tests/testthat/_snaps/nm.md
In kestrel99/pmxTools: Pharmacometric and Pharmacokinetic Toolkit
read_nm
Code
read_nm("testData/runR001.xml")
Message <simpleMessage>
Reading testData/runR001.xml
Output
$start_datetime
$start_datetime[[1]]
[1] "2021-02-04T17:29:28.815"
$control_stream
$control_stream[[1]]
[1] "\n$PROB BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n$INPUT ID TIME DV=DROP LNDV=DV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n$DATA BOLUS_1CPT.csv IGNORE=@ IGNORE (SD.EQ.0)\n$SUBR ADVAN1,TRANS2\n$PK\n CL=THETA(1)*EXP(ETA(1))\n V=THETA(2)*EXP(ETA(2))\n S1=V\n$ERROR (ONLY OBSERVATIONS)\n IPRED=LOG(0.0025)\n W=THETA(3)\n IF (F.GT.0) IPRED=LOG(F)\n IRES=IPRED-DV\n IWRES=IRES/W\n Y=IPRED+W*ERR(1)\n$THETA (0,5,15) (0,90,200) (0,0.3,1)\n;# CL V RSV\n$OMEGA 0.15 0.15\n;# IIV_CL IIV_V\n$SIGMA 1 FIX\n;# RSV_FIX\n$EST NSIG=3 PRINT=5 MAX=9999 NOABORT POSTHOC METHOD=COND INTER NOOBT\n$COV\n$TABLE ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2\n IPRED IRES IWRES CWRESI\n ONEHEADER NOPRINT FILE=runR001.csv\n"
$nmtran
$nmtran[[1]]
[1] "\n\n WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1\n\n (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.\n"
$nonmem
$nonmem$license_information
$nonmem$license_information[[1]]
[1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n"
$nonmem$program_information
$nonmem$program_information[[1]]
[1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n"
$nonmem$problem
$nonmem$problem$problem_title
$nonmem$problem$problem_title[[1]]
[1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001"
$nonmem$problem$problem_information
$nonmem$problem$problem_information[[1]]
[1] "\n\n PROBLEM NO.: 1\n BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n0DATA CHECKOUT RUN: NO\n DATA SET LOCATED ON UNIT NO.: 2\n THIS UNIT TO BE REWOUND: NO\n NO. OF DATA RECS IN DATA SET: 2400\n NO. OF DATA ITEMS IN DATA SET: 13\n ID DATA ITEM IS DATA ITEM NO.: 1\n DEP VARIABLE IS DATA ITEM NO.: 3\n MDV DATA ITEM IS DATA ITEM NO.: 4\n0INDICES PASSED TO SUBROUTINE PRED:\n 6 2 5 0 0 0 13 0 0 0 0\n0LABELS FOR DATA ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n0(NONBLANK) LABELS FOR PRED-DEFINED ITEMS:\n CL V IPRED IRES IWRES\n0FORMAT FOR DATA:\n (E4.0,2E7.0,E2.0,E7.0,E2.0,E7.0,E6.0,E5.0,2E3.0,2E2.0)\n\n TOT. NO. OF OBS RECS: 2276\n TOT. NO. OF INDIVIDUALS: 120\n0LENGTH OF THETA: 3\n0DEFAULT THETA BOUNDARY TEST OMITTED: NO\n0OMEGA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 2\n0DEFAULT OMEGA BOUNDARY TEST OMITTED: YES\n0SIGMA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 1\n0DEFAULT SIGMA BOUNDARY TEST OMITTED: NO\n0INITIAL ESTIMATE OF THETA:\n LOWER BOUND INITIAL EST UPPER BOUND\n 0.0000E+00 0.5000E+01 0.1500E+02\n 0.0000E+00 0.9000E+02 0.2000E+03\n 0.0000E+00 0.3000E+00 0.1000E+01\n0INITIAL ESTIMATE OF OMEGA:\n 0.1500E+00\n 0.0000E+00 0.1500E+00\n0INITIAL ESTIMATE OF SIGMA:\n 0.1000E+01\n0SIGMA CONSTRAINED TO BE THIS INITIAL ESTIMATE\n0COVARIANCE STEP OMITTED: NO\n EIGENVLS. PRINTED: NO\n SPECIAL COMPUTATION: NO\n COMPRESSED FORMAT: NO\n GRADIENT METHOD USED: NOSLOW\n SIGDIGITS ETAHAT (SIGLO): -1\n SIGDIGITS GRADIENTS (SIGL): -1\n EXCLUDE COV FOR FOCE (NOFCOV): NO\n Cholesky Transposition of R Matrix (CHOLROFF):0\n KNUTHSUMOFF: -1\n RESUME COV ANALYSIS (RESUME): NO\n SIR SAMPLE SIZE (SIRSAMPLE):\n NON-LINEARLY TRANSFORM THETAS DURING COV (THBND): 1\n PRECONDTIONING CYCLES (PRECOND): 0\n PRECONDTIONING TYPES (PRECONDS): TOS\n FORCED PRECONDTIONING CYCLES (PFCOND):0\n PRECONDTIONING TYPE (PRETYPE): 0\n FORCED POS. DEFINITE SETTING DURING PRECONDITIONING: (FPOSDEF):0\n SIMPLE POS. DEFINITE SETTING: (POSDEF):-1\n0TABLES STEP OMITTED: NO\n NO. OF TABLES: 1\n SEED NUMBER (SEED): 11456\n RANMETHOD: 3U\n MC SAMPLES (ESAMPLE): 300\n WRES SQUARE ROOT TYPE (WRESCHOL): EIGENVALUE\n0-- TABLE 1 --\n0RECORDS ONLY: ALL\n04 COLUMNS APPENDED: YES\n PRINTED: NO\n HEADERS: ONE\n FILE TO BE FORWARDED: NO\n FORMAT: S1PE11.4\n IDFORMAT:\n LFORMAT:\n RFORMAT:\n FIXED_EFFECT_ETAS:\n0USER-CHOSEN ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2 IPRED IRES IWRES CWRESI\n1DOUBLE PRECISION PREDPP VERSION 7.5.0\n\n ONE COMPARTMENT MODEL (ADVAN1)\n0MAXIMUM NO. OF BASIC PK PARAMETERS: 2\n0BASIC PK PARAMETERS (AFTER TRANSLATION):\n ELIMINATION RATE (K) IS BASIC PK PARAMETER NO.: 1\n\n TRANSLATOR WILL CONVERT PARAMETERS\n CLEARANCE (CL) AND VOLUME (V) TO K (TRANS2)\n0COMPARTMENT ATTRIBUTES\n COMPT. NO. FUNCTION INITIAL ON/OFF DOSE DEFAULT DEFAULT\n STATUS ALLOWED ALLOWED FOR DOSE FOR OBS.\n 1 CENTRAL ON NO YES YES YES\n 2 OUTPUT OFF YES NO NO NO\n1\n ADDITIONAL PK PARAMETERS - ASSIGNMENT OF ROWS IN GG\n COMPT. NO. INDICES\n SCALE BIOAVAIL. ZERO-ORDER ZERO-ORDER ABSORB\n FRACTION RATE DURATION LAG\n 1 3 * * * *\n 2 * - - - -\n - PARAMETER IS NOT ALLOWED FOR THIS MODEL\n * PARAMETER IS NOT SUPPLIED BY PK SUBROUTINE;\n WILL DEFAULT TO ONE IF APPLICABLE\n0DATA ITEM INDICES USED BY PRED ARE:\n EVENT ID DATA ITEM IS DATA ITEM NO.: 6\n TIME DATA ITEM IS DATA ITEM NO.: 2\n DOSE AMOUNT DATA ITEM IS DATA ITEM NO.: 5\n COMPT. NO. DATA ITEM IS DATA ITEM NO.: 13\n\n0PK SUBROUTINE CALLED WITH EVERY EVENT RECORD.\n PK SUBROUTINE NOT CALLED AT NONEVENT (ADDITIONAL OR LAGGED) DOSE TIMES.\n0DURING SIMULATION, ERROR SUBROUTINE CALLED WITH EVERY EVENT RECORD.\n OTHERWISE, ERROR SUBROUTINE CALLED ONLY WITH OBSERVATION EVENTS.\n"
$nonmem$problem$problem_options
list()
attr(,"data_checkout_run")
[1] "no"
attr(,"data_unit")
[1] "2"
attr(,"data_rewind")
[1] "no"
attr(,"data_nrec")
[1] "2400"
attr(,"data_nitems")
[1] "13"
attr(,"data_id")
[1] "1"
attr(,"data_l2")
[1] "0"
attr(,"data_dv")
[1] "3"
attr(,"data_mdv")
[1] "4"
attr(,"data_mrg")
[1] "0"
attr(,"data_raw")
[1] "0"
attr(,"data_rpt")
[1] "0"
attr(,"data_sub_array1")
[1] "0"
attr(,"data_sub_array2")
[1] "0"
attr(,"data_sub_array3")
[1] "0"
attr(,"data_pred_indices")
[1] "6,2,5,0,0,0,13,0,0,0,0"
attr(,"data_format")
[1] "(e4.0,2e7.0,e2.0,e7.0,e2.0,e7.0,e6.0,e5.0,2e3.0,2e2.0)"
attr(,"data_nobs")
[1] "2276"
attr(,"data_nind")
[1] "120"
attr(,"data_mdv100")
[1] "0"
attr(,"nthetat")
[1] "3"
attr(,"theta_bound_test_omitted")
[1] "no"
attr(,"omega_diagdim")
[1] "2"
attr(,"omega_bound_test_omitted")
[1] "no"
attr(,"sigma_diagdim")
[1] "1"
attr(,"sigma_bound_test_omitted")
[1] "no"
attr(,"cov_omitted")
[1] "no"
attr(,"cov_matrix")
[1] "rsr"
attr(,"cov_eigen_print")
[1] "no"
attr(,"cov_special")
[1] "no"
attr(,"cov_compressed")
[1] "no"
attr(,"cov_slow_gradient")
[1] "noslow"
attr(,"cov_siglocov")
[1] "-1"
attr(,"cov_siglcov")
[1] "-1"
attr(,"cov_tol")
[1] "-1"
attr(,"cov_atol")
[1] "-1"
attr(,"cov_nofcov")
[1] "no"
attr(,"cov_cholroff")
[1] "0"
attr(,"cov_knuthsumoff")
[1] "-1"
attr(,"cov_resume")
[1] "no"
attr(,"cov_sirsample")
[1] "BLANK"
attr(,"cov_thbnd")
[1] "1"
attr(,"cov_precond")
[1] "0"
attr(,"cov_preconds")
[1] "tos"
attr(,"cov_pfcond")
[1] "0"
attr(,"cov_pretype")
[1] "0"
attr(,"cov_fposdef")
[1] "0"
attr(,"cov_posdef")
[1] "-1"
attr(,"tab_omitted")
[1] "no"
attr(,"tab_number")
[1] "1"
attr(,"tab_seed")
[1] "11456"
attr(,"tab_clockseed")
[1] "11456"
attr(,"tab_ranmethod")
[1] "3u"
attr(,"tab_esample")
[1] "300"
attr(,"tab_wres")
[1] "eigenvalue"
attr(,"tab_fixedetas_01")
[1] "BLANK"
attr(,"pred_advan")
[1] "1"
attr(,"pred_evid")
[1] "6"
attr(,"pred_time")
[1] "2"
attr(,"pred_amt")
[1] "5"
attr(,"pred_cmt")
[1] "13"
$nonmem$problem$theta_lb
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "3"
$nonmem$problem$theta_in
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "5.00000000000000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "90.0000000000000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "0.300000000000000"
attr(,"name")
[1] "3"
$nonmem$problem$theta_ub
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "15.0000000000000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "200.000000000000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "1.00000000000000"
attr(,"name")
[1] "3"
$nonmem$problem$estimation
$nonmem$problem$estimation$parallel_est
list()
attr(,"parafile")
[1] "C:\\MPI\\node6.pnm"
attr(,"protocol")
[1] "MPI"
attr(,"nodes")
[1] "6"
$nonmem$problem$estimation$table_series
$nonmem$problem$estimation$table_series[[1]]
[1] "1"
$nonmem$problem$estimation$estimation_method
$nonmem$problem$estimation$estimation_method[[1]]
[1] "focei"
$nonmem$problem$estimation$estimation_title
$nonmem$problem$estimation$estimation_title[[1]]
[1] "First Order Conditional Estimation with Interaction"
$nonmem$problem$estimation$estimation_information
$nonmem$problem$estimation$estimation_information[[1]]
[1] "\n ESTIMATION STEP OMITTED: NO\n ANALYSIS TYPE: POPULATION\n NUMBER OF SADDLE POINT RESET ITERATIONS: 0\n GRADIENT METHOD USED: NOSLOW\n CONDITIONAL ESTIMATES USED: YES\n CENTERED ETA: NO\n EPS-ETA INTERACTION: YES\n LAPLACIAN OBJ. FUNC.: NO\n NO. OF FUNCT. EVALS. ALLOWED: 9999\n NO. OF SIG. FIGURES REQUIRED: 3\n INTERMEDIATE PRINTOUT: YES\n ESTIMATE OUTPUT TO MSF: NO\n ABORT WITH PRED EXIT CODE 1: NO\n IND. OBJ. FUNC. VALUES SORTED: NO\n NUMERICAL DERIVATIVE\n FILE REQUEST (NUMDER): NONE\n MAP (ETAHAT) ESTIMATION METHOD (OPTMAP): 0\n ETA HESSIAN EVALUATION METHOD (ETADER): 0\n INITIAL ETA FOR MAP ESTIMATION (MCETA): 0\n SIGDIGITS FOR MAP ESTIMATION (SIGLO): 100\n GRADIENT SIGDIGITS OF\n FIXED EFFECTS PARAMETERS (SIGL): 100\n NOPRIOR SETTING (NOPRIOR): 0\n NOCOV SETTING (NOCOV): OFF\n DERCONT SETTING (DERCONT): OFF\n FINAL ETA RE-EVALUATION (FNLETA): 1\n EXCLUDE NON-INFLUENTIAL (NON-INFL.) ETAS\n IN SHRINKAGE (ETASTYPE): NO\n NON-INFL. ETA CORRECTION (NONINFETA): 0\n RAW OUTPUT FILE (FILE): runR001.ext\n EXCLUDE TITLE (NOTITLE): NO\n EXCLUDE COLUMN LABELS (NOLABEL): NO\n FORMAT FOR ADDITIONAL FILES (FORMAT): S1PE12.5\n PARAMETER ORDER FOR OUTPUTS (ORDER): TSOL\n KNUTHSUMOFF: 0\n INCLUDE LNTWOPI: NO\n INCLUDE CONSTANT TERM TO PRIOR (PRIORC): NO\n INCLUDE CONSTANT TERM TO OMEGA (ETA) (OLNTWOPI):NO\n ADDITIONAL CONVERGENCE TEST (CTYPE=4)?: NO\n EM OR BAYESIAN METHOD USED: NONE\n\n"
$nonmem$problem$estimation$estimation_options
list()
attr(,"estim_omitted")
[1] "no"
attr(,"analysis_type")
[1] "pop"
attr(,"saddle_reset")
[1] "0"
attr(,"saddle_hess")
[1] "0"
attr(,"slow_gradient")
[1] "noslow"
attr(,"cond_estim")
[1] "yes"
attr(,"centered_eta")
[1] "no"
attr(,"epseta_interaction")
[1] "yes"
attr(,"laplace")
[1] "no"
attr(,"predflag")
[1] "0"
attr(,"maxfn")
[1] "9999"
attr(,"nsig")
[1] "3"
attr(,"msfo")
[1] "no"
attr(,"abort")
[1] "no"
attr(,"objsort")
[1] "no"
attr(,"numder")
[1] "0"
attr(,"optmap")
[1] "0"
attr(,"etader")
[1] "0"
attr(,"mceta")
[1] "0"
attr(,"siglo")
[1] "100"
attr(,"sigl")
[1] "100"
attr(,"noprior")
[1] "0"
attr(,"nocov")
[1] "0"
attr(,"dercont")
[1] "0"
attr(,"atol")
[1] "0"
attr(,"fnleta")
[1] "1"
attr(,"etastype")
[1] "0"
attr(,"noninfeta")
[1] "0"
attr(,"file")
[1] "runr001.ext"
attr(,"notitle")
[1] "0"
attr(,"nolabel")
[1] "0"
attr(,"format")
[1] "s1pe12.5"
attr(,"order")
[1] "tsol"
attr(,"knuthsumoff")
[1] "0"
attr(,"lntwopi")
[1] "0"
attr(,"priorc")
[1] "0"
attr(,"olntwopi")
[1] "0"
attr(,"ctype")
[1] "0"
$nonmem$problem$estimation$monitor
$nonmem$problem$estimation$monitor$obj
$nonmem$problem$estimation$monitor$obj[[1]]
[1] "-3465.72885682371"
attr(,"iteration")
[1] "0"
$nonmem$problem$estimation$monitor$obj
$nonmem$problem$estimation$monitor$obj[[1]]
[1] "-4111.52222574939"
attr(,"iteration")
[1] "5"
$nonmem$problem$estimation$monitor$obj
$nonmem$problem$estimation$monitor$obj[[1]]
[1] "-4125.77900367604"
attr(,"iteration")
[1] "10"
$nonmem$problem$estimation$monitor$obj
$nonmem$problem$estimation$monitor$obj[[1]]
[1] "-4126.11481640313"
attr(,"iteration")
[1] "14"
$nonmem$problem$estimation$termination_status
$nonmem$problem$estimation$termination_status[[1]]
[1] "0"
$nonmem$problem$estimation$termination_nfuncevals
$nonmem$problem$estimation$termination_nfuncevals[[1]]
[1] "114"
$nonmem$problem$estimation$termination_sigdigits
$nonmem$problem$estimation$termination_sigdigits[[1]]
[1] "3.02298445301969"
$nonmem$problem$estimation$termination_information
$nonmem$problem$estimation$termination_information[[1]]
[1] "\n0MINIMIZATION SUCCESSFUL\n NO. OF FUNCTION EVALUATIONS USED: 114\n NO. OF SIG. DIGITS IN FINAL EST.: 3.0\n"
$nonmem$problem$estimation$termination_txtmsg
$nonmem$problem$estimation$termination_txtmsg$val
$nonmem$problem$estimation$termination_txtmsg$val[[1]]
[1] "37"
attr(,"name")
[1] "1"
$nonmem$problem$estimation$etabar
$nonmem$problem$estimation$etabar$row
$nonmem$problem$estimation$etabar$row$col
$nonmem$problem$estimation$etabar$row$col[[1]]
[1] "4.765711648433239E-004"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabar$row$col
$nonmem$problem$estimation$etabar$row$col[[1]]
[1] "-1.516261194686842E-003"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etabarse
$nonmem$problem$estimation$etabarse$row
$nonmem$problem$estimation$etabarse$row$col
$nonmem$problem$estimation$etabarse$row$col[[1]]
[1] "2.398354777032987E-002"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabarse$row$col
$nonmem$problem$estimation$etabarse$row$col[[1]]
[1] "2.719347789006172E-002"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etabarn
$nonmem$problem$estimation$etabarn$row
$nonmem$problem$estimation$etabarn$row$col
$nonmem$problem$estimation$etabarn$row$col[[1]]
[1] "120"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabarn$row$col
$nonmem$problem$estimation$etabarn$row$col[[1]]
[1] "120"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etabarpval
$nonmem$problem$estimation$etabarpval$row
$nonmem$problem$estimation$etabarpval$row$col
$nonmem$problem$estimation$etabarpval$row$col[[1]]
[1] "0.984146393573823"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabarpval$row$col
$nonmem$problem$estimation$etabarpval$row$col[[1]]
[1] "0.955534240611886"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etashrinksd
$nonmem$problem$estimation$etashrinksd$row
$nonmem$problem$estimation$etashrinksd$row$col
$nonmem$problem$estimation$etashrinksd$row$col[[1]]
[1] "1.37215788183357"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etashrinksd$row$col
$nonmem$problem$estimation$etashrinksd$row$col[[1]]
[1] "1.46175485792922"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etashrinkvr
$nonmem$problem$estimation$etashrinkvr$row
$nonmem$problem$estimation$etashrinkvr$row$col
$nonmem$problem$estimation$etashrinkvr$row$col[[1]]
[1] "2.72548759114038"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etashrinkvr$row$col
$nonmem$problem$estimation$etashrinkvr$row$col[[1]]
[1] "2.90214244321166"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$ebvshrinksd
$nonmem$problem$estimation$ebvshrinksd$row
$nonmem$problem$estimation$ebvshrinksd$row$col
$nonmem$problem$estimation$ebvshrinksd$row$col[[1]]
[1] "1.58000136432566"
attr(,"cname")
[1] "EBV1"
$nonmem$problem$estimation$ebvshrinksd$row$col
$nonmem$problem$estimation$ebvshrinksd$row$col[[1]]
[1] "1.76289476258970"
attr(,"cname")
[1] "EBV2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$ebvshrinkvr
$nonmem$problem$estimation$ebvshrinkvr$row
$nonmem$problem$estimation$ebvshrinkvr$row$col
$nonmem$problem$estimation$ebvshrinkvr$row$col[[1]]
[1] "3.13503868553859"
attr(,"cname")
[1] "EBV1"
$nonmem$problem$estimation$ebvshrinkvr$row$col
$nonmem$problem$estimation$ebvshrinkvr$row$col[[1]]
[1] "3.49471154573972"
attr(,"cname")
[1] "EBV2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$relativeinf
$nonmem$problem$estimation$relativeinf$row
$nonmem$problem$estimation$relativeinf$row$col
$nonmem$problem$estimation$relativeinf$row$col[[1]]
[1] "96.8120802973034"
attr(,"cname")
[1] "REL1"
$nonmem$problem$estimation$relativeinf$row$col
$nonmem$problem$estimation$relativeinf$row$col[[1]]
[1] "96.4526037915573"
attr(,"cname")
[1] "REL2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$epsshrinksd
$nonmem$problem$estimation$epsshrinksd$row
$nonmem$problem$estimation$epsshrinksd$row$col
$nonmem$problem$estimation$epsshrinksd$row$col[[1]]
[1] "5.22027080681049"
attr(,"cname")
[1] "EPS1"
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$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA1"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA2"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
attr(,"rname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "74.0494905940748"
attr(,"cname")
[1] "THETA1"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "-2.35947484707118"
attr(,"cname")
[1] "THETA2"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "2423.71409515852"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "159.617096229120"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "6825.27392229574"
attr(,"cname")
[1] "OMEGA(2,2)"
attr(,"rname")
[1] "OMEGA(2,2)"
$nonmem$problem$estimation$invcovariance$row
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA1"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA2"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(2,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "SIGMA(1,1)"
attr(,"rname")
[1] "SIGMA(1,1)"
attr(,"number")
[1] "1"
attr(,"type")
[1] "0"
$nonmem$problem$post_process_times
$nonmem$problem$post_process_times$post_elapsed_time
$nonmem$problem$post_process_times$post_elapsed_time[[1]]
[1] "0.08"
$nonmem$problem$post_process_times$finaloutput_elapsed_time
$nonmem$problem$post_process_times$finaloutput_elapsed_time[[1]]
[1] "0.20"
attr(,"number")
[1] "1"
attr(,"subproblem")
[1] "0"
attr(,"superproblem1")
[1] "0"
attr(,"iteration1")
[1] "0"
attr(,"superproblem2")
[1] "0"
attr(,"iteration2")
[1] "0"
attr(,"version")
[1] "7.5.0"
$stop_datetime
$stop_datetime[[1]]
[1] "2021-02-04T17:29:31.574"
$total_cputime
$total_cputime[[1]]
[1] "7.266"
attr(,"schemaLocation")
[1] "http://namespaces.oreilly.com/xmlnut/address output.xsd"
attr(,"xmlns:xsi")
[1] "http://www.w3.org/2001/XMLSchema-instance"
attr(,"xmlns:nm")
[1] "http://namespaces.oreilly.com/xmlnut/address"
rnm
Code
rnm(index = "001", prefix = "runR", pathNM = "testData", ext = ".res", extmod = ".ctl")
Output
$Theta
Parameter Estimate SE CV CIL CIU P
1 THETA1 3.980130 0.09897590 2.486750 3.7861408 4.1741192 0
2 THETA2 68.219400 1.92949000 2.828360 64.4376691 72.0011309 0
3 THETA3 0.199472 0.00280475 1.406087 0.1939748 0.2049692 0
$Eta
Eta Estimate SE CV EtaCV Shrinkage
1 1 0.0715555 0.00912817 12.75677 26.74986 1.37216
2 2 0.0921585 0.01220090 13.23904 30.35762 1.46175
$Epsilon
Epsilon Estimate SE CV EpsCV Shrinkage
1 1 1 0 0 100 5.22027
$CorTheta
THETA1 THETA2 THETA3
1 1.00000000 0.109072 0.00138964
2 0.10907200 1.000000 0.12310700
3 0.00138964 0.123107 1.00000000
$CorOmega
Eta1 Eta2
Eta1 1.000 0.000
Eta2 0.000 1.000
$CorSigma
Eps1
Eps1 1.000
$OmegaMatrix
[,1] [,2]
[1,] 0.0715555 0.0000000
[2,] 0.0000000 0.0921585
$SigmaMatrix
[,1]
[1,] 1
$CovMatrixTheta
THETA1 THETA2 THETA3
1 9.79623e-03 0.020829800 3.85768e-07
2 2.08298e-02 3.722920000 6.66221e-04
3 3.85768e-07 0.000666221 7.86662e-06
$CovMatrix
THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1.
1 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0
2 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0
3 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0
4 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
5 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0
6 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
7 -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0
OMEGA.2.2.
1 -9.96425e-05
2 8.11546e-04
3 -2.60664e-06
4 0.00000e+00
5 -2.55098e-06
6 0.00000e+00
7 1.48861e-04
$OFV
[1] -4126.115
$ThetaString
Parameter Estimate SE CV Estimate (95% CI) P
1 THETA1 3.98 0.0990 2.5% 3.98 (3.79/4.17) < 0.00001
2 THETA2 68.2 1.93 2.8% 68.2 (64.4/72.0) < 0.00001
3 THETA3 0.199 0.00280 1.4% 0.199 (0.194/0.205) < 0.00001
$EtaString
Eta Estimate SE CV 100*sqrt(Omega) Shrinkage
1 1 0.0716 0.00913 12.8% 26.7% 1.4%
2 2 0.0922 0.0122 13.2% 30.4% 1.5%
$EpsString
Epsilon Estimate SE CV 100*sqrt(Omega) Shrinkage
1 1 1.00 (Fixed) 5.2%
$RunTime
[1] 17.35
$conditionN
NULL
read_nmcov
Code
read_nmcov("testData/runR001.cov")
Message <simpleMessage>
Reading testData/runR001.cov
Output
THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1.
[1,] 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0
[2,] 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0
[3,] 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0
[4,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
[5,] 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0
[6,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
[7,] -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0
OMEGA.2.2.
[1,] -9.96425e-05
[2,] 8.11546e-04
[3,] -2.60664e-06
[4,] 0.00000e+00
[5,] -2.55098e-06
[6,] 0.00000e+00
[7,] 1.48861e-04
read_nmext
Code
read_nmext("testData/runR001.ext")
Message <simpleMessage>
Reading testData/runR001.ext
Output
$Termination
NULL
$OFV
[1] -4126.115
$Thetas
[1] 3.980130 68.219400 0.199472
$Omega
$Omega[[1]]
[1] 0.0715555
$Omega[[2]]
[1] 0.0000000 0.0921585
$Sigma
$Sigma[[1]]
[1] 1
$seThetas
[1] 0.09897590 1.92949000 0.00280475
$seOmega
$seOmega[[1]]
[1] 0.00912817
$seOmega[[2]]
[1] NA 0.0122009
$seSigma
$seSigma[[1]]
[1] NA
$raw_lst
[1] "TABLE NO. 1: First Order Conditional Estimation with Interaction: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0"
[2] " ITERATION THETA1 THETA2 THETA3 SIGMA(1,1) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OBJ"
[3] " 0 5.00000E+00 9.00000E+01 3.00000E-01 1.00000E+00 1.50000E-01 0.00000E+00 1.50000E-01 -3465.72885682371"
[4] " 5 3.83588E+00 6.72641E+01 1.91725E-01 1.00000E+00 7.13261E-02 0.00000E+00 1.29166E-01 -4111.52222574939"
[5] " 10 3.94172E+00 6.73826E+01 1.99381E-01 1.00000E+00 7.15277E-02 0.00000E+00 9.19553E-02 -4125.77900367604"
[6] " 14 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313"
[7] " -1000000000 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313"
[8] " -1000000001 9.89759E-02 1.92949E+00 2.80475E-03 1.00000E+10 9.12817E-03 1.00000E+10 1.22009E-02 0.000000000000000E+000"
[9] " -1000000004 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 2.67499E-01 0.00000E+00 3.03576E-01 0.000000000000000E+000"
[10] " -1000000005 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+10 1.70621E-02 1.00000E+10 2.00952E-02 0.000000000000000E+000"
[11] " -1000000006 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 0.000000000000000E+000"
[12] " -1000000007 0.00000E+00 3.70000E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.000000000000000E+000"
[13] " -1000000008 3.88104E-02 -2.92122E-03 -4.33821E-01 0.00000E+00 -4.03024E-01 0.00000E+00 1.44149E-01 0.000000000000000E+000"
get_est_table
Code
get_est_table(nm1, thetaLabels = c("CL", "V", "KA"), omegaLabels = c("CL", "V"),
sigmaLabels = "Residual")
Output
Parameter Estimate RSE CI95 Shrinkage
1 CL 3.9800 2.49 3.79-4.17 -
2 V 68.2000 2.83 64.4-72.0 -
3 KA 0.1990 1.41 0.194-0.205 -
4 CL 0.0716 12.80 0.0537-0.0894 1.37
5 OM2,1 0.0000 NA <NA> -
6 V 0.0922 13.20 0.0682-0.116 1.46
7 Residual 1.0000 NA --- 5.22
get_probinfo
Code
get_probinfo(nm1)
Output
$prob_title
[1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001"
$prog_info
[1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n"
$lic_info
[1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n"
$prob_times
startTime stopTime elapsedTime
1 2021-02-04T17:29:31.574 2021-02-04T17:29:31.574 7.266
$prob_info
nRecords nOBS nIND nTHETA nOMEGA nSIGMA COV_STEP_OMITTED COV_MATRIX
1 2400 2276 120 3 NA 1 NO rsr
$est_info
final_objective_function estimation_method
1 -4126.11 focei
estimation_title estimation_elapsed_time
1 First Order Conditional Estimation with Interaction 0.83
termination_status condition_number
1 SUCCESSFUL NA
sample_uncertainty
Code
sample_uncert("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Reading testData/runR001.cov
Output
V1 V2 V3 V4 V5 V6 V7
1 4.165433 69.39547 0.2027448 1 0.06848604 0 0.09347681
2 3.980225 69.50231 0.1994999 1 0.07953186 0 0.08515790
3 4.008908 67.31330 0.2020217 1 0.04367090 0 0.08225640
4 4.001296 68.48560 0.2047266 1 0.07295125 0 0.09326988
5 3.978739 67.59651 0.1971732 1 0.08556432 0 0.08930405
6 4.042743 71.34557 0.1996294 1 0.05363680 0 0.10454367
7 3.969076 69.34515 0.1982914 1 0.07396419 0 0.09076399
8 3.869667 69.34122 0.1993334 1 0.06957219 0 0.08570421
9 4.083545 68.47258 0.2010389 1 0.07686870 0 0.08509724
10 4.153517 68.51932 0.2009742 1 0.06672599 0 0.11383226
11 4.028990 67.55515 0.2025752 1 0.06291851 0 0.08666884
12 4.095689 67.97826 0.2024989 1 0.07236835 0 0.09128803
13 4.028240 71.82350 0.2024290 1 0.07231574 0 0.09965155
14 3.983857 65.11927 0.1980753 1 0.07718695 0 0.09164850
15 3.942173 67.80190 0.2045056 1 0.06681079 0 0.08288682
16 3.945592 68.78126 0.1997871 1 0.06646189 0 0.10900627
17 3.842798 68.74961 0.2024411 1 0.06104701 0 0.09405646
18 3.843747 67.80288 0.2056648 1 0.07270782 0 0.07868634
19 4.005418 67.09663 0.2037665 1 0.07063172 0 0.10041499
20 3.988539 67.15033 0.2015780 1 0.06780923 0 0.09632218
21 4.315006 68.16353 0.1958835 1 0.07113135 0 0.10648345
22 3.975249 68.53082 0.2040278 1 0.08818818 0 0.08984173
23 3.921943 69.60221 0.1979640 1 0.07267085 0 0.12511286
24 3.983742 67.76555 0.2031760 1 0.06717891 0 0.10367067
25 3.895660 69.47939 0.1993874 1 0.06817941 0 0.08973712
26 3.958638 69.74054 0.1949952 1 0.07217236 0 0.09218806
27 3.985585 68.95600 0.1997755 1 0.06356015 0 0.10439573
28 3.920165 70.13811 0.1952001 1 0.07006469 0 0.06607858
29 4.135315 69.01056 0.1978472 1 0.07398465 0 0.07513122
30 3.827007 68.56629 0.2015357 1 0.05506670 0 0.09303089
31 3.893408 67.49121 0.1975671 1 0.04499286 0 0.08351562
32 4.025988 70.45182 0.1990793 1 0.07242308 0 0.09782781
33 4.019942 70.96364 0.2014000 1 0.08447572 0 0.08777964
34 3.884504 66.55993 0.1971079 1 0.07450460 0 0.08856721
35 3.996054 66.93821 0.1985125 1 0.06129866 0 0.08274537
36 4.081618 68.97580 0.2001548 1 0.07202699 0 0.09638920
37 3.993148 65.10763 0.1985139 1 0.06485045 0 0.07416839
38 3.908453 65.67802 0.1990315 1 0.06266032 0 0.09186744
39 3.935636 66.32350 0.2013148 1 0.07732190 0 0.08450629
40 3.803549 66.89265 0.1998202 1 0.06222067 0 0.09201371
41 3.794152 65.91168 0.2045937 1 0.08406271 0 0.09105954
42 3.966106 69.23118 0.1967659 1 0.06171561 0 0.09058125
43 3.889720 71.25744 0.1962289 1 0.07186124 0 0.10326919
44 4.154339 67.57126 0.1984505 1 0.06970990 0 0.09025829
45 3.930934 65.24055 0.1965228 1 0.07108583 0 0.08314434
46 3.846555 65.76844 0.1990567 1 0.07902672 0 0.07322697
47 3.758647 65.37698 0.1983753 1 0.08090015 0 0.07478860
48 4.209726 67.88323 0.1984188 1 0.07493575 0 0.08783786
49 4.077548 68.53444 0.1997585 1 0.06783113 0 0.07974986
50 3.901412 65.80751 0.2001533 1 0.06834075 0 0.08115616
sample_omega
Code
sample_omega("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Output
OMEGA1 OMEGA2
1 -0.485774017 -0.185195155
2 0.019057330 -0.201841117
3 -0.092220115 0.142531846
4 -0.053452246 -0.041899840
5 -0.005860621 0.097999946
6 -0.122117141 -0.491895640
7 0.047158306 -0.177104223
8 0.317216216 -0.176399096
9 -0.277511640 -0.039923984
10 -0.466124693 -0.047340588
11 -0.143078090 0.104464520
12 -0.317857393 0.037836851
13 -0.075626875 -0.567076755
14 -0.057431324 0.487740577
15 0.096573312 0.065719009
16 0.102980688 -0.088367559
17 0.381530989 -0.083297510
18 0.364015055 0.065651205
19 -0.085608934 0.176622932
20 -0.039014555 0.168189713
21 -0.910806987 0.008494193
22 0.017880132 -0.048991123
23 0.180236394 -0.217507094
24 -0.016373515 0.071400401
25 0.248784681 -0.198159213
26 0.081610619 -0.239302183
27 -0.003202234 -0.115894102
28 0.191494306 -0.301816487
29 -0.410335617 -0.124609535
30 0.421659420 -0.054440752
31 0.224514080 0.114643305
32 -0.090473167 -0.351267547
33 -0.066580283 -0.431786741
34 0.234546310 0.261169214
35 -0.063058274 0.201557182
36 -0.264244743 -0.119094904
37 -0.083333567 0.489565129
38 0.156144909 0.399898917
39 0.091808239 0.298321052
40 0.459855852 0.208893265
41 0.470330694 0.363237058
42 0.053542262 -0.159170186
43 0.292422796 -0.477895354
44 -0.483526786 0.101818212
45 0.088062709 0.468706416
46 0.325173266 0.385727743
47 0.558226034 0.447393843
48 -0.629438185 0.052686743
49 -0.260387425 -0.049650628
50 0.176918857 0.379532347
sample_sigma
Code
sample_sigma("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Output
SIGMA1
1 -0.61004507
2 -0.66487797
3 0.46950931
4 -0.13802084
5 0.32281829
6 -1.62033672
7 -0.58339300
8 -0.58107027
9 -0.13151224
10 -0.15594302
11 0.34411303
12 0.12463708
13 -1.86798828
14 1.60664967
15 0.21648276
16 -0.29108857
17 -0.27438750
18 0.21625940
19 0.58180760
20 0.55402802
21 0.02798043
22 -0.16137999
23 -0.71648273
24 0.23519764
25 -0.65274953
26 -0.78827719
27 -0.38176282
28 -0.99420344
29 -0.41047204
30 -0.17933143
31 0.37764262
32 -1.15709850
33 -1.42233404
34 0.86030864
35 0.66394267
36 -0.39230648
37 1.61265986
38 1.31729344
39 0.98268924
40 0.68810821
41 1.19652685
42 -0.52431711
43 -1.57421885
44 0.33539591
45 1.54394989
46 1.27061266
47 1.47374486
48 0.17355361
49 -0.16355245
50 1.25020461
kestrel99/pmxTools documentation built on Feb. 25, 2023, 1:26 p.m.
R Package Documentation
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read_nm
Code
read_nm("testData/runR001.xml")
Message <simpleMessage>
Reading testData/runR001.xml
Output
$start_datetime
$start_datetime[[1]]
[1] "2021-02-04T17:29:28.815"
$control_stream
$control_stream[[1]]
[1] "\n$PROB BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n$INPUT ID TIME DV=DROP LNDV=DV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n$DATA BOLUS_1CPT.csv IGNORE=@ IGNORE (SD.EQ.0)\n$SUBR ADVAN1,TRANS2\n$PK\n CL=THETA(1)*EXP(ETA(1))\n V=THETA(2)*EXP(ETA(2))\n S1=V\n$ERROR (ONLY OBSERVATIONS)\n IPRED=LOG(0.0025)\n W=THETA(3)\n IF (F.GT.0) IPRED=LOG(F)\n IRES=IPRED-DV\n IWRES=IRES/W\n Y=IPRED+W*ERR(1)\n$THETA (0,5,15) (0,90,200) (0,0.3,1)\n;# CL V RSV\n$OMEGA 0.15 0.15\n;# IIV_CL IIV_V\n$SIGMA 1 FIX\n;# RSV_FIX\n$EST NSIG=3 PRINT=5 MAX=9999 NOABORT POSTHOC METHOD=COND INTER NOOBT\n$COV\n$TABLE ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2\n IPRED IRES IWRES CWRESI\n ONEHEADER NOPRINT FILE=runR001.csv\n"
$nmtran
$nmtran[[1]]
[1] "\n\n WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1\n\n (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.\n"
$nonmem
$nonmem$license_information
$nonmem$license_information[[1]]
[1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n"
$nonmem$program_information
$nonmem$program_information[[1]]
[1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n"
$nonmem$problem
$nonmem$problem$problem_title
$nonmem$problem$problem_title[[1]]
[1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001"
$nonmem$problem$problem_information
$nonmem$problem$problem_information[[1]]
[1] "\n\n PROBLEM NO.: 1\n BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001\n0DATA CHECKOUT RUN: NO\n DATA SET LOCATED ON UNIT NO.: 2\n THIS UNIT TO BE REWOUND: NO\n NO. OF DATA RECS IN DATA SET: 2400\n NO. OF DATA ITEMS IN DATA SET: 13\n ID DATA ITEM IS DATA ITEM NO.: 1\n DEP VARIABLE IS DATA ITEM NO.: 3\n MDV DATA ITEM IS DATA ITEM NO.: 4\n0INDICES PASSED TO SUBROUTINE PRED:\n 6 2 5 0 0 0 13 0 0 0 0\n0LABELS FOR DATA ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI SSX IIX SD CMT\n0(NONBLANK) LABELS FOR PRED-DEFINED ITEMS:\n CL V IPRED IRES IWRES\n0FORMAT FOR DATA:\n (E4.0,2E7.0,E2.0,E7.0,E2.0,E7.0,E6.0,E5.0,2E3.0,2E2.0)\n\n TOT. NO. OF OBS RECS: 2276\n TOT. NO. OF INDIVIDUALS: 120\n0LENGTH OF THETA: 3\n0DEFAULT THETA BOUNDARY TEST OMITTED: NO\n0OMEGA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 2\n0DEFAULT OMEGA BOUNDARY TEST OMITTED: YES\n0SIGMA HAS SIMPLE DIAGONAL FORM WITH DIMENSION: 1\n0DEFAULT SIGMA BOUNDARY TEST OMITTED: NO\n0INITIAL ESTIMATE OF THETA:\n LOWER BOUND INITIAL EST UPPER BOUND\n 0.0000E+00 0.5000E+01 0.1500E+02\n 0.0000E+00 0.9000E+02 0.2000E+03\n 0.0000E+00 0.3000E+00 0.1000E+01\n0INITIAL ESTIMATE OF OMEGA:\n 0.1500E+00\n 0.0000E+00 0.1500E+00\n0INITIAL ESTIMATE OF SIGMA:\n 0.1000E+01\n0SIGMA CONSTRAINED TO BE THIS INITIAL ESTIMATE\n0COVARIANCE STEP OMITTED: NO\n EIGENVLS. PRINTED: NO\n SPECIAL COMPUTATION: NO\n COMPRESSED FORMAT: NO\n GRADIENT METHOD USED: NOSLOW\n SIGDIGITS ETAHAT (SIGLO): -1\n SIGDIGITS GRADIENTS (SIGL): -1\n EXCLUDE COV FOR FOCE (NOFCOV): NO\n Cholesky Transposition of R Matrix (CHOLROFF):0\n KNUTHSUMOFF: -1\n RESUME COV ANALYSIS (RESUME): NO\n SIR SAMPLE SIZE (SIRSAMPLE):\n NON-LINEARLY TRANSFORM THETAS DURING COV (THBND): 1\n PRECONDTIONING CYCLES (PRECOND): 0\n PRECONDTIONING TYPES (PRECONDS): TOS\n FORCED PRECONDTIONING CYCLES (PFCOND):0\n PRECONDTIONING TYPE (PRETYPE): 0\n FORCED POS. DEFINITE SETTING DURING PRECONDITIONING: (FPOSDEF):0\n SIMPLE POS. DEFINITE SETTING: (POSDEF):-1\n0TABLES STEP OMITTED: NO\n NO. OF TABLES: 1\n SEED NUMBER (SEED): 11456\n RANMETHOD: 3U\n MC SAMPLES (ESAMPLE): 300\n WRES SQUARE ROOT TYPE (WRESCHOL): EIGENVALUE\n0-- TABLE 1 --\n0RECORDS ONLY: ALL\n04 COLUMNS APPENDED: YES\n PRINTED: NO\n HEADERS: ONE\n FILE TO BE FORWARDED: NO\n FORMAT: S1PE11.4\n IDFORMAT:\n LFORMAT:\n RFORMAT:\n FIXED_EFFECT_ETAS:\n0USER-CHOSEN ITEMS:\n ID TIME LNDV MDV AMT EVID DOSE VI CLI CL V ETA1 ETA2 IPRED IRES IWRES CWRESI\n1DOUBLE PRECISION PREDPP VERSION 7.5.0\n\n ONE COMPARTMENT MODEL (ADVAN1)\n0MAXIMUM NO. OF BASIC PK PARAMETERS: 2\n0BASIC PK PARAMETERS (AFTER TRANSLATION):\n ELIMINATION RATE (K) IS BASIC PK PARAMETER NO.: 1\n\n TRANSLATOR WILL CONVERT PARAMETERS\n CLEARANCE (CL) AND VOLUME (V) TO K (TRANS2)\n0COMPARTMENT ATTRIBUTES\n COMPT. NO. FUNCTION INITIAL ON/OFF DOSE DEFAULT DEFAULT\n STATUS ALLOWED ALLOWED FOR DOSE FOR OBS.\n 1 CENTRAL ON NO YES YES YES\n 2 OUTPUT OFF YES NO NO NO\n1\n ADDITIONAL PK PARAMETERS - ASSIGNMENT OF ROWS IN GG\n COMPT. NO. INDICES\n SCALE BIOAVAIL. ZERO-ORDER ZERO-ORDER ABSORB\n FRACTION RATE DURATION LAG\n 1 3 * * * *\n 2 * - - - -\n - PARAMETER IS NOT ALLOWED FOR THIS MODEL\n * PARAMETER IS NOT SUPPLIED BY PK SUBROUTINE;\n WILL DEFAULT TO ONE IF APPLICABLE\n0DATA ITEM INDICES USED BY PRED ARE:\n EVENT ID DATA ITEM IS DATA ITEM NO.: 6\n TIME DATA ITEM IS DATA ITEM NO.: 2\n DOSE AMOUNT DATA ITEM IS DATA ITEM NO.: 5\n COMPT. NO. DATA ITEM IS DATA ITEM NO.: 13\n\n0PK SUBROUTINE CALLED WITH EVERY EVENT RECORD.\n PK SUBROUTINE NOT CALLED AT NONEVENT (ADDITIONAL OR LAGGED) DOSE TIMES.\n0DURING SIMULATION, ERROR SUBROUTINE CALLED WITH EVERY EVENT RECORD.\n OTHERWISE, ERROR SUBROUTINE CALLED ONLY WITH OBSERVATION EVENTS.\n"
$nonmem$problem$problem_options
list()
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[1] "no"
attr(,"data_unit")
[1] "2"
attr(,"data_rewind")
[1] "no"
attr(,"data_nrec")
[1] "2400"
attr(,"data_nitems")
[1] "13"
attr(,"data_id")
[1] "1"
attr(,"data_l2")
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attr(,"data_dv")
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attr(,"data_mdv")
[1] "4"
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attr(,"data_raw")
[1] "0"
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[1] "0"
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[1] "0"
attr(,"data_pred_indices")
[1] "6,2,5,0,0,0,13,0,0,0,0"
attr(,"data_format")
[1] "(e4.0,2e7.0,e2.0,e7.0,e2.0,e7.0,e6.0,e5.0,2e3.0,2e2.0)"
attr(,"data_nobs")
[1] "2276"
attr(,"data_nind")
[1] "120"
attr(,"data_mdv100")
[1] "0"
attr(,"nthetat")
[1] "3"
attr(,"theta_bound_test_omitted")
[1] "no"
attr(,"omega_diagdim")
[1] "2"
attr(,"omega_bound_test_omitted")
[1] "no"
attr(,"sigma_diagdim")
[1] "1"
attr(,"sigma_bound_test_omitted")
[1] "no"
attr(,"cov_omitted")
[1] "no"
attr(,"cov_matrix")
[1] "rsr"
attr(,"cov_eigen_print")
[1] "no"
attr(,"cov_special")
[1] "no"
attr(,"cov_compressed")
[1] "no"
attr(,"cov_slow_gradient")
[1] "noslow"
attr(,"cov_siglocov")
[1] "-1"
attr(,"cov_siglcov")
[1] "-1"
attr(,"cov_tol")
[1] "-1"
attr(,"cov_atol")
[1] "-1"
attr(,"cov_nofcov")
[1] "no"
attr(,"cov_cholroff")
[1] "0"
attr(,"cov_knuthsumoff")
[1] "-1"
attr(,"cov_resume")
[1] "no"
attr(,"cov_sirsample")
[1] "BLANK"
attr(,"cov_thbnd")
[1] "1"
attr(,"cov_precond")
[1] "0"
attr(,"cov_preconds")
[1] "tos"
attr(,"cov_pfcond")
[1] "0"
attr(,"cov_pretype")
[1] "0"
attr(,"cov_fposdef")
[1] "0"
attr(,"cov_posdef")
[1] "-1"
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[1] "no"
attr(,"tab_number")
[1] "1"
attr(,"tab_seed")
[1] "11456"
attr(,"tab_clockseed")
[1] "11456"
attr(,"tab_ranmethod")
[1] "3u"
attr(,"tab_esample")
[1] "300"
attr(,"tab_wres")
[1] "eigenvalue"
attr(,"tab_fixedetas_01")
[1] "BLANK"
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[1] "1"
attr(,"pred_evid")
[1] "6"
attr(,"pred_time")
[1] "2"
attr(,"pred_amt")
[1] "5"
attr(,"pred_cmt")
[1] "13"
$nonmem$problem$theta_lb
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_lb$val
$nonmem$problem$theta_lb$val[[1]]
[1] "0.000000000000000E+000"
attr(,"name")
[1] "3"
$nonmem$problem$theta_in
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "5.00000000000000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "90.0000000000000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_in$val
$nonmem$problem$theta_in$val[[1]]
[1] "0.300000000000000"
attr(,"name")
[1] "3"
$nonmem$problem$theta_ub
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "15.0000000000000"
attr(,"name")
[1] "1"
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "200.000000000000"
attr(,"name")
[1] "2"
$nonmem$problem$theta_ub$val
$nonmem$problem$theta_ub$val[[1]]
[1] "1.00000000000000"
attr(,"name")
[1] "3"
$nonmem$problem$estimation
$nonmem$problem$estimation$parallel_est
list()
attr(,"parafile")
[1] "C:\\MPI\\node6.pnm"
attr(,"protocol")
[1] "MPI"
attr(,"nodes")
[1] "6"
$nonmem$problem$estimation$table_series
$nonmem$problem$estimation$table_series[[1]]
[1] "1"
$nonmem$problem$estimation$estimation_method
$nonmem$problem$estimation$estimation_method[[1]]
[1] "focei"
$nonmem$problem$estimation$estimation_title
$nonmem$problem$estimation$estimation_title[[1]]
[1] "First Order Conditional Estimation with Interaction"
$nonmem$problem$estimation$estimation_information
$nonmem$problem$estimation$estimation_information[[1]]
[1] "\n ESTIMATION STEP OMITTED: NO\n ANALYSIS TYPE: POPULATION\n NUMBER OF SADDLE POINT RESET ITERATIONS: 0\n GRADIENT METHOD USED: NOSLOW\n CONDITIONAL ESTIMATES USED: YES\n CENTERED ETA: NO\n EPS-ETA INTERACTION: YES\n LAPLACIAN OBJ. FUNC.: NO\n NO. OF FUNCT. EVALS. ALLOWED: 9999\n NO. OF SIG. FIGURES REQUIRED: 3\n INTERMEDIATE PRINTOUT: YES\n ESTIMATE OUTPUT TO MSF: NO\n ABORT WITH PRED EXIT CODE 1: NO\n IND. OBJ. FUNC. VALUES SORTED: NO\n NUMERICAL DERIVATIVE\n FILE REQUEST (NUMDER): NONE\n MAP (ETAHAT) ESTIMATION METHOD (OPTMAP): 0\n ETA HESSIAN EVALUATION METHOD (ETADER): 0\n INITIAL ETA FOR MAP ESTIMATION (MCETA): 0\n SIGDIGITS FOR MAP ESTIMATION (SIGLO): 100\n GRADIENT SIGDIGITS OF\n FIXED EFFECTS PARAMETERS (SIGL): 100\n NOPRIOR SETTING (NOPRIOR): 0\n NOCOV SETTING (NOCOV): OFF\n DERCONT SETTING (DERCONT): OFF\n FINAL ETA RE-EVALUATION (FNLETA): 1\n EXCLUDE NON-INFLUENTIAL (NON-INFL.) ETAS\n IN SHRINKAGE (ETASTYPE): NO\n NON-INFL. ETA CORRECTION (NONINFETA): 0\n RAW OUTPUT FILE (FILE): runR001.ext\n EXCLUDE TITLE (NOTITLE): NO\n EXCLUDE COLUMN LABELS (NOLABEL): NO\n FORMAT FOR ADDITIONAL FILES (FORMAT): S1PE12.5\n PARAMETER ORDER FOR OUTPUTS (ORDER): TSOL\n KNUTHSUMOFF: 0\n INCLUDE LNTWOPI: NO\n INCLUDE CONSTANT TERM TO PRIOR (PRIORC): NO\n INCLUDE CONSTANT TERM TO OMEGA (ETA) (OLNTWOPI):NO\n ADDITIONAL CONVERGENCE TEST (CTYPE=4)?: NO\n EM OR BAYESIAN METHOD USED: NONE\n\n"
$nonmem$problem$estimation$estimation_options
list()
attr(,"estim_omitted")
[1] "no"
attr(,"analysis_type")
[1] "pop"
attr(,"saddle_reset")
[1] "0"
attr(,"saddle_hess")
[1] "0"
attr(,"slow_gradient")
[1] "noslow"
attr(,"cond_estim")
[1] "yes"
attr(,"centered_eta")
[1] "no"
attr(,"epseta_interaction")
[1] "yes"
attr(,"laplace")
[1] "no"
attr(,"predflag")
[1] "0"
attr(,"maxfn")
[1] "9999"
attr(,"nsig")
[1] "3"
attr(,"msfo")
[1] "no"
attr(,"abort")
[1] "no"
attr(,"objsort")
[1] "no"
attr(,"numder")
[1] "0"
attr(,"optmap")
[1] "0"
attr(,"etader")
[1] "0"
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[1] "0"
attr(,"siglo")
[1] "100"
attr(,"sigl")
[1] "100"
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[1] "0"
attr(,"nocov")
[1] "0"
attr(,"dercont")
[1] "0"
attr(,"atol")
[1] "0"
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[1] "1"
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[1] "0"
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[1] "0"
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[1] "runr001.ext"
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[1] "0"
attr(,"nolabel")
[1] "0"
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[1] "s1pe12.5"
attr(,"order")
[1] "tsol"
attr(,"knuthsumoff")
[1] "0"
attr(,"lntwopi")
[1] "0"
attr(,"priorc")
[1] "0"
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[1] "0"
attr(,"ctype")
[1] "0"
$nonmem$problem$estimation$monitor
$nonmem$problem$estimation$monitor$obj
$nonmem$problem$estimation$monitor$obj[[1]]
[1] "-3465.72885682371"
attr(,"iteration")
[1] "0"
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[1] "-4111.52222574939"
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[1] "5"
$nonmem$problem$estimation$monitor$obj
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[1] "-4125.77900367604"
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[1] "10"
$nonmem$problem$estimation$monitor$obj
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[1] "-4126.11481640313"
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[1] "14"
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$nonmem$problem$estimation$termination_status[[1]]
[1] "0"
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$nonmem$problem$estimation$termination_nfuncevals[[1]]
[1] "114"
$nonmem$problem$estimation$termination_sigdigits
$nonmem$problem$estimation$termination_sigdigits[[1]]
[1] "3.02298445301969"
$nonmem$problem$estimation$termination_information
$nonmem$problem$estimation$termination_information[[1]]
[1] "\n0MINIMIZATION SUCCESSFUL\n NO. OF FUNCTION EVALUATIONS USED: 114\n NO. OF SIG. DIGITS IN FINAL EST.: 3.0\n"
$nonmem$problem$estimation$termination_txtmsg
$nonmem$problem$estimation$termination_txtmsg$val
$nonmem$problem$estimation$termination_txtmsg$val[[1]]
[1] "37"
attr(,"name")
[1] "1"
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$nonmem$problem$estimation$etabar$row$col
$nonmem$problem$estimation$etabar$row$col[[1]]
[1] "4.765711648433239E-004"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabar$row$col
$nonmem$problem$estimation$etabar$row$col[[1]]
[1] "-1.516261194686842E-003"
attr(,"cname")
[1] "ETA2"
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[1] "SUBPOP1"
$nonmem$problem$estimation$etabarse
$nonmem$problem$estimation$etabarse$row
$nonmem$problem$estimation$etabarse$row$col
$nonmem$problem$estimation$etabarse$row$col[[1]]
[1] "2.398354777032987E-002"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etabarse$row$col
$nonmem$problem$estimation$etabarse$row$col[[1]]
[1] "2.719347789006172E-002"
attr(,"cname")
[1] "ETA2"
attr(,"rname")
[1] "SUBPOP1"
$nonmem$problem$estimation$etabarn
$nonmem$problem$estimation$etabarn$row
$nonmem$problem$estimation$etabarn$row$col
$nonmem$problem$estimation$etabarn$row$col[[1]]
[1] "120"
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[1] "ETA1"
$nonmem$problem$estimation$etabarn$row$col
$nonmem$problem$estimation$etabarn$row$col[[1]]
[1] "120"
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[1] "ETA2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$etabarpval$row
$nonmem$problem$estimation$etabarpval$row$col
$nonmem$problem$estimation$etabarpval$row$col[[1]]
[1] "0.984146393573823"
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[1] "ETA1"
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$nonmem$problem$estimation$etabarpval$row$col[[1]]
[1] "0.955534240611886"
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[1] "ETA2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$etashrinksd$row
$nonmem$problem$estimation$etashrinksd$row$col
$nonmem$problem$estimation$etashrinksd$row$col[[1]]
[1] "1.37215788183357"
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[1] "ETA1"
$nonmem$problem$estimation$etashrinksd$row$col
$nonmem$problem$estimation$etashrinksd$row$col[[1]]
[1] "1.46175485792922"
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[1] "ETA2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$etashrinkvr$row
$nonmem$problem$estimation$etashrinkvr$row$col
$nonmem$problem$estimation$etashrinkvr$row$col[[1]]
[1] "2.72548759114038"
attr(,"cname")
[1] "ETA1"
$nonmem$problem$estimation$etashrinkvr$row$col
$nonmem$problem$estimation$etashrinkvr$row$col[[1]]
[1] "2.90214244321166"
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[1] "ETA2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$ebvshrinksd$row
$nonmem$problem$estimation$ebvshrinksd$row$col
$nonmem$problem$estimation$ebvshrinksd$row$col[[1]]
[1] "1.58000136432566"
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[1] "EBV1"
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$nonmem$problem$estimation$ebvshrinksd$row$col[[1]]
[1] "1.76289476258970"
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[1] "EBV2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$ebvshrinkvr$row$col
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[1] "3.13503868553859"
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[1] "EBV1"
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[1] "3.49471154573972"
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[1] "EBV2"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$relativeinf$row$col
$nonmem$problem$estimation$relativeinf$row$col[[1]]
[1] "96.8120802973034"
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[1] "REL1"
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[1] "96.4526037915573"
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[1] "SUBPOP1"
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$nonmem$problem$estimation$epsshrinksd$row$col[[1]]
[1] "5.22027080681049"
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[1] "EPS1"
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[1] "SUBPOP1"
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[1] "10.1680293406566"
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[1] "THETA2"
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$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
attr(,"rname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "74.0494905940748"
attr(,"cname")
[1] "THETA1"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "-2.35947484707118"
attr(,"cname")
[1] "THETA2"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "2423.71409515852"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "159.617096229120"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "6825.27392229574"
attr(,"cname")
[1] "OMEGA(2,2)"
attr(,"rname")
[1] "OMEGA(2,2)"
$nonmem$problem$estimation$invcovariance$row
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA1"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA2"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "THETA3"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,1)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(1,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "OMEGA(2,2)"
$nonmem$problem$estimation$invcovariance$row$col
$nonmem$problem$estimation$invcovariance$row$col[[1]]
[1] "0.000000000000000E+000"
attr(,"cname")
[1] "SIGMA(1,1)"
attr(,"rname")
[1] "SIGMA(1,1)"
attr(,"number")
[1] "1"
attr(,"type")
[1] "0"
$nonmem$problem$post_process_times
$nonmem$problem$post_process_times$post_elapsed_time
$nonmem$problem$post_process_times$post_elapsed_time[[1]]
[1] "0.08"
$nonmem$problem$post_process_times$finaloutput_elapsed_time
$nonmem$problem$post_process_times$finaloutput_elapsed_time[[1]]
[1] "0.20"
attr(,"number")
[1] "1"
attr(,"subproblem")
[1] "0"
attr(,"superproblem1")
[1] "0"
attr(,"iteration1")
[1] "0"
attr(,"superproblem2")
[1] "0"
attr(,"iteration2")
[1] "0"
attr(,"version")
[1] "7.5.0"
$stop_datetime
$stop_datetime[[1]]
[1] "2021-02-04T17:29:31.574"
$total_cputime
$total_cputime[[1]]
[1] "7.266"
attr(,"schemaLocation")
[1] "http://namespaces.oreilly.com/xmlnut/address output.xsd"
attr(,"xmlns:xsi")
[1] "http://www.w3.org/2001/XMLSchema-instance"
attr(,"xmlns:nm")
[1] "http://namespaces.oreilly.com/xmlnut/address"
rnm
Code
rnm(index = "001", prefix = "runR", pathNM = "testData", ext = ".res", extmod = ".ctl")
Output
$Theta
Parameter Estimate SE CV CIL CIU P
1 THETA1 3.980130 0.09897590 2.486750 3.7861408 4.1741192 0
2 THETA2 68.219400 1.92949000 2.828360 64.4376691 72.0011309 0
3 THETA3 0.199472 0.00280475 1.406087 0.1939748 0.2049692 0
$Eta
Eta Estimate SE CV EtaCV Shrinkage
1 1 0.0715555 0.00912817 12.75677 26.74986 1.37216
2 2 0.0921585 0.01220090 13.23904 30.35762 1.46175
$Epsilon
Epsilon Estimate SE CV EpsCV Shrinkage
1 1 1 0 0 100 5.22027
$CorTheta
THETA1 THETA2 THETA3
1 1.00000000 0.109072 0.00138964
2 0.10907200 1.000000 0.12310700
3 0.00138964 0.123107 1.00000000
$CorOmega
Eta1 Eta2
Eta1 1.000 0.000
Eta2 0.000 1.000
$CorSigma
Eps1
Eps1 1.000
$OmegaMatrix
[,1] [,2]
[1,] 0.0715555 0.0000000
[2,] 0.0000000 0.0921585
$SigmaMatrix
[,1]
[1,] 1
$CovMatrixTheta
THETA1 THETA2 THETA3
1 9.79623e-03 0.020829800 3.85768e-07
2 2.08298e-02 3.722920000 6.66221e-04
3 3.85768e-07 0.000666221 7.86662e-06
$CovMatrix
THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1.
1 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0
2 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0
3 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0
4 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
5 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0
6 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
7 -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0
OMEGA.2.2.
1 -9.96425e-05
2 8.11546e-04
3 -2.60664e-06
4 0.00000e+00
5 -2.55098e-06
6 0.00000e+00
7 1.48861e-04
$OFV
[1] -4126.115
$ThetaString
Parameter Estimate SE CV Estimate (95% CI) P
1 THETA1 3.98 0.0990 2.5% 3.98 (3.79/4.17) < 0.00001
2 THETA2 68.2 1.93 2.8% 68.2 (64.4/72.0) < 0.00001
3 THETA3 0.199 0.00280 1.4% 0.199 (0.194/0.205) < 0.00001
$EtaString
Eta Estimate SE CV 100*sqrt(Omega) Shrinkage
1 1 0.0716 0.00913 12.8% 26.7% 1.4%
2 2 0.0922 0.0122 13.2% 30.4% 1.5%
$EpsString
Epsilon Estimate SE CV 100*sqrt(Omega) Shrinkage
1 1 1.00 (Fixed) 5.2%
$RunTime
[1] 17.35
$conditionN
NULL
read_nmcov
Code
read_nmcov("testData/runR001.cov")
Message <simpleMessage>
Reading testData/runR001.cov
Output
THETA1 THETA2 THETA3 SIGMA.1.1. OMEGA.1.1. OMEGA.2.1.
[1,] 9.79623e-03 0.020829800 3.85768e-07 0 1.81304e-05 0
[2,] 2.08298e-02 3.722920000 6.66221e-04 0 5.51038e-04 0
[3,] 3.85768e-07 0.000666221 7.86662e-06 0 1.67878e-06 0
[4,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
[5,] 1.81304e-05 0.000551038 1.67878e-06 0 8.33235e-05 0
[6,] 0.00000e+00 0.000000000 0.00000e+00 0 0.00000e+00 0
[7,] -9.96425e-05 0.000811546 -2.60664e-06 0 -2.55098e-06 0
OMEGA.2.2.
[1,] -9.96425e-05
[2,] 8.11546e-04
[3,] -2.60664e-06
[4,] 0.00000e+00
[5,] -2.55098e-06
[6,] 0.00000e+00
[7,] 1.48861e-04
read_nmext
Code
read_nmext("testData/runR001.ext")
Message <simpleMessage>
Reading testData/runR001.ext
Output
$Termination
NULL
$OFV
[1] -4126.115
$Thetas
[1] 3.980130 68.219400 0.199472
$Omega
$Omega[[1]]
[1] 0.0715555
$Omega[[2]]
[1] 0.0000000 0.0921585
$Sigma
$Sigma[[1]]
[1] 1
$seThetas
[1] 0.09897590 1.92949000 0.00280475
$seOmega
$seOmega[[1]]
[1] 0.00912817
$seOmega[[2]]
[1] NA 0.0122009
$seSigma
$seSigma[[1]]
[1] NA
$raw_lst
[1] "TABLE NO. 1: First Order Conditional Estimation with Interaction: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0"
[2] " ITERATION THETA1 THETA2 THETA3 SIGMA(1,1) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OBJ"
[3] " 0 5.00000E+00 9.00000E+01 3.00000E-01 1.00000E+00 1.50000E-01 0.00000E+00 1.50000E-01 -3465.72885682371"
[4] " 5 3.83588E+00 6.72641E+01 1.91725E-01 1.00000E+00 7.13261E-02 0.00000E+00 1.29166E-01 -4111.52222574939"
[5] " 10 3.94172E+00 6.73826E+01 1.99381E-01 1.00000E+00 7.15277E-02 0.00000E+00 9.19553E-02 -4125.77900367604"
[6] " 14 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313"
[7] " -1000000000 3.98013E+00 6.82194E+01 1.99472E-01 1.00000E+00 7.15555E-02 0.00000E+00 9.21585E-02 -4126.11481640313"
[8] " -1000000001 9.89759E-02 1.92949E+00 2.80475E-03 1.00000E+10 9.12817E-03 1.00000E+10 1.22009E-02 0.000000000000000E+000"
[9] " -1000000004 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 2.67499E-01 0.00000E+00 3.03576E-01 0.000000000000000E+000"
[10] " -1000000005 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+10 1.70621E-02 1.00000E+10 2.00952E-02 0.000000000000000E+000"
[11] " -1000000006 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 0.000000000000000E+000"
[12] " -1000000007 0.00000E+00 3.70000E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.000000000000000E+000"
[13] " -1000000008 3.88104E-02 -2.92122E-03 -4.33821E-01 0.00000E+00 -4.03024E-01 0.00000E+00 1.44149E-01 0.000000000000000E+000"
get_est_table
Code
get_est_table(nm1, thetaLabels = c("CL", "V", "KA"), omegaLabels = c("CL", "V"),
sigmaLabels = "Residual")
Output
Parameter Estimate RSE CI95 Shrinkage
1 CL 3.9800 2.49 3.79-4.17 -
2 V 68.2000 2.83 64.4-72.0 -
3 KA 0.1990 1.41 0.194-0.205 -
4 CL 0.0716 12.80 0.0537-0.0894 1.37
5 OM2,1 0.0000 NA <NA> -
6 V 0.0922 13.20 0.0682-0.116 1.46
7 Residual 1.0000 NA --- 5.22
get_probinfo
Code
get_probinfo(nm1)
Output
$prob_title
[1] "BOLUS_1CPT_VCL SINGLE DOSE FOCE INTER (120 Ind/2276 Obs) runR001"
$prog_info
[1] "\n1NONLINEAR MIXED EFFECTS MODEL PROGRAM (NONMEM) VERSION 7.5.0\n ORIGINALLY DEVELOPED BY STUART BEAL, LEWIS SHEINER, AND ALISON BOECKMANN\n CURRENT DEVELOPERS ARE ROBERT BAUER, ICON DEVELOPMENT SOLUTIONS,\n AND ALISON BOECKMANN. IMPLEMENTATION, EFFICIENCY, AND STANDARDIZATION\n PERFORMED BY NOUS INFOSYSTEMS.\n"
$lic_info
[1] "\nLicense Registered to: Occams\nExpiration Date: 14 JUN 2021\nCurrent Date: 4 FEB 2021\nDays until program expires : 130\n"
$prob_times
startTime stopTime elapsedTime
1 2021-02-04T17:29:31.574 2021-02-04T17:29:31.574 7.266
$prob_info
nRecords nOBS nIND nTHETA nOMEGA nSIGMA COV_STEP_OMITTED COV_MATRIX
1 2400 2276 120 3 NA 1 NO rsr
$est_info
final_objective_function estimation_method
1 -4126.11 focei
estimation_title estimation_elapsed_time
1 First Order Conditional Estimation with Interaction 0.83
termination_status condition_number
1 SUCCESSFUL NA
sample_uncertainty
Code
sample_uncert("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Reading testData/runR001.cov
Output
V1 V2 V3 V4 V5 V6 V7
1 4.165433 69.39547 0.2027448 1 0.06848604 0 0.09347681
2 3.980225 69.50231 0.1994999 1 0.07953186 0 0.08515790
3 4.008908 67.31330 0.2020217 1 0.04367090 0 0.08225640
4 4.001296 68.48560 0.2047266 1 0.07295125 0 0.09326988
5 3.978739 67.59651 0.1971732 1 0.08556432 0 0.08930405
6 4.042743 71.34557 0.1996294 1 0.05363680 0 0.10454367
7 3.969076 69.34515 0.1982914 1 0.07396419 0 0.09076399
8 3.869667 69.34122 0.1993334 1 0.06957219 0 0.08570421
9 4.083545 68.47258 0.2010389 1 0.07686870 0 0.08509724
10 4.153517 68.51932 0.2009742 1 0.06672599 0 0.11383226
11 4.028990 67.55515 0.2025752 1 0.06291851 0 0.08666884
12 4.095689 67.97826 0.2024989 1 0.07236835 0 0.09128803
13 4.028240 71.82350 0.2024290 1 0.07231574 0 0.09965155
14 3.983857 65.11927 0.1980753 1 0.07718695 0 0.09164850
15 3.942173 67.80190 0.2045056 1 0.06681079 0 0.08288682
16 3.945592 68.78126 0.1997871 1 0.06646189 0 0.10900627
17 3.842798 68.74961 0.2024411 1 0.06104701 0 0.09405646
18 3.843747 67.80288 0.2056648 1 0.07270782 0 0.07868634
19 4.005418 67.09663 0.2037665 1 0.07063172 0 0.10041499
20 3.988539 67.15033 0.2015780 1 0.06780923 0 0.09632218
21 4.315006 68.16353 0.1958835 1 0.07113135 0 0.10648345
22 3.975249 68.53082 0.2040278 1 0.08818818 0 0.08984173
23 3.921943 69.60221 0.1979640 1 0.07267085 0 0.12511286
24 3.983742 67.76555 0.2031760 1 0.06717891 0 0.10367067
25 3.895660 69.47939 0.1993874 1 0.06817941 0 0.08973712
26 3.958638 69.74054 0.1949952 1 0.07217236 0 0.09218806
27 3.985585 68.95600 0.1997755 1 0.06356015 0 0.10439573
28 3.920165 70.13811 0.1952001 1 0.07006469 0 0.06607858
29 4.135315 69.01056 0.1978472 1 0.07398465 0 0.07513122
30 3.827007 68.56629 0.2015357 1 0.05506670 0 0.09303089
31 3.893408 67.49121 0.1975671 1 0.04499286 0 0.08351562
32 4.025988 70.45182 0.1990793 1 0.07242308 0 0.09782781
33 4.019942 70.96364 0.2014000 1 0.08447572 0 0.08777964
34 3.884504 66.55993 0.1971079 1 0.07450460 0 0.08856721
35 3.996054 66.93821 0.1985125 1 0.06129866 0 0.08274537
36 4.081618 68.97580 0.2001548 1 0.07202699 0 0.09638920
37 3.993148 65.10763 0.1985139 1 0.06485045 0 0.07416839
38 3.908453 65.67802 0.1990315 1 0.06266032 0 0.09186744
39 3.935636 66.32350 0.2013148 1 0.07732190 0 0.08450629
40 3.803549 66.89265 0.1998202 1 0.06222067 0 0.09201371
41 3.794152 65.91168 0.2045937 1 0.08406271 0 0.09105954
42 3.966106 69.23118 0.1967659 1 0.06171561 0 0.09058125
43 3.889720 71.25744 0.1962289 1 0.07186124 0 0.10326919
44 4.154339 67.57126 0.1984505 1 0.06970990 0 0.09025829
45 3.930934 65.24055 0.1965228 1 0.07108583 0 0.08314434
46 3.846555 65.76844 0.1990567 1 0.07902672 0 0.07322697
47 3.758647 65.37698 0.1983753 1 0.08090015 0 0.07478860
48 4.209726 67.88323 0.1984188 1 0.07493575 0 0.08783786
49 4.077548 68.53444 0.1997585 1 0.06783113 0 0.07974986
50 3.901412 65.80751 0.2001533 1 0.06834075 0 0.08115616
sample_omega
Code
sample_omega("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Output
OMEGA1 OMEGA2
1 -0.485774017 -0.185195155
2 0.019057330 -0.201841117
3 -0.092220115 0.142531846
4 -0.053452246 -0.041899840
5 -0.005860621 0.097999946
6 -0.122117141 -0.491895640
7 0.047158306 -0.177104223
8 0.317216216 -0.176399096
9 -0.277511640 -0.039923984
10 -0.466124693 -0.047340588
11 -0.143078090 0.104464520
12 -0.317857393 0.037836851
13 -0.075626875 -0.567076755
14 -0.057431324 0.487740577
15 0.096573312 0.065719009
16 0.102980688 -0.088367559
17 0.381530989 -0.083297510
18 0.364015055 0.065651205
19 -0.085608934 0.176622932
20 -0.039014555 0.168189713
21 -0.910806987 0.008494193
22 0.017880132 -0.048991123
23 0.180236394 -0.217507094
24 -0.016373515 0.071400401
25 0.248784681 -0.198159213
26 0.081610619 -0.239302183
27 -0.003202234 -0.115894102
28 0.191494306 -0.301816487
29 -0.410335617 -0.124609535
30 0.421659420 -0.054440752
31 0.224514080 0.114643305
32 -0.090473167 -0.351267547
33 -0.066580283 -0.431786741
34 0.234546310 0.261169214
35 -0.063058274 0.201557182
36 -0.264244743 -0.119094904
37 -0.083333567 0.489565129
38 0.156144909 0.399898917
39 0.091808239 0.298321052
40 0.459855852 0.208893265
41 0.470330694 0.363237058
42 0.053542262 -0.159170186
43 0.292422796 -0.477895354
44 -0.483526786 0.101818212
45 0.088062709 0.468706416
46 0.325173266 0.385727743
47 0.558226034 0.447393843
48 -0.629438185 0.052686743
49 -0.260387425 -0.049650628
50 0.176918857 0.379532347
sample_sigma
Code
sample_sigma("testData/runR001.xml", n = 50, seed = 740727)
Message <simpleMessage>
Reading testData/runR001.xml
Output
SIGMA1
1 -0.61004507
2 -0.66487797
3 0.46950931
4 -0.13802084
5 0.32281829
6 -1.62033672
7 -0.58339300
8 -0.58107027
9 -0.13151224
10 -0.15594302
11 0.34411303
12 0.12463708
13 -1.86798828
14 1.60664967
15 0.21648276
16 -0.29108857
17 -0.27438750
18 0.21625940
19 0.58180760
20 0.55402802
21 0.02798043
22 -0.16137999
23 -0.71648273
24 0.23519764
25 -0.65274953
26 -0.78827719
27 -0.38176282
28 -0.99420344
29 -0.41047204
30 -0.17933143
31 0.37764262
32 -1.15709850
33 -1.42233404
34 0.86030864
35 0.66394267
36 -0.39230648
37 1.61265986
38 1.31729344
39 0.98268924
40 0.68810821
41 1.19652685
42 -0.52431711
43 -1.57421885
44 0.33539591
45 1.54394989
46 1.27061266
47 1.47374486
48 0.17355361
49 -0.16355245
50 1.25020461
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