Hi I am having some problems running a covariate analysis with my colleage using R with the NonMem program we are using for a graduate school project. R and NonMem run fine without adding in the covariates, but the program is giving us a problem when the covariate analysis is added. We think the problem is with the R code to run the covariate data analysis. We have the control stream, R code (along with the error), and data attached. If anyone can help we would really appreciate it. Thank you very much. Michael
R Code: # load MItools from within R library(MItools) ProjectDir <- "~/EssentialsOpenCourseware/continuous_PKPD/Examples" NMcom <- "nm6osxg77big.pl" cov <- c("AGE", "BW") # run NONMEM using 3032.ctl NONR(ProjectDir=ProjectDir, NMcom=NMcom, dvname="Test (mcg/L)", diag=1, covplt=1, b=3032, boot=0, nochecksum=TRUE, grp=c("FLAG") ) ERROR MESSAGE: ld warning: for symbol _cm41_ tentative definition of size 32 from /usr/local/nm6osxg77big/nm/nonmem.a(INITL.o) is is smaller than the real definition of size 28 from /usr/local/nm6osxg77big/nm/BLKDAT.o /usr/local/nm6osxg77big/test/nm6osxg77big.pl is starting /Users/mpdubb/EssentialsOpenCourseware/continuous_PKPD/Examples/3033/nonmem.exe /usr/local/nm6osxg77big/test/nm6osxg77big.pl is complete No TAD item for run 3033. Error in as.vector(x, mode) : invalid 'mode' argument Run 3033 complete. NONR complete. CONTROL STREAM (in NONMEM): $PROB RUN# 3033 EFFECT COMP POPULATION PK-PD MODEL 2 $INPUT C REPL ID ARM TIME AGE BW GNDR DV MDV FLAG AMT EVID ;FLAG 1 = PK, FLAG 2=PD, ;CMT 1=GUT, 2=CENTRAL ;DV =PK ORDERED BY ID, TIME $DATA ../projectRSD1.csv IGNORE=C $SUBROUTINE ADVAN2 TRANS2 INFN=../MItoolsRunlogNM6.for $ABB COMRES=8 $PK FLA2=FLAG TVKA=THETA(1) TVCL=THETA(2) TVV=THETA(3) CL=TVCL*EXP(ETA(1)) V=TVV*EXP(ETA(2)) KA=TVKA*EXP(ETA(3)) S2=V $ERROR EMAX=THETA(4)*EXP(ETA(4)) EC50=THETA(5)*EXP(ETA(5)) N = THETA(6)*EXP(ETA(6)) EFF= (EMAX*F**N)/(EC50**N+F**N) + ERR(2) CONC= F + F*ERR(1) Y = CONC*(2-FLAG) + EFF*(FLAG-1) IPRED=Y " LAST " COM(1)=G(1,1) " COM(2)=G(2,1) " COM(3)=G(3,1) " COM(4)=G(4,1) " COM(5)=G(5,1) " COM(6)=G(6,1) " COM(7)=HH(1,1) " COM(8)=HH(2,1) $THETA (0, 1.7) ;KA (0, 4.7) ;CL (0, 38) ;V (0.0, .5) ; EMAX (0.0, 100) ; EC50 (0.0, 1, 10) ; N $OMEGA 0.04 0.04 0.04 0.04 0.04 0.04 $SIGMA 0.04 5 $ESTIMATION MAXEVAL=9999 NOABORT METHOD=0 POSTHOC PRINT=5 $COVARIANCE $TABLE ID TIME AGE BW GNDR TVKA TVV TVCL ETA1 ETA2 ETA3 EVID NOPRINT ONEHEADER FILE=TABLE.PAR $TABLE NOPRINT FILE=../3033.TAB ONEHEADER ID TIME AGE BW GNDR KA V CL TVKA TVCL TVV FLAG FLA2 EVID EFF CONC IPRED FLAG $TABLE NOPRINT ONEHEADER FILE=../3033par.TAB ID TIME AGE BW GNDR KA V CL TVKA TVCL TVV EMAX EC50 ETA1 ETA2 ETA3 EVID $TABLE ID TIME COM(1)=G11 COM(2)=G21 COM(3)=G31 COM(4)=G41 COM(5)=G51 COM(6)=G61 COM(7)=H11 COM(8)=H21 IPRED MDV NOPRINT ONEHEADER FILE=cwtab1.deriv
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