730 fax 373 7556 http www health auckland ac nz pharmacology staff nholford From Wang Yaning WangYA cder fda gov Subject NMusers How does NONMEM DES work Date Tue December 21 2004 Nick I just want to make sure I correctly understand your response By default NONMEM uses the value of C2 1 in your example at TIME2 as the

    Original URL path: http://nonmem.org/nonmem/nm/99dec212004.html (2016-04-25)
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  • [NMusers] pediatric PK studies for pediatric exclusivity
    to partner in clinical program has passed what kind of a pediatric study design should one use Assuming that this study needs to be conducted in healthy children and the drug has a relatively long half life of about 12 to 24 hours A traditional PK study with 8 or more blood draws approx sample size 24 OR A population PK approach with a slightly larger sample size but significantly less number of samples approx sample size of 36 to 48 There are trade offs for both approaches cost pop PK being more expensive than traditional PK ethical sensitivities and considerations and enrollment more will be needed for pop PK versus reduced number of blood draws and decreased discomfort distress potentially easier IRB approval for pop PK Appreciate feedback from the group Best Regards Dolly Dolly A Parasrampuria PhD Clinical Pharmacology M C 263 McNeil Consumer Specialty Pharmaceuticals 7050 Camp Hill Rd Fort Washington PA 19034 2299 Tel 215 273 7760 Fax 215 273 4127 From Suliman Al Fayoumi alfayoumi hotmail com Subject RE NMusers pediatric PK studies for pediatric exclusivity Date Fri December 10 2004 12 25 pm Hi Dolly Both traditional and Pop PK studies have been utilized

    Original URL path: http://nonmem.org/nonmem/nm/99dec102004.html (2016-04-25)
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  • [NMusers] SAS vs S-Plus
    has closed both offer nonlinear mixed effects models GAM analysis etc They are virtually the same S plus still has the edge graphics wise However of all the programming languages I have studied S plus is one of the craziest and not the most easy to learn SAS is far easier to learn and has the advantage in the all statistical analyses in support of an NDA will be done within SAS Most companies have a site license for SAS and so using it will not cost a department much if anything S plus is a couple of thousand dollars I also have to say that SAS has the regulatory edge in terms of acceptance over S plus Comments Pete Peter L Bonate PhD FCP Director Pharmacokinetics ILEX Oncology 4545 Horizon Hill Blvd San Antonio TX 78229 phone 210 949 8662 fax 210 949 8219 email pbonate ilexonc com From Bachman William MYD bachmanw iconus com Subject RE NMusers A vs S Plus Date Wed December 8 2004 3 05 pm You forgot the biggest one cost Only major pharma can afford to implement it across the board S Plus is affordable R is free William J Bachman Ph D Manager Pharmacometrics Research and Development GloboMax The Strategic Pharmaceutical Development Division of ICON plc 7250 Parkway Drive Suite 430 Hanover MD 21076 410 782 2212 bachmanw iconus com From Sam Liao sliao pharmaxresearch com Subject RE NMusers A vs S Plus Date Wed December 8 2004 3 50 pm Hi Bill and nmv users I would like to ask if any S Plus or R users in this group know of any function to use in solving differential equations in PKPD models I prefer to use S Plus in Monte Carlo simulation of PKPD models But so far only limited

    Original URL path: http://nonmem.org/nonmem/nm/99dec082004.html (2016-04-25)
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