Replies: 1 comment 6 replies
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Hi @WXX155367 First check:
If so, then this is an error in the If you have other files not only is the import more stable but the retained digits in the NONMEM input are more accurate than the numbers in the listing file. If you can supply the |
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6 replies
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Hi @WXX155367 The version of |
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Thanks for your answering. I have updated my package in the latest version (0.1.10) by "devtools::install_github("nlmixr2/nonmem2rx")", but it still can't show the thetaMat and other information in the output. Did I use the correct package? |
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The version seems to match; it works for me: library(nonmem2rx)
m <- readRDS("~/src/nonmem2rx/tests/testthat/test-lst-import-1.rds")
print(head(m))
#> [1] "di 12-03-2019"
#> [2] "14:40"
#> [3] ";; 1. Based on: 0102"
#> [4] ";; 2. Description: AMIKACIN PK RUN0102 FINAL MODEL"
#> [5] ";----------------------------------"
#> [6] "$PROBLEM AMIKACIN PK"
f <- withr::with_tempdir({
writeLines(m, "run0112.lst")
nonmem2rx("run0112.lst")
})
#> ℹ getting information from 'run0112.lst'
#> ℹ reading in lst file
#> ℹ getting information from lst file
#> ℹ done
#> ℹ done
#> ℹ splitting control stream by records
#> ℹ done
#> ℹ Processing record $INPUT
#> ℹ Processing record $gTHETA
#> ℹ Processing record $OMEGA
#> ℹ Processing record $SIGMA
#> ℹ Processing record $PROBLEM
#> ℹ Processing record $DATA
#> ℹ Processing record $SUBROUTINES
#> ℹ Processing record $PK
#> ℹ Processing record $ERROR
#> ℹ Processing record $ESTIMATION
#> ℹ Ignore record $ESTIMATION
#> ℹ Processing record $COVARIANCE
#> ℹ Ignore record $COVARIANCE
#> ℹ Processing record $TABLE
#> ℹ change initial estimate of `theta1` to `0.189`
#> ℹ change initial estimate of `theta2` to `1.81`
#> ℹ change initial estimate of `theta3` to `16`
#> ℹ change initial estimate of `theta4` to `0.769`
#> ℹ change initial estimate of `theta5` to `12.6`
#> ℹ change initial estimate of `theta6` to `0.856`
#> ℹ change initial estimate of `theta7` to `0.858`
#> ℹ change initial estimate of `theta8` to `0.421`
#> ℹ change initial estimate of `theta9` to `0`
#> ℹ change initial estimate of `theta10` to `1`
#> ℹ change initial estimate of `theta11` to `4.51e-05`
#> ℹ change initial estimate of `theta12` to `0.903`
#> ℹ change initial estimate of `theta13` to `0`
#> ℹ change initial estimate of `theta14` to `1`
#> ℹ change initial estimate of `theta15` to `1`
#> ℹ change initial estimate of `theta16` to `0`
#> ℹ change initial estimate of `theta17` to `0`
#> ℹ change initial estimate of `theta18` to `0`
#> ℹ change initial estimate of `theta19` to `1`
#> ℹ change initial estimate of `theta20` to `1`
#> ℹ change initial estimate of `theta21` to `0`
#> ℹ change initial estimate of `theta22` to `0`
#> ℹ change initial estimate of `theta23` to `0`
#> ℹ change initial estimate of `theta24` to `-0.529`
#> ℹ change initial estimate of `theta25` to `0`
#> ℹ change initial estimate of `theta26` to `0`
#> ℹ change initial estimate of `theta27` to `0`
#> ℹ change initial estimate of `theta28` to `0`
#> ℹ change initial estimate of `theta29` to `1`
#> ℹ change initial estimate of `theta30` to `1`
#> ℹ change initial estimate of `theta31` to `-2.13`
#> ℹ some correlations may have been dropped for the variables: `eta1`, `eta2`
#> ℹ the piping should specify the needed covariances directly
#> ℹ change initial estimate of `eta1` to `0.138`
#> ℹ add covariance between `eta2` and `eta1` with initial estimate `0.0388`
#> ℹ change initial estimate of `eta2` to `0.0322`
#> ℹ done
#> ℹ changing most variables to lower case
#> ℹ done
#> ℹ replace theta names
#> ℹ done
#> ℹ replace eta names
#> ℹ done (no labels)
# The thetaMat should not be NULL
print(f$thetaMat)
#> exponential t.CL t.V1 t.Q t.V2 t.CKEP2
#> exponential 4.86e-04 -5.34e-04 -2.58e-03 8.45e-04 2.63e-02 3.90e-04
#> t.CL -5.34e-04 1.39e-02 2.25e-02 -5.27e-03 -4.18e-01 -5.45e-03
#> t.V1 -2.58e-03 2.25e-02 2.69e-01 -8.09e-03 -4.79e-01 -6.07e-03
#> t.Q 8.45e-04 -5.27e-03 -8.09e-03 7.51e-03 3.20e-01 6.11e-03
#> t.V2 2.63e-02 -4.18e-01 -4.79e-01 3.20e-01 2.08e+01 3.35e-01
#> t.CKEP2 3.90e-04 -5.45e-03 -6.07e-03 6.11e-03 3.35e-01 1.08e-02
#> theta7 -6.06e-04 9.54e-04 1.51e-02 1.67e-03 1.04e-01 8.36e-03
#> theta8 -1.45e-04 -9.84e-04 -1.66e-02 -2.75e-04 5.48e-02 2.95e-04
#> theta9 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta10 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta11 -2.74e-08 3.91e-09 1.27e-06 -1.34e-07 2.96e-07 -2.04e-07
#> theta12 1.05e-04 -7.14e-04 -1.37e-02 -2.41e-04 9.85e-03 -1.94e-04
#> t.APAC 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.INDI 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta15 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta16 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta17 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta18 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.COPD 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.IMMU 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.HEMA 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta22 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.TEMP 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.TOPR 2.28e-04 9.48e-04 7.50e-03 -1.30e-03 -3.79e-02 -8.16e-04
#> theta25 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta26 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta27 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta28 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta29 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.HEDI 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.SODI 9.58e-04 -4.52e-03 -1.08e-02 5.56e-03 7.29e-03 2.50e-03
#> eta1 3.96e-04 -3.13e-03 -6.14e-03 1.48e-03 8.81e-02 -1.11e-04
#> omega1.2 4.90e-05 -3.77e-04 -6.80e-04 5.44e-05 6.08e-03 -3.61e-04
#> eta2 -2.15e-04 4.61e-04 4.43e-03 -6.61e-04 -2.37e-02 -4.94e-04
#> eps1 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
#> theta7 theta8 theta9 theta10 theta11 theta12 t.APAC
#> exponential -6.06e-04 -1.45e-04 0 0 -2.74e-08 1.05e-04 0
#> t.CL 9.54e-04 -9.84e-04 0 0 3.91e-09 -7.14e-04 0
#> t.V1 1.51e-02 -1.66e-02 0 0 1.27e-06 -1.37e-02 0
#> t.Q 1.67e-03 -2.75e-04 0 0 -1.34e-07 -2.41e-04 0
#> t.V2 1.04e-01 5.48e-02 0 0 2.96e-07 9.85e-03 0
#> t.CKEP2 8.36e-03 2.95e-04 0 0 -2.04e-07 -1.94e-04 0
#> theta7 3.09e-02 1.13e-02 0 0 1.43e-08 -1.18e-03 0
#> theta8 1.13e-02 2.84e-02 0 0 4.48e-07 2.53e-03 0
#> theta9 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta10 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta11 1.43e-08 4.48e-07 0 0 1.28e-10 -5.84e-08 0
#> theta12 -1.18e-03 2.53e-03 0 0 -5.84e-08 5.11e-03 0
#> t.APAC 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.INDI 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta15 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta16 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta17 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta18 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.COPD 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.IMMU 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.HEMA 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta22 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.TEMP 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.TOPR -1.51e-03 -7.53e-03 0 0 -1.97e-07 -1.32e-03 0
#> theta25 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta26 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta27 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta28 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> theta29 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.HEDI 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.SODI -8.71e-03 6.49e-03 0 0 -2.07e-06 4.92e-03 0
#> eta1 -2.19e-03 2.06e-04 0 0 2.60e-08 2.87e-04 0
#> omega1.2 -7.07e-04 3.30e-04 0 0 2.64e-08 7.10e-05 0
#> eta2 3.57e-04 2.08e-04 0 0 5.10e-08 -9.36e-05 0
#> eps1 0.00e+00 0.00e+00 0 0 0.00e+00 0.00e+00 0
#> t.INDI theta15 theta16 theta17 theta18 t.COPD t.IMMU t.HEMA theta22
#> exponential 0 0 0 0 0 0 0 0 0
#> t.CL 0 0 0 0 0 0 0 0 0
#> t.V1 0 0 0 0 0 0 0 0 0
#> t.Q 0 0 0 0 0 0 0 0 0
#> t.V2 0 0 0 0 0 0 0 0 0
#> t.CKEP2 0 0 0 0 0 0 0 0 0
#> theta7 0 0 0 0 0 0 0 0 0
#> theta8 0 0 0 0 0 0 0 0 0
#> theta9 0 0 0 0 0 0 0 0 0
#> theta10 0 0 0 0 0 0 0 0 0
#> theta11 0 0 0 0 0 0 0 0 0
#> theta12 0 0 0 0 0 0 0 0 0
#> t.APAC 0 0 0 0 0 0 0 0 0
#> t.INDI 0 0 0 0 0 0 0 0 0
#> theta15 0 0 0 0 0 0 0 0 0
#> theta16 0 0 0 0 0 0 0 0 0
#> theta17 0 0 0 0 0 0 0 0 0
#> theta18 0 0 0 0 0 0 0 0 0
#> t.COPD 0 0 0 0 0 0 0 0 0
#> t.IMMU 0 0 0 0 0 0 0 0 0
#> t.HEMA 0 0 0 0 0 0 0 0 0
#> theta22 0 0 0 0 0 0 0 0 0
#> t.TEMP 0 0 0 0 0 0 0 0 0
#> t.TOPR 0 0 0 0 0 0 0 0 0
#> theta25 0 0 0 0 0 0 0 0 0
#> theta26 0 0 0 0 0 0 0 0 0
#> theta27 0 0 0 0 0 0 0 0 0
#> theta28 0 0 0 0 0 0 0 0 0
#> theta29 0 0 0 0 0 0 0 0 0
#> t.HEDI 0 0 0 0 0 0 0 0 0
#> t.SODI 0 0 0 0 0 0 0 0 0
#> eta1 0 0 0 0 0 0 0 0 0
#> omega1.2 0 0 0 0 0 0 0 0 0
#> eta2 0 0 0 0 0 0 0 0 0
#> eps1 0 0 0 0 0 0 0 0 0
#> t.TEMP t.TOPR theta25 theta26 theta27 theta28 theta29 t.HEDI
#> exponential 0 2.28e-04 0 0 0 0 0 0
#> t.CL 0 9.48e-04 0 0 0 0 0 0
#> t.V1 0 7.50e-03 0 0 0 0 0 0
#> t.Q 0 -1.30e-03 0 0 0 0 0 0
#> t.V2 0 -3.79e-02 0 0 0 0 0 0
#> t.CKEP2 0 -8.16e-04 0 0 0 0 0 0
#> theta7 0 -1.51e-03 0 0 0 0 0 0
#> theta8 0 -7.53e-03 0 0 0 0 0 0
#> theta9 0 0.00e+00 0 0 0 0 0 0
#> theta10 0 0.00e+00 0 0 0 0 0 0
#> theta11 0 -1.97e-07 0 0 0 0 0 0
#> theta12 0 -1.32e-03 0 0 0 0 0 0
#> t.APAC 0 0.00e+00 0 0 0 0 0 0
#> t.INDI 0 0.00e+00 0 0 0 0 0 0
#> theta15 0 0.00e+00 0 0 0 0 0 0
#> theta16 0 0.00e+00 0 0 0 0 0 0
#> theta17 0 0.00e+00 0 0 0 0 0 0
#> theta18 0 0.00e+00 0 0 0 0 0 0
#> t.COPD 0 0.00e+00 0 0 0 0 0 0
#> t.IMMU 0 0.00e+00 0 0 0 0 0 0
#> t.HEMA 0 0.00e+00 0 0 0 0 0 0
#> theta22 0 0.00e+00 0 0 0 0 0 0
#> t.TEMP 0 0.00e+00 0 0 0 0 0 0
#> t.TOPR 0 2.40e-02 0 0 0 0 0 0
#> theta25 0 0.00e+00 0 0 0 0 0 0
#> theta26 0 0.00e+00 0 0 0 0 0 0
#> theta27 0 0.00e+00 0 0 0 0 0 0
#> theta28 0 0.00e+00 0 0 0 0 0 0
#> theta29 0 0.00e+00 0 0 0 0 0 0
#> t.HEDI 0 0.00e+00 0 0 0 0 0 0
#> t.SODI 0 -3.63e-03 0 0 0 0 0 0
#> eta1 0 -3.23e-05 0 0 0 0 0 0
#> omega1.2 0 -3.57e-04 0 0 0 0 0 0
#> eta2 0 1.92e-04 0 0 0 0 0 0
#> eps1 0 0.00e+00 0 0 0 0 0 0
#> t.SODI eta1 omega1.2 eta2 eps1
#> exponential 9.58e-04 3.96e-04 4.90e-05 -2.15e-04 0
#> t.CL -4.52e-03 -3.13e-03 -3.77e-04 4.61e-04 0
#> t.V1 -1.08e-02 -6.14e-03 -6.80e-04 4.43e-03 0
#> t.Q 5.56e-03 1.48e-03 5.44e-05 -6.61e-04 0
#> t.V2 7.29e-03 8.81e-02 6.08e-03 -2.37e-02 0
#> t.CKEP2 2.50e-03 -1.11e-04 -3.61e-04 -4.94e-04 0
#> theta7 -8.71e-03 -2.19e-03 -7.07e-04 3.57e-04 0
#> theta8 6.49e-03 2.06e-04 3.30e-04 2.08e-04 0
#> theta9 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta10 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta11 -2.07e-06 2.60e-08 2.64e-08 5.10e-08 0
#> theta12 4.92e-03 2.87e-04 7.10e-05 -9.36e-05 0
#> t.APAC 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.INDI 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta15 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta16 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta17 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta18 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.COPD 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.IMMU 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.HEMA 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta22 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.TEMP 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.TOPR -3.63e-03 -3.23e-05 -3.57e-04 1.92e-04 0
#> theta25 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta26 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta27 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta28 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> theta29 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.HEDI 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
#> t.SODI 3.56e-01 2.03e-03 -8.04e-05 -1.16e-03 0
#> eta1 2.03e-03 1.84e-03 3.94e-04 -1.79e-04 0
#> omega1.2 -8.04e-05 3.94e-04 1.78e-04 3.79e-05 0
#> eta2 -1.16e-03 -1.79e-04 3.79e-05 2.60e-04 0
#> eps1 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0
# You can see it in the full model object
print(f)
#> ── rxode2-based solved PK 2-compartment model ──────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> exponential t.CL t.V1 t.Q t.V2 t.CKEP2
#> 1.89e-01 1.81e+00 1.60e+01 7.69e-01 1.26e+01 8.56e-01
#> theta7 theta8 theta9 theta10 theta11 theta12
#> 8.58e-01 4.21e-01 0.00e+00 1.00e+00 4.51e-05 9.03e-01
#> t.APAC t.INDI theta15 theta16 theta17 theta18
#> 0.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00 0.00e+00
#> t.COPD t.IMMU t.HEMA theta22 t.TEMP t.TOPR
#> 1.00e+00 1.00e+00 0.00e+00 0.00e+00 0.00e+00 -5.29e-01
#> theta25 theta26 theta27 theta28 theta29 t.HEDI
#> 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.00e+00 1.00e+00
#> t.SODI
#> -2.13e+00
#>
#> Omega ($omega):
#> eta1 eta2
#> eta1 0.1380 0.0388
#> eta2 0.0388 0.0322
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name Rate Off Internal #
#> 1 1 central TRUE FALSE 1
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- c(";; 1. Based on: 0102", ";; 2. Description: AMIKACIN PK RUN0102 FINAL MODEL",
#> ";----------------------------------", "AMIKACIN PK",
#> ";----------------------------------", ";MISSING DATA UNTIL 10% ARE IMPUTED WITH MEDIAN")
#> dfObs <- 280
#> dfSub <- 97
#> sigma <- lotri({
#> eps1 ~ 1
#> })
#> thetaMat <- lotri({
#> exponential ~ c(exponential = 0.000486)
#> t.CL ~ c(exponential = -0.000534, t.CL = 0.0139)
#> t.V1 ~ c(exponential = -0.00258, t.CL = 0.0225, t.V1 = 0.269)
#> t.Q ~ c(exponential = 0.000845, t.CL = -0.00527, t.V1 = -0.00809,
#> t.Q = 0.00751)
#> t.V2 ~ c(exponential = 0.0263, t.CL = -0.418, t.V1 = -0.479,
#> t.Q = 0.32, t.V2 = 20.8)
#> t.CKEP2 ~ c(exponential = 0.00039, t.CL = -0.00545, t.V1 = -0.00607,
#> t.Q = 0.00611, t.V2 = 0.335, t.CKEP2 = 0.0108)
#> theta7 ~ c(exponential = -0.000606, t.CL = 0.000954,
#> t.V1 = 0.0151, t.Q = 0.00167, t.V2 = 0.104, t.CKEP2 = 0.00836,
#> theta7 = 0.0309)
#> theta8 ~ c(exponential = -0.000145, t.CL = -0.000984,
#> t.V1 = -0.0166, t.Q = -0.000275, t.V2 = 0.0548, t.CKEP2 = 0.000295,
#> theta7 = 0.0113, theta8 = 0.0284)
#> theta9 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0)
#> theta10 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0)
#> theta11 ~ c(exponential = -2.74e-08, t.CL = 3.91e-09,
#> t.V1 = 1.27e-06, t.Q = -1.34e-07, t.V2 = 2.96e-07,
#> t.CKEP2 = -2.04e-07, theta7 = 1.43e-08, theta8 = 4.48e-07,
#> theta9 = 0, theta10 = 0, theta11 = 1.28e-10)
#> theta12 ~ c(exponential = 0.000105, t.CL = -0.000714,
#> t.V1 = -0.0137, t.Q = -0.000241, t.V2 = 0.00985,
#> t.CKEP2 = -0.000194, theta7 = -0.00118, theta8 = 0.00253,
#> theta9 = 0, theta10 = 0, theta11 = -5.84e-08, theta12 = 0.00511)
#> t.APAC ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0)
#> t.INDI ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0)
#> theta15 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0)
#> theta16 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0)
#> theta17 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0)
#> theta18 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0)
#> t.COPD ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0)
#> t.IMMU ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0)
#> t.HEMA ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0)
#> theta22 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0)
#> t.TEMP ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0)
#> t.TOPR ~ c(exponential = 0.000228, t.CL = 0.000948, t.V1 = 0.0075,
#> t.Q = -0.0013, t.V2 = -0.0379, t.CKEP2 = -0.000816,
#> theta7 = -0.00151, theta8 = -0.00753, theta9 = 0,
#> theta10 = 0, theta11 = -1.97e-07, theta12 = -0.00132,
#> t.APAC = 0, t.INDI = 0, theta15 = 0, theta16 = 0,
#> theta17 = 0, theta18 = 0, t.COPD = 0, t.IMMU = 0,
#> t.HEMA = 0, theta22 = 0, t.TEMP = 0, t.TOPR = 0.024)
#> theta25 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0)
#> theta26 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0,
#> theta26 = 0)
#> theta27 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0,
#> theta26 = 0, theta27 = 0)
#> theta28 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0,
#> theta26 = 0, theta27 = 0, theta28 = 0)
#> theta29 ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0,
#> theta26 = 0, theta27 = 0, theta28 = 0, theta29 = 0)
#> t.HEDI ~ c(exponential = 0, t.CL = 0, t.V1 = 0, t.Q = 0,
#> t.V2 = 0, t.CKEP2 = 0, theta7 = 0, theta8 = 0, theta9 = 0,
#> theta10 = 0, theta11 = 0, theta12 = 0, t.APAC = 0,
#> t.INDI = 0, theta15 = 0, theta16 = 0, theta17 = 0,
#> theta18 = 0, t.COPD = 0, t.IMMU = 0, t.HEMA = 0,
#> theta22 = 0, t.TEMP = 0, t.TOPR = 0, theta25 = 0,
#> theta26 = 0, theta27 = 0, theta28 = 0, theta29 = 0,
#> t.HEDI = 0)
#> t.SODI ~ c(exponential = 0.000958, t.CL = -0.00452, t.V1 = -0.0108,
#> t.Q = 0.00556, t.V2 = 0.00729, t.CKEP2 = 0.0025,
#> theta7 = -0.00871, theta8 = 0.00649, theta9 = 0,
#> theta10 = 0, theta11 = -2.07e-06, theta12 = 0.00492,
#> t.APAC = 0, t.INDI = 0, theta15 = 0, theta16 = 0,
#> theta17 = 0, theta18 = 0, t.COPD = 0, t.IMMU = 0,
#> t.HEMA = 0, theta22 = 0, t.TEMP = 0, t.TOPR = -0.00363,
#> theta25 = 0, theta26 = 0, theta27 = 0, theta28 = 0,
#> theta29 = 0, t.HEDI = 0, t.SODI = 0.356)
#> eta1 ~ c(exponential = 0.000396, t.CL = -0.00313, t.V1 = -0.00614,
#> t.Q = 0.00148, t.V2 = 0.0881, t.CKEP2 = -0.000111,
#> theta7 = -0.00219, theta8 = 0.000206, theta9 = 0,
#> theta10 = 0, theta11 = 2.6e-08, theta12 = 0.000287,
#> t.APAC = 0, t.INDI = 0, theta15 = 0, theta16 = 0,
#> theta17 = 0, theta18 = 0, t.COPD = 0, t.IMMU = 0,
#> t.HEMA = 0, theta22 = 0, t.TEMP = 0, t.TOPR = -3.23e-05,
#> theta25 = 0, theta26 = 0, theta27 = 0, theta28 = 0,
#> theta29 = 0, t.HEDI = 0, t.SODI = 0.00203, eta1 = 0.00184)
#> omega1.2 ~ c(exponential = 4.9e-05, t.CL = -0.000377,
#> t.V1 = -0.00068, t.Q = 5.44e-05, t.V2 = 0.00608,
#> t.CKEP2 = -0.000361, theta7 = -0.000707, theta8 = 0.00033,
#> theta9 = 0, theta10 = 0, theta11 = 2.64e-08, theta12 = 7.1e-05,
#> t.APAC = 0, t.INDI = 0, theta15 = 0, theta16 = 0,
#> theta17 = 0, theta18 = 0, t.COPD = 0, t.IMMU = 0,
#> t.HEMA = 0, theta22 = 0, t.TEMP = 0, t.TOPR = -0.000357,
#> theta25 = 0, theta26 = 0, theta27 = 0, theta28 = 0,
#> theta29 = 0, t.HEDI = 0, t.SODI = -8.04e-05, eta1 = 0.000394,
#> omega1.2 = 0.000178)
#> eta2 ~ c(exponential = -0.000215, t.CL = 0.000461, t.V1 = 0.00443,
#> t.Q = -0.000661, t.V2 = -0.0237, t.CKEP2 = -0.000494,
#> theta7 = 0.000357, theta8 = 0.000208, theta9 = 0,
#> theta10 = 0, theta11 = 5.1e-08, theta12 = -9.36e-05,
#> t.APAC = 0, t.INDI = 0, theta15 = 0, theta16 = 0,
#> theta17 = 0, theta18 = 0, t.COPD = 0, t.IMMU = 0,
#> t.HEMA = 0, theta22 = 0, t.TEMP = 0, t.TOPR = 0.000192,
#> theta25 = 0, theta26 = 0, theta27 = 0, theta28 = 0,
#> theta29 = 0, t.HEDI = 0, t.SODI = -0.00116, eta1 = -0.000179,
#> omega1.2 = 3.79e-05, eta2 = 0.00026)
#> eps1 ~ 0
#> })
#> validation <- "could not read in input data; validation skipped"
#> ini({
#> exponential <- c(0, 0.189)
#> label("1 exponential error")
#> t.CL <- c(0, 1.81)
#> label("2 CL")
#> t.V1 <- c(0, 16)
#> label("3 V1")
#> t.Q <- c(0, 0.769)
#> label("4 Q")
#> t.V2 <- c(0, 12.6)
#> label("5 V2")
#> t.CKEP2 <- c(-2, 0.856)
#> label("6 CKEP2 on CL")
#> theta7 <- c(-2, 0.858)
#> label("7 BMI on CL")
#> theta8 <- c(-2, 0.421)
#> label("8 BMI on V1")
#> theta9 <- fix(0)
#> label("9 BALA2 on CL")
#> theta10 <- fix(1)
#> label("10 MISS BALA2")
#> theta11 <- c(-1e-04, 4.51e-05)
#> label("11 BALA2 on V1")
#> theta12 <- c(0, 0.903)
#> label("12 MISS BALA2")
#> t.APAC <- fix(0)
#> label("13 APAC on CL")
#> t.INDI <- fix(1)
#> label("14 INDI on CL")
#> theta15 <- fix(1)
#> label("15 GROU on CL")
#> theta16 <- fix(0)
#> label("16 MAP on CL")
#> theta17 <- fix(0)
#> label("17 SOFA on CL")
#> theta18 <- fix(0)
#> label("18 SOFA2 on CL")
#> t.COPD <- fix(1)
#> label("19 COPD on V1")
#> t.IMMU <- fix(1)
#> label("20 IMMU on V1")
#> t.HEMA <- fix(0)
#> label("21 HEMA on V1")
#> theta22 <- fix(0)
#> label("22 SOFA2 on V1")
#> t.TEMP <- fix(0)
#> label("23 TEMP on V1")
#> t.TOPR <- c(-2, -0.529)
#> label("24 TOPR on V1")
#> theta25 <- fix(0)
#> label("25 MAP on V2")
#> theta26 <- fix(0)
#> label("26 SOFA on V2")
#> theta27 <- fix(0)
#> label("27 SOFA2 on V2")
#> theta28 <- fix(0)
#> label("28 BMI on V2")
#> theta29 <- fix(1)
#> label("29 GROU on V2")
#> t.HEDI <- fix(1)
#> label("30 HEDI on CL")
#> t.SODI <- c(-4, -2.13)
#> label("31 SODI on V1")
#> eta1 ~ 0.138
#> eta2 ~ c(0.0388, 0.0322)
#> })
#> model({
#> flg1 <- 1
#> if (BALA2 == 99999)
#> flg1 <- 0
#> flg2 <- 0
#> if (INDI == 1)
#> flg2 <- 1
#> flg3 <- 0
#> if (GROU == 1)
#> flg3 <- 1
#> flg4 <- 0
#> if (COPD == 1)
#> flg4 <- 1
#> flg5 <- 0
#> if (IMMU == 1)
#> flg5 <- 1
#> flg6 <- 0
#> if (HEDI == 1)
#> flg6 <- 1
#> rxm.vcl1 <- t.CL * (CKEP2/52)^t.CKEP2 * (BMI/24)^theta7 *
#> ((1 + theta9 * (BALA2 - 2796.5) * flg1) * theta10^(1 -
#> flg1))
#> rxm.vcl2 <- rxm.vcl1 * (APAC/25)^t.APAC * t.INDI^flg2 *
#> theta15^flg3 * (MAP/67)^theta16 * (SOFA/7)^theta17
#> rxm.vcl3 <- rxm.vcl2 * (SOFA2/8)^theta18 * t.HEDI^flg6
#> cl <- rxm.vcl3 * exp(eta1)
#> rxm.vvv1 <- t.V1 * (BMI/24)^theta8 * ((1 + theta11 *
#> (BALA2 - 2796.5) * flg1) * theta12^(1 - flg1))
#> rxm.vvv2 <- rxm.vvv1 * t.COPD^flg4 * t.IMMU^flg5 * (HEMA/0.3605)^t.HEMA *
#> (SOFA2/8)^theta22
#> rxm.vvv3 <- rxm.vvv2 * (TEMP/37.8)^t.TEMP * (TOPR/66)^t.TOPR *
#> (SODI/138.25)^t.SODI
#> v1 <- rxm.vvv3 * exp(eta2)
#> tvq <- t.Q
#> q <- tvq
#> tvv2 <- t.V2 * (MAP/67)^theta25 * (SOFA/7)^theta26 *
#> (SOFA2/8)^theta27 * (BMI/24)^theta28 * theta29^flg3
#> v2 <- tvv2
#> scale1 <- v1
#> rxlincmt1 <- linCmt()
#> scale1 <- scale1/v1
#> f <- rxlincmt1/scale1
#> ipred <- f
#> if (W == 0)
#> W <- 1
#> ipred ~ prop(exponential)
#> })
#> }
#> ── nonmem2rx translation notes ($notes): ──
#> • there are duplicate eta names, not renaming duplicate parameters
#> • there are duplicate theta names, not renaming duplicate parameters
#> ── nonmem2rx extra properties: ──
#> other properties include: $etaData
#> captured NONMEM table outputs: $predData, $ipredData
#> NONMEM/rxode2 comparison data: $iwresCompare, $predCompare, $ipredCompare
#> NONMEM/rxode2 composite comparison: $predAtol, $predRtol, $ipredAtol, $ipredRtol, $iwresAtol, $iwresRtolCreated on 2026-02-18 with reprex v2.1.1 |
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Thanks for your reply. Can I ask what is ".rds" in m <- readRDS("~/src/nonmem2rx/tests/testthat/test-lst-import-1.rds")? |
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Sure, the You can see it at the top of the script. m <- readRDS("~/src/nonmem2rx/tests/testthat/test-lst-import-1.rds")
print(head(m))
#> [1] "di 12-03-2019"
#> [2] "14:40"
#> [3] ";; 1. Based on: 0102"
#> [4] ";; 2. Description: AMIKACIN PK RUN0102 FINAL MODEL"
#> [5] ";----------------------------------"
#> [6] "$PROBLEM AMIKACIN PK" |
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Hi developers. Sorry for bother you. I am a beginner of “nonmem2rx” to do the simulation. I am writing this post to ask for help about “nonmem2rx”.
When I tried to use "nonmem2rx" and "rxode2" to consider parameter uncertainty in simulation, there is no thetaMat in my output. I only use ".lst" and "mod" to do the simulation in a certain folder with nonmem2rx, because I don't have another NONMEM files in this folder. So is this why I can't see thetaMat, dfObs, and dfSub in the output? Or I miss something in ".lst" file? Thanks in advance. Look forward to the reply.
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