Get the most accurate information you can get from NONMEM
Usage
nminfo(
file,
mod = ".mod",
xml = ".xml",
ext = ".ext",
cov = ".cov",
phi = ".phi",
lst = ".lst",
useXml = TRUE,
useExt = TRUE,
useCov = TRUE,
usePhi = TRUE,
useLst = TRUE,
strictLst = FALSE,
verbose = FALSE
)Arguments
- file
nonmem file, like control stream, phi. This function will remove the extension to try to get the right information. It preferentially selects the most accurate estimates from the file.
- mod
the NONMEM output extension, defaults to
.mod- xml
the NONMEM xml file extension , defaults to
.xml- ext
the NONMEM ext file extension, defaults to
.ext- cov
the NONMEM covariance file extension, defaults to
.cov- phi
the NONMEM eta/phi file extension, defaults to
.phi- lst
the NONMEM output extension, defaults to
.lst- useXml
if present, use the NONMEM xml file to import much of the NONMEM information
- useExt
if present, use the NONMEM ext file to extract parameter estimates (default
TRUE), otherwise defaults to parameter estimates extracted in the NONMEM output- useCov
if present, use the NONMEM cov file to import the covariance, otherwise import the covariance with list file
- usePhi
if present, use the NONMEM phi file to extract etas (default
TRUE), otherwise defaults to etas in the tables (if present)- useLst
if present, use the NONMEM lst file to extract NONMEM information
- strictLst
The list parsing needs to be correct for a successful load (default
FALSE).- verbose
this is a flag to be more verbose when reading information in, by default this is
FALSE
Examples
nminfo(system.file("mods/cpt/runODE032.res", package="nonmem2rx"))
#> $theta
#> theta1 theta2 theta3 theta4 theta5
#> 1.3703404 4.1981491 1.3800349 3.8765734 0.1964461
#>
#> $omega
#> eta1 eta2 eta3 eta4
#> eta1 0.1012514 0.00000000 0.0000000 0.00000000
#> eta2 0.0000000 0.09938724 0.0000000 0.00000000
#> eta3 0.0000000 0.00000000 0.1013027 0.00000000
#> eta4 0.0000000 0.00000000 0.0000000 0.07304975
#>
#> $cov
#> theta1 theta2 theta3 theta4 theta5
#> theta1 8.876810e-04 -1.055098e-04 1.844162e-04 -1.202337e-04 5.278300e-08
#> theta2 -1.055098e-04 8.714095e-04 -1.061946e-04 -5.066632e-05 -1.565618e-05
#> theta3 1.844162e-04 -1.061946e-04 2.993363e-03 1.652516e-04 5.993313e-06
#> theta4 -1.202337e-04 -5.066632e-05 1.652516e-04 1.213465e-03 -2.539912e-05
#> theta5 5.278300e-08 -1.565618e-05 5.993313e-06 -2.539912e-05 9.942182e-06
#> eta1 -4.712728e-05 4.696667e-05 -3.642709e-05 2.547962e-05 -8.168847e-06
#> omega.1.2 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> omega.1.3 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> omega.1.4 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> eta2 -7.371560e-05 2.566338e-05 -8.083493e-05 1.369999e-05 -4.365635e-06
#> omega.2.3 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> omega.2.4 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> eta3 6.633832e-05 -8.190016e-05 5.489848e-04 1.683555e-04 1.591222e-06
#> omega.3.4 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> eta4 -9.496613e-06 1.101079e-04 -3.065372e-04 -9.128974e-05 3.187703e-06
#> eps1 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> eta1 omega.1.2 omega.1.3 omega.1.4 eta2 omega.2.3
#> theta1 -4.712728e-05 0 0 0 -7.371560e-05 0
#> theta2 4.696667e-05 0 0 0 2.566338e-05 0
#> theta3 -3.642709e-05 0 0 0 -8.083493e-05 0
#> theta4 2.547962e-05 0 0 0 1.369999e-05 0
#> theta5 -8.168847e-06 0 0 0 -4.365635e-06 0
#> eta1 1.692964e-04 0 0 0 8.751806e-06 0
#> omega.1.2 0.000000e+00 0 0 0 0.000000e+00 0
#> omega.1.3 0.000000e+00 0 0 0 0.000000e+00 0
#> omega.1.4 0.000000e+00 0 0 0 0.000000e+00 0
#> eta2 8.751806e-06 0 0 0 1.512503e-04 0
#> omega.2.3 0.000000e+00 0 0 0 0.000000e+00 0
#> omega.2.4 0.000000e+00 0 0 0 0.000000e+00 0
#> eta3 3.487139e-05 0 0 0 4.315929e-07 0
#> omega.3.4 0.000000e+00 0 0 0 0.000000e+00 0
#> eta4 1.366281e-05 0 0 0 -1.950959e-05 0
#> eps1 0.000000e+00 0 0 0 0.000000e+00 0
#> omega.2.4 eta3 omega.3.4 eta4 eps1
#> theta1 0 6.633832e-05 0 -9.496613e-06 0
#> theta2 0 -8.190016e-05 0 1.101079e-04 0
#> theta3 0 5.489848e-04 0 -3.065372e-04 0
#> theta4 0 1.683555e-04 0 -9.128974e-05 0
#> theta5 0 1.591222e-06 0 3.187703e-06 0
#> eta1 0 3.487139e-05 0 1.366281e-05 0
#> omega.1.2 0 0.000000e+00 0 0.000000e+00 0
#> omega.1.3 0 0.000000e+00 0 0.000000e+00 0
#> omega.1.4 0 0.000000e+00 0 0.000000e+00 0
#> eta2 0 4.315929e-07 0 -1.950959e-05 0
#> omega.2.3 0 0.000000e+00 0 0.000000e+00 0
#> omega.2.4 0 0.000000e+00 0 0.000000e+00 0
#> eta3 0 9.590290e-04 0 -1.297699e-04 0
#> omega.3.4 0 0.000000e+00 0 0.000000e+00 0
#> eta4 0 -1.297699e-04 0 5.101895e-04 0
#> eps1 0 0.000000e+00 0 0.000000e+00 0
#>
#> $objf
#> [1] 20167.64
#>
#> $nobs
#> [1] 2280
#>
#> $nsub
#> [1] 120
#>
#> $nmtran
#> [1] "\n\n WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1\n\n (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.\n"
#>
#> $termInfo
#> [1] "\n0MINIMIZATION SUCCESSFUL\n NO. OF FUNCTION EVALUATIONS USED: 320\n NO. OF SIG. DIGITS IN FINAL EST.: 2.5\n"
#>
#> $nonmem
#> [1] "7.4.3"
#>
#> $time
#> [1] 100.95
#>
#> $tere
#> [1] " Elapsed estimation time in seconds: 71.95\n Elapsed covariance time in seconds: 28.38\n Elapsed postprocess time in seconds: 0.43"
#>
#> $control
#> [1] ""
#> [2] "$PROB BOLUS_2CPT_CLV1QV2 SINGLE DOSE FOCEI (120 Ind/2280 Obs) runODE032"
#> [3] "$INPUT ID TIME DV LNDV MDV AMT EVID DOSE V1I CLI QI V2I SSX IIX SD CMT"
#> [4] "$DATA BOLUS_2CPT.csv IGNORE=@ IGNORE (SD.EQ.0)"
#> [5] "$SUBR ADVAN13 TOL=6"
#> [6] "$MODEL"
#> [7] " COMP=(CENTRAL,DEFOBS,DEFDOSE)"
#> [8] " COMP=(PERI)"
#> [9] "$PK"
#> [10] " CL=EXP(THETA(1)+ETA(1))"
#> [11] " V=EXP(THETA(2)+ETA(2))"
#> [12] " Q=EXP(THETA(3)+ETA(3))"
#> [13] " V2=EXP(THETA(4)+ETA(4))"
#> [14] " V1=V"
#> [15] " S1=V"
#> [16] "\t\t K21=Q/V2"
#> [17] "\t\t K12=Q/V"
#> [18] "$DES"
#> [19] " DADT(1)= K21*A(2)-K12*A(1)-CL*A(1)/V1"
#> [20] " DADT(2)=-K21*A(2)+K12*A(1) \t\t"
#> [21] "$ERROR"
#> [22] " IPRED = F"
#> [23] " RESCV = THETA(5)"
#> [24] " W = IPRED*RESCV"
#> [25] " IRES = DV-IPRED"
#> [26] " IWRES = IRES/W"
#> [27] " Y = IPRED+W*EPS(1)"
#> [28] "$THETA 1.6 ;log Cl"
#> [29] "$THETA 4.5 ;log Vc"
#> [30] "$THETA 1.6 ;log Q"
#> [31] "$THETA 4 ;log Vp"
#> [32] "$THETA (0,0.3,1) ;RSV"
#> [33] "$OMEGA 0.15 0.15 0.15 0.15"
#> [34] "$SIGMA 1 FIX"
#> [35] "$EST NSIG=2 SIGL=6 PRINT=5 MAX=9999 NOABORT POSTHOC METHOD=COND INTER NOOBT"
#> [36] "$COV"
#> [37] "$TABLE ID TIME LNDV MDV AMT EVID DOSE V1I CLI QI V2I CL V Q V2 ETA1 ETA2 ETA3 ETA4"
#> [38] " IPRED IRES IWRES CWRESI"
#> [39] " ONEHEADER NOPRINT FILE=runODE032.csv"
#>
#> $eta
#> ID eta1 eta2 eta3 eta4
#> 1 1 -0.14424000 0.37464400 0.06501120 0.240662000
#> 2 2 0.56765200 -0.17515700 0.35129700 0.068655100
#> 3 3 0.47739800 -0.05753220 -0.07838230 -0.029594800
#> 4 4 -0.59588800 0.40511500 0.06595780 -0.104262000
#> 5 5 -0.32363600 0.27545000 0.02914670 0.251918000
#> 6 6 0.23277900 0.16120000 -0.00238193 0.064909600
#> 7 7 0.60699200 0.01759660 0.11880500 -0.028699900
#> 8 8 0.31283200 -0.53217800 -0.06375310 -0.221174000
#> 9 9 0.29495300 0.05832140 0.10949400 0.231407000
#> 10 10 0.14195300 -0.24786400 -0.17256300 -0.254001000
#> 11 11 -0.27053800 -0.23474000 -0.15745700 0.170349000
#> 12 12 -0.42602800 0.42758100 0.07017320 -0.075792800
#> 13 13 0.08017620 0.75176000 -0.00136251 0.045172700
#> 14 14 -0.12636300 -0.10582300 -0.08585340 0.020315600
#> 15 15 0.38692100 0.15867700 -0.00800554 0.108208000
#> 16 16 0.27036200 0.18321400 -0.00419876 0.374298000
#> 17 17 0.23923600 -0.32492200 -0.40412600 0.249456000
#> 18 18 -0.00269962 0.15345600 0.08357370 0.229613000
#> 19 19 0.13841300 -0.54122300 -0.03773240 0.296767000
#> 20 20 -0.46801300 -0.20000400 0.22992100 0.519881000
#> 21 21 0.28046300 0.19223800 -0.24784800 -0.053553600
#> 22 22 -0.00235221 0.10750900 -0.01570640 -0.170039000
#> 23 23 0.43714700 -0.09834960 0.20282200 -0.291774000
#> 24 24 -0.22670500 0.10172000 -0.06534150 0.019352400
#> 25 25 0.33364600 0.05095240 0.12533900 -0.284328000
#> 26 26 -0.15186700 -0.26233000 0.02811900 -0.065962400
#> 27 27 -0.28479700 -0.07478660 -0.02914140 -0.074459200
#> 28 28 0.04748590 0.17603800 0.11330300 0.116149000
#> 29 29 0.11232300 -0.42770200 -0.12393100 0.112370000
#> 30 30 -0.10120700 0.24156700 0.18911800 0.022527100
#> 31 31 0.26038200 -0.31787200 -0.46396000 -0.057012300
#> 32 32 0.02265670 -0.12159100 0.09948040 -0.044713800
#> 33 33 -0.31068700 -0.50537800 0.11857700 -0.072940000
#> 34 34 0.15974200 -0.00581950 -0.14293700 0.026960100
#> 35 35 0.05689450 -0.18707700 0.13855200 -0.038802000
#> 36 36 -0.04149100 0.01467420 0.24871300 0.235971000
#> 37 37 -0.28270600 0.18864700 -0.14675500 0.002239020
#> 38 38 -0.39544100 -0.17566300 0.03086270 0.160316000
#> 39 39 -0.44801000 -0.23339500 -0.05457800 0.034569300
#> 40 40 -0.40352400 0.71639900 0.03388700 -0.050975100
#> 41 41 -0.09660390 0.37159800 -0.14032900 -0.163309000
#> 42 42 0.40655200 -0.19898700 0.09422060 0.014364700
#> 43 43 0.06365490 -0.23971500 0.18403100 0.024279300
#> 44 44 0.73216500 0.15155300 0.08640920 -0.070061900
#> 45 45 0.69482300 -0.33599300 -0.45285800 0.327398000
#> 46 46 -0.15903400 -0.49138700 0.08631480 -0.326643000
#> 47 47 -0.32692500 0.52906500 0.15525900 -0.002167200
#> 48 48 0.34205600 0.43590800 0.10205300 0.117408000
#> 49 49 0.15624900 0.12570800 -0.18659000 0.162904000
#> 50 50 0.20167200 -0.27862400 -0.10363700 -0.611866000
#> 51 51 0.28569900 -0.05298130 -0.31277400 0.482237000
#> 52 52 -0.17925200 0.23186600 0.13349000 0.110341000
#> 53 53 -0.20669600 -0.28473000 0.14233500 0.082932900
#> 54 54 -0.14132400 0.37939300 -0.05261020 0.029393800
#> 55 55 -0.11181300 -0.32678600 0.16299000 -0.070609600
#> 56 56 -0.63672900 0.58485000 0.10498900 0.013498600
#> 57 57 -0.21507100 -0.22916600 -0.28756200 0.178900000
#> 58 58 0.35806700 -0.05416930 0.40838100 -0.276384000
#> 59 59 0.05910530 -0.44828200 -0.12018000 0.218146000
#> 60 60 0.10759500 -0.04209500 0.29418100 -0.106099000
#> 61 61 0.37837000 -0.07172710 -0.08466650 0.199045000
#> 62 62 -0.27696000 -0.14019400 -0.10502100 0.037360700
#> 63 63 -0.72832600 0.33906900 0.15471800 -0.157963000
#> 64 64 0.38560500 -0.12710600 0.12557100 -0.306528000
#> 65 65 0.16094300 -0.16399700 -0.15446100 0.044445100
#> 66 66 0.69667500 0.34464000 0.13533300 -0.455244000
#> 67 67 0.44275200 0.12776100 0.36124600 -0.412007000
#> 68 68 -0.19654600 0.11443100 0.10645000 -0.590975000
#> 69 69 -0.05818240 -0.08413010 -0.05650970 0.263846000
#> 70 70 0.14952100 0.39368100 -0.04981730 0.191504000
#> 71 71 -0.33740700 0.10570800 0.19619900 0.155928000
#> 72 72 -0.69872100 -0.51533700 0.04396320 0.000846648
#> 73 73 0.01076690 0.61540700 0.09002220 0.178556000
#> 74 74 0.20712900 -0.21042600 -0.05817590 0.137012000
#> 75 75 0.36452900 0.00945768 0.01538820 -0.102007000
#> 76 76 -0.06147530 -0.01864860 0.03956850 0.025404600
#> 77 77 0.14755500 -0.33821000 0.08060850 -0.104637000
#> 78 78 0.05043080 -0.14039200 -0.06552990 0.037271100
#> 79 79 -0.13078600 -0.28282800 0.17856900 -0.255775000
#> 80 80 -0.04714240 0.13484500 0.18002800 0.108969000
#> 81 81 0.03155160 -0.21060600 0.14035000 0.089137500
#> 82 82 0.37108300 -0.31208900 -0.23774900 0.026305200
#> 83 83 0.25148300 0.61218800 0.10758100 -0.176849000
#> 84 84 -0.18963100 0.04943880 -0.04214050 0.102070000
#> 85 85 0.33298700 0.27384800 0.16310000 0.033666000
#> 86 86 -0.23812200 -0.16038400 -0.08634300 -0.058731500
#> 87 87 0.38391600 0.04119620 -0.27643800 0.147468000
#> 88 88 -0.10298800 0.19976700 -0.15661500 -0.200062000
#> 89 89 -0.15166600 0.41495400 0.09549760 -0.065032300
#> 90 90 0.01407440 0.29514700 0.19409100 0.135821000
#> 91 91 -0.41928800 -0.60078300 -0.32863400 0.113174000
#> 92 92 -0.06073560 -0.19536500 0.16977300 -0.191269000
#> 93 93 -0.08957630 0.22526300 0.09766250 0.051171900
#> 94 94 -0.59527900 0.44926000 0.09443550 -0.091018700
#> 95 95 -0.52511800 0.04418750 -0.49548800 -0.187676000
#> 96 96 0.00218837 -0.08893150 0.05216140 -0.087904800
#> 97 97 -0.01221490 -0.62926800 -0.21896700 0.167880000
#> 98 98 -0.06611430 -0.48380600 0.25682800 0.089878300
#> 99 99 0.28847000 -0.12401300 0.31547400 -0.042283500
#> 100 100 0.16767600 -0.18271000 0.12634200 -0.288271000
#> 101 101 0.13754700 -0.01918670 0.28368400 0.137620000
#> 102 102 0.27452300 0.47222900 0.07034760 0.106941000
#> 103 103 -0.11568100 0.11760300 0.18951200 -0.043268100
#> 104 104 0.06801260 0.05801770 -0.04669300 -0.144975000
#> 105 105 -0.16200900 0.16523000 0.48384200 0.205917000
#> 106 106 -0.10389900 0.39249200 -0.01162800 0.112158000
#> 107 107 -0.46541000 -0.16248700 -0.22631000 0.026516500
#> 108 108 -0.56156500 -0.20425100 0.08323350 -0.067884700
#> 109 109 -0.02578220 0.29599700 -0.03974570 0.154768000
#> 110 110 0.05554480 -0.76315700 -0.49552200 0.011846900
#> 111 111 -0.50922900 0.07079820 -0.10147900 -0.116094000
#> 112 112 -0.19079300 0.30565000 -0.02401360 -0.072402000
#> 113 113 -0.03288730 -0.26397800 0.41920200 -0.419513000
#> 114 114 0.17266700 -0.21803900 -0.23855700 -0.024368500
#> 115 115 0.07875010 0.12835600 0.11664400 -0.218375000
#> 116 116 -0.32527700 0.16564300 -0.00834690 0.059186700
#> 117 117 -0.05887220 -0.37614800 0.09676570 -0.281402000
#> 118 118 -0.13482900 0.25191100 -0.22708900 -0.139859000
#> 119 119 0.10252400 -0.40742900 -0.28432200 0.146728000
#> 120 120 0.55679800 -0.17809900 -0.18922100 -0.178665000
#>
#> $uses
#> [1] "xml" "ext" "phi" "lst"
#>
#> $thetaSource
#> [1] "xml"
#>
#> $omegaSource
#> [1] "xml"
#>
#> $covSource
#> [1] "xml"
#>
#> $objfSource
#> [1] "xml"
#>
#> $sigma
#> eps1
#> eps1 1
#>
#> $sigmaSource
#> [1] "ext"
#>