Get the most accurate information you can get from NONMEM
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
)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.
the NONMEM output extension, defaults to .mod
the NONMEM xml file extension , defaults to .xml
the NONMEM ext file extension, defaults to .ext
the NONMEM covariance file extension, defaults to .cov
the NONMEM eta/phi file extension, defaults to .phi
the NONMEM output extension, defaults to .lst
if present, use the NONMEM xml file to import much of the NONMEM information
if present, use the NONMEM ext file to extract
parameter estimates (default TRUE), otherwise defaults to
parameter estimates extracted in the NONMEM output
if present, use the NONMEM cov file to import the covariance, otherwise import the covariance with list file
if present, use the NONMEM phi file to extract etas
(default TRUE), otherwise defaults to etas in the tables (if
present)
if present, use the NONMEM lst file to extract NONMEM information
The list parsing needs to be correct for a
successful load (default FALSE).
this is a flag to be more verbose when reading information in, by default this is FALSE
list of NONMEM information
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"
#>