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  • [NMusers] NONMEM Bug Overview - AAPS
    site They are available in PowerPoint format or in a version that can be viewed directly from the web for Unix users http www cognigencorp com perspective presentationsinternet kp 36 369 html Regards Luann Phillips Director Pharmacometrics R D Cognigen Corporation From Leonid Gibiansky leonidg metrumrg com Subject RE NMusers NONMEM Bug Overview AAPS Date Fri November 19 2004 2 42 pm My presentation on the same session is available

    Original URL path: http://nonmem.org/nonmem/nm/98nov192004.html (2016-04-25)
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  • [NMusers] Something wrong in US FDA guidance?
    1 53 0 2 0 25 0 02 0 2 0 5 5 13 0 2 0 75 8 92 0 2 1 24 56 0 2 1 5 19 21 0 2 2 1 8 0 2 4 43 07 0 2 6 41 56 0 3 0 25 13 87 0 3 0 5 15 03 0 3 0 75 18 39 0 3 1 16 25 0 3 1 5 15 44 0 3 2 23 74 0 3 4 24 8 0 3 6 21 79 0 4 0 25 27 27 0 4 0 5 3 71 0 4 0 75 43 82 0 4 1 44 39 0 4 1 5 77 04 0 4 2 66 8 0 4 4 62 96 0 4 6 71 6 0 5 0 25 10 65 0 5 0 5 7 72 0 5 0 75 23 42 0 5 1 20 37 0 5 1 5 19 95 0 5 2 32 0 5 4 32 81 0 5 6 61 51 0 6 0 25 10 41 0 6 0 5 5 94 0 6 0 75 2 29 0 6 1 8 92 0 6 1 5 20 64 0 6 2 19 52 0 6 4 8 52 0 6 6 19 01 0 7 0 25 4 2 0 7 0 5 12 31 0 7 0 75 1 34 0 7 1 18 84 0 7 1 5 42 7 0 7 2 37 29 0 7 4 45 46 0 7 6 37 24 0 8 0 25 11 95 0 8 0 5 7 45 0 8 0 75 5 95 0 8 1 8 78 0 8 1 5 1 26 0 8 2 48 83 0 8 4 71 77 0 8 6 8 14 0 9 0 25 12 36 0 9 0 5 12 95 0 9 0 75 1 88 0 9 1 43 35 0 9 1 5 20 97 0 9 2 39 79 0 9 4 57 55 0 9 6 34 18 0 10 0 25 1 15 0 10 0 5 39 45 0 10 0 75 40 68 0 10 1 16 19 0 10 1 5 6 87 0 10 2 10 75 0 10 4 37 64 0 10 6 35 01 0 11 0 25 30 03 0 11 0 5 39 56 0 11 0 75 61 06 0 11 1 43 58 0 11 1 5 40 73 0 11 2 62 01 0 11 4 27 82 0 11 6 33 6 0 12 0 25 7 25 0 12 0 5 14 73 0 12 0 75 21 09 0 12 1 10 81 0 12 1 5 0 51 0 12 2 10 51 0 12 4 14 89 0 12 6 16 14 0 Kyun Seop Bae MD PhD Clinical Research Center Asan Medical Center Pungnap dong Songpa

    Original URL path: http://nonmem.org/nonmem/nm/99nov192004.html (2016-04-25)
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  • [NMusers] PD lag time in $DES
    initialise the response compartment Please let me know if this is what you wanted Thanks Mathangi From Perez Ruixo Juan Jose PRDBE JPEREZRU PRDBE jnj com Subject RE NMusers PD lag time in DES Date Thursday 18 November 2004 11 33 Dear Jim You may want to have a look to a recent PAGE presentation NONMEM Implementation of Cell Lifespan Models for Hematological Drug Effects http www page meeting org page page2004 Kimko pdf Juan Jose Perez Ruixo PhD Advanced PK PD Modelling Simulation Johnson Johnson Pharmaceutical Research Development Beerse Belgium From mark e sale gsk com Subject RE NMusers PD lag time in DES Date Thu November 18 2004 10 46 am Jim This isn t easy In simulation packages a pipe is created by a long series of concatenated compartments in ACSL is was 50 as in DADT 1 K A 1 DADT 2 K A 1 K A 2 DADT 3 K A 2 K A 3 DADT 50 K A 49 K A 50 50 compartments will give a very nice square wave delay effect but is numerically very difficult for estimation even though there is only one parameter which describes the delay I ve used a smaller number of compartments 2 or 3 but that doesn t really give a lag delay more of smudging sort of effect In PRED you can just do LAG THETA the use T LAG But there is not as far as I know an easy way to store what the value was at T LAG using DES Mark Sale M D Global Director Research Modeling and Simulation GlaxoSmithKline 919 483 1808 Mobile 919 522 6668 From Nick Holford n holford auckland ac nz Subject RE NMusers PD lag time in DES Date Thu November 25 2004 4 20 am

    Original URL path: http://nonmem.org/nonmem/nm/99nov172004.html (2016-04-25)
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  • [NMusers] Negative values in 95%CI on ETAs
    fda gov Subject RE NMusers Negative values in 95 CI on ETAs Date Tue November 16 2004 2 43 pm Hello Manoj A couple of quick comments 1 It is better to parameterize models in terms of CL V Q VSS or V peripheral instead of the parameterization you have chosen 2 You could try different values of Ka and check how it influences the results 3 What is the estimation procedure you are using Venkatesh Atul Bhattaram Pharmacometrics DPE 1 OCPB CDER FDA From MANOJ KHURANA manoj2570 yahoo com Subject RE NMusers Negative values in 95 CI on ETAs Date Tue November 16 2004 3 27 pm Hi All Thanks for your input I initially tried parametrization in terms of CL and V realizing they are meaningful parameters but I dont know for what reason it didnt work even after fixing KA to different values and I had underpredicted concentrations all over the data I am using method 0 FO By the way the data I have is rich so please advice if FO or FOCE would be appropriate Thanks MK From Sam Liao sliao pharmaxresearch com Subject RE NMusers Negative values in 95 CI on ETAs Date Tue November 16 2004 4 24 pm Hi Manoj I think the problem may be the initial estimates you used It is more critical when you have a two compartment model Also I would use FOCE for rich dataset Sam Liao PharMax Research From MADABUSHI RAJANIKANTH Subject RE NMusers Negative values in 95 CI on ETAs Date Tue November 16 2004 6 06 pm Hi Manoj Since you say the data is rich and you are fixing Ka you should be using FOCE Moreover FOCE is a better method of estimation than FO quick and dirty raj From Nick Holford n

    Original URL path: http://nonmem.org/nonmem/nm/99nov162004.html (2016-04-25)
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  • [NMusers] Updated NMTRAN bug VIII
    as D DV A LOG D XIII Steady state kinetics will not be computed when 1 there are multiple problem specifications 2 with the second or subsequent problem specification SS is listed first in the INPT record 3 an SS routine is not listed in the SUBROUTINES record Work around Construct a new data set such that 2 above will not happen That is the new data set will be exactly like the old data set except for having a new column that is exactly like the first column in the original data set and the new column will be placed after the first column Actually the first column itself can be deleted but if it is not use DROP with the first column Work around Include the name of the SS routine in the SUBROUTINES record XIV NM TRAN translation of clock times to elapsed times can be faulty All elapsed times resulting from clock time translation should have two digits to the right of the decimal point Certain elapsed times greater than 999 99 hours 41 6 days are unpredictably and mistakenly truncated so that they contain only one digit to the right of the decimal point See discussion in the NONMEM Archive http www cognigencorp com nonmem nm 99apr192002 html Fix In routine READ3 replace the line ELSEIF VALUE KK J GE 1000 0 AND WIDE NE Y THEN with ELSEIF VALUE KK J GE 1000 0 AND WIDE NE Y AND NSP EQ 1 THEN XV The error message DATA WIDE CANNOT BE USED FILE CONTAINS MORE THAN 9999 RECS may appear but it should not appear when 1 the WIDE option appears on the DATA record 2 there are more than 9999 records in the data set See discussion in the NONMEM Archive http www cognigencorp com nonmem nm 99apr192002 html Fix In routine READF delete this statement IF INOBS GT 9999 AND WIDE EQ Y CALL ERRMSG 283 1 XVI NM TRAN translation of TIME data items is faulty when 1 NM TRAN infers that the data are single subject data 2 the name ID is listed in the INPUT record as ID or ID L1 3 some synonym A B and or DATE DROP preceeds ID in the INPUT record Time translation occurs when either clock times are present in the NM TRAN data set or DATE items appear Usually when time translation occurs with single subject data ID does not appear in the INPUT record though L1 may appear in which case the TIME data item on the first record of the data set is translated to 0 and subsequent TIME data items are translated to times relative to 0 When ID is listed in the INPUT record with every data record where the ID data item changes value the TIME data item is translated to 0 and subsequent TIME data items up to the next change in ID value are translated to times relative to 0 Due to the bug if ID is listed near the beginning of the INPUT record different data from the ID data items are used in the process of time translation If the ID is listed near the end of the INPUT record the ID data items are ignored in the process of time translation i e all TIME data items subsequent to the one on the first data record are translated to times relative to 0 Work around Construct a new data set such that 3 above will not happen That is the new data set will be exactly like the old data set except for having a new column that is exactly like the column in the original data set with the ID data items column C and the new column will be placed before the columns with the A type data items and or the DATE data items Actually column C itself can be deleted but if it is not give this column a name N different from ID and use N DROP Work around Avoid using the synonym A B XVII The constant LNP4 in files TSIZES is set at installation time to the default value of 1000 An error occurs during compilation of generated code when LNP4 is set to a value greater than 9999 However a value greater than 9999 is of little practical value When the option COMRES n n 0 is used in the ABBREVIATED record or when verbatim code is used and when LNP4 is set to a value greater than 1000 an error occurs during compilation of generated code Fix In routine GENCOM replace the two lines of code WRITE LINE A I4 4 A DIMENSION COM COMMAX LL 19 with WRITE LINE A I6 6 A DIMENSION COM COMMAX LL 21 XVIII The data may be mistakenly interpreted as single subject data when 1 there are multiple problem specifications 2 in the second or subsequent problem specification a MSFI record appears without the NPOP option With the problem specification where the MSFI record appears without the NPOP option the data are misinterpreted as single subject data An error message will make it clear that the data are being misinterpreted Work around Include the NPOP option XIX Fatal error message 386 spuriously arises when abbreviated code such as IF condition statement is used where 1 the condition includes a test of ICALL or COMACT and either 2a the statement is a WRITE PRINT statement that uses either ICALL or COMACT in the output list or 2b the statement is an assignment statement that uses either ICALL or COMACT as a right hand quantity Work around Instead of the above IF statement use IF condition THEN statement ENDIF XX There arises a faulty end of record condition when 1 a superproblem is used 2 the data set is too large Work around Try reinstalling NONMEM setting LIM1 the size of buffer 1 to a value large enough that for each of the problems in the superproblem the

    Original URL path: http://nonmem.org/nonmem/nm/99nov152004.html (2016-04-25)
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  • [NMusers] sample size
    Subject RE NMusers sample size Date Sun November 14 2004 5 38 pm Hi Vijay Pascal Mats In addition to the comments already you could compute the amount of information in your current design and then get a feeling for how well a population method would be able to solve your problem This would allow you to assess whether the design is sufficient to meet your needs vs the slightly different question does a particular tool e g NONMEM perform well with the data that you have To do this you would need to have some feeling as to what the most likely model and parameter values are and it may well turn out that in some circumstances it is possible to learn about some parameters from as little as 4 intensively sampled subjects If you have the sampling design and some feeling for the likely model s and parameter values then I am happy to compute the information from the design for you Steve Stephen Duffull School of Pharmacy University of Queensland Brisbane 4072 Australia Tel 61 7 3365 8808 Fax 61 7 3365 1688 University Provider Number 00025B Email sduffull pharmacy uq edu au www http www uq edu au pharmacy sduffull duffull htm PFIM http www uq edu au pharmacy sduffull pfim htm MCMC PK example http www uq edu au pharmacy sduffull MCMC eg htm From Mats Karlsson Subject RE NMusers sample size Date Mon November 15 2004 4 16 am Hi Steve Vijay wrote I have plasma concentration time data from 4 large mammals Would it not be more straightforward and logical to actually analyse the data rather than guess upon the model and then use an approximation to investigate how well the design can characterize it Best regards Mats Mats Karlsson PhD Professor of Pharmacometrics Div of Pharmacokinetics and Drug Therapy Dept of Pharmaceutical Biosciences Faculty of Pharmacy Uppsala University Box 591 SE 751 24 Uppsala Sweden phone 46 18 471 4105 fax 46 18 471 4003 mats karlsson farmbio uu se From Steve Duffull sduffull pharmacy uq edu au Subject RE NMusers sample size Date Mon November 15 2004 4 23 am Mats If you know nothing about the drug then I agree However if the experiment was supposed to be answering a question then it is possible that the investigators may know something in which case the design could be assessed this assessment could also answer the yet to be asked question how many more animals are needed to answer the question of interest Steve Stephen Duffull School of Pharmacy University of Queensland Brisbane 4072 Australia Tel 61 7 3365 8808 Fax 61 7 3365 1688 University Provider Number 00025B Email sduffull pharmacy uq edu au www http www uq edu au pharmacy sduffull duffull htm PFIM http www uq edu au pharmacy sduffull pfim htm MCMC PK example http www uq edu au pharmacy sduffull MCMC eg htm From GIRARD PASCAL PASCAL GIRARD adm univ lyon1 fr Subject RE NMusers sample

    Original URL path: http://nonmem.org/nonmem/nm/98nov112004.html (2016-04-25)
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  • [NMusers] Open note to Nick Holford about WFN installation subdirectories
    used for Also CrossGraphs has been sold to PPD and is US 3 000 seat Do you or others know of any useful alternatives to viewing NONMEM output in addition to Mats XPOSE SPlus combination Many thanks Paul nmusers my apologies for the listserve posting if you are not using wfn but I thought that it was of general enough relevance to post here PRH 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 Nick Holford Subject RE NMusers Open note to Nick Holford about WFN installation subdirectories Date Fri November 12 2004 12 54 am Paul Thanks for your question about the sub directories They are used to store different compiled versions of NONMEM This lets you choose between a version which allows more obs subject e g 50t by calling wfn e g wfn g77 50t Please look at http wfn sourceforge net wfnnmver htm for details I am aware that CG is no longer available for any practical use because of the pricing Like Steve Duffull I am exploring alternatives I am hoping to

    Original URL path: http://nonmem.org/nonmem/nm/99nov112004.html (2016-04-25)
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  • [NMusers] Apple G5
    don t see anything in the Archives Have a great weekend Paul 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 David Bourne david boomer org Subject RE NMusers Apple G5 Date Mon December 6 2004 5 05 pm Hello Paul I have put a SETUP file

    Original URL path: http://nonmem.org/nonmem/nm/99nov052004.html (2016-04-25)
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