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Don't show as much of the mlx list
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@mattfidler
mattfidler committed May 1, 2024
1 parent 84c595a commit 9e65833
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4 changes: 3 additions & 1 deletion README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,9 @@ mlx <- mlxtran(mlxtranFile)
mlx
# this can be converted to a list
head(as.list(mlx))
mlx <- as.list(mlx)
mlx$DATAFILE$FILEINFO$FILEINFO
```

## Translating models from the Monolix model library
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323 changes: 24 additions & 299 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,15 @@ rx <- monolix2rx(mlxtranFile)
#> ℹ imported monolix and translated to rxode2 compatible data ($monolixData)
#> ℹ imported monolix ETAS (_SAEM) imported to rxode2 compatible data ($etaData)
#> ℹ imported monolix pred/ipred data to compare ($predIpredData)
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> In file included from /usr/share/R/include/R.h:71,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2parse.h:33,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2/include/rxode2.h:9,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2_model_shared.h:3,
#> from rx_3eaac9dbb7c8e82fd82febcc413da174_.c:117:
#> /usr/share/R/include/R_ext/Complex.h:80:6: warning: ISO C99 doesn’t support unnamed structs/unions [-Wpedantic]
#> 80 | };
#> | ^
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
Expand Down Expand Up @@ -218,310 +227,17 @@ mlx
#> ; $MODEL$LONGITUDINAL$EQUATION

# this can be converted to a list
head(as.list(mlx))
#> $mlxtran
#> [1] ""
#>
#> $DATAFILE
#> $DATAFILE$DATAFILE
#> list()
#>
#> $DATAFILE$FILEINFO
#> $DATAFILE$FILEINFO$FILEINFO
#> $DATAFILE$FILEINFO$FILEINFO$file
mlx <- as.list(mlx)

mlx$DATAFILE$FILEINFO$FILEINFO
#> $file
#> [1] "data/theophylline_data.txt"
#>
#> $DATAFILE$FILEINFO$FILEINFO$header
#> $header
#> [1] "ID" "AMT" "TIME" "CONC" "WEIGHT" "SEX"
#>
#> $DATAFILE$FILEINFO$FILEINFO$delimiter
#> $delimiter
#> [1] "tab"
#>
#>
#>
#> $DATAFILE$CONTENT
#> $DATAFILE$CONTENT$CONTENT
#> $DATAFILE$CONTENT$CONTENT$use1
#> identifier time eventidentifier
#> "ID" "TIME" NA
#> amount interdoseinterval censored
#> "AMT" NA NA
#> limit observationtype administration
#> NA NA NA
#> steadystate observation occasion
#> NA "CONC" NA
#> rate additionaldose missingdependentvariable
#> NA NA NA
#>
#> $DATAFILE$CONTENT$CONTENT$cont
#> [1] "WEIGHT"
#>
#> $DATAFILE$CONTENT$CONTENT$cat
#> $DATAFILE$CONTENT$CONTENT$cat$SEX
#> $DATAFILE$CONTENT$CONTENT$cat$SEX$cat
#> character(0)
#>
#> $DATAFILE$CONTENT$CONTENT$cat$SEX$quote
#> logical(0)
#>
#>
#>
#> $DATAFILE$CONTENT$CONTENT$reg
#> character(0)
#>
#> $DATAFILE$CONTENT$CONTENT$nbdoses
#> [1] 7
#>
#> $DATAFILE$CONTENT$CONTENT$yname
#> character(0)
#>
#> $DATAFILE$CONTENT$CONTENT$ynameQuote
#> logical(0)
#>
#> $DATAFILE$CONTENT$CONTENT$ytype
#> character(0)
#>
#> $DATAFILE$CONTENT$CONTENT$ytypeQuote
#> logical(0)
#>
#> $DATAFILE$CONTENT$CONTENT$name
#> [1] "CONC"
#>
#> $DATAFILE$CONTENT$CONTENT$type
#> [1] "continuous"
#>
#>
#>
#>
#> $MODEL
#> $MODEL$MODEL
#> list()
#>
#> $MODEL$INDIVIDUAL
#> $MODEL$INDIVIDUAL$INDIVIDUAL
#> $MODEL$INDIVIDUAL$INDIVIDUAL$input
#> [1] "ka_pop" "omega_ka" "V_pop" "omega_V" "Cl_pop" "omega_Cl"
#>
#> $MODEL$INDIVIDUAL$INDIVIDUAL$cat
#> NULL
#>
#> $MODEL$INDIVIDUAL$INDIVIDUAL$reg
#> character(0)
#>
#> $MODEL$INDIVIDUAL$INDIVIDUAL$file
#> character(0)
#>
#>
#> $MODEL$INDIVIDUAL$DEFINITION
#> $MODEL$INDIVIDUAL$DEFINITION$vars
#> $MODEL$INDIVIDUAL$DEFINITION$vars$ka
#> $MODEL$INDIVIDUAL$DEFINITION$vars$ka$distribution
#> [1] "lognormal"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$ka$typical
#> [1] "ka_pop"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$ka$sd
#> [1] "omega_ka"
#>
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$V
#> $MODEL$INDIVIDUAL$DEFINITION$vars$V$distribution
#> [1] "lognormal"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$V$typical
#> [1] "V_pop"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$V$sd
#> [1] "omega_V"
#>
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$Cl
#> $MODEL$INDIVIDUAL$DEFINITION$vars$Cl$distribution
#> [1] "lognormal"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$Cl$typical
#> [1] "Cl_pop"
#>
#> $MODEL$INDIVIDUAL$DEFINITION$vars$Cl$sd
#> [1] "omega_Cl"
#>
#>
#>
#> $MODEL$INDIVIDUAL$DEFINITION$fixed
#> numeric(0)
#>
#> $MODEL$INDIVIDUAL$DEFINITION$cor
#> [1] level v1 v2 est
#> <0 rows> (or 0-length row.names)
#>
#> $MODEL$INDIVIDUAL$DEFINITION$est
#> type name fixed level
#> 1 typical ka_pop FALSE pop
#> 2 sd omega_ka FALSE id
#> 3 typical V_pop FALSE pop
#> 4 sd omega_V FALSE id
#> 5 typical Cl_pop FALSE pop
#> 6 sd omega_Cl FALSE id
#>
#> $MODEL$INDIVIDUAL$DEFINITION$rx
#> [1] "ka <- exp(ka_pop + omega_ka)" "V <- exp(V_pop + omega_V)"
#> [3] "Cl <- exp(Cl_pop + omega_Cl)"
#>
#>
#>
#> $MODEL$LONGITUDINAL
#> $MODEL$LONGITUDINAL$LONGITUDINAL
#> $MODEL$LONGITUDINAL$LONGITUDINAL$input
#> [1] "a" "b" "ka" "V" "Cl"
#>
#> $MODEL$LONGITUDINAL$LONGITUDINAL$cat
#> NULL
#>
#> $MODEL$LONGITUDINAL$LONGITUDINAL$reg
#> character(0)
#>
#> $MODEL$LONGITUDINAL$LONGITUDINAL$file
#> [1] "oral1_1cpt_kaVCl.txt"
#>
#>
#> $MODEL$LONGITUDINAL$DEFINITION
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$var
#> [1] "CONC"
#>
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$dist
#> [1] "normal"
#>
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$pred
#> [1] "Cc"
#>
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$err
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$err$errName
#> [1] "combined1"
#>
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$err$typical
#> [1] "a" "b"
#>
#>
#> $MODEL$LONGITUDINAL$DEFINITION$endpoint[[1]]$autocor
#> character(0)
#>
#>
#>
#> $MODEL$LONGITUDINAL$DEFINITION$fixed
#> numeric(0)
#>
#>
#> $MODEL$LONGITUDINAL$EQUATION
#> $MODEL$LONGITUDINAL$EQUATION[[1]]
#> [1] "; PK model definition\nCc = pkmodel(ka, V, Cl)"
#>
#>
#> $MODEL$LONGITUDINAL$OUTPUT
#> $MODEL$LONGITUDINAL$OUTPUT$output
#> [1] "Cc"
#>
#> $MODEL$LONGITUDINAL$OUTPUT$table
#> character(0)
#>
#>
#>
#>
#> $FIT
#> $FIT$FIT
#> data dataQuote model modelQuote
#> 1 CONC FALSE CONC FALSE
#>
#>
#> $PARAMETER
#> $PARAMETER$PARAMETER
#> name value method
#> 1 Cl_pop 0.1 MLE
#> 2 V_pop 0.5 MLE
#> 3 a 1.0 MLE
#> 4 b 0.3 MLE
#> 5 ka_pop 1.0 MLE
#> 6 omega_Cl 1.0 MLE
#> 7 omega_V 1.0 MLE
#> 8 omega_ka 1.0 MLE
#>
#>
#> $MONOLIX
#> $MONOLIX$MONOLIX
#> list()
#>
#> $MONOLIX$TASKS
#> $MONOLIX$TASKS$TASKS
#> $MONOLIX$TASKS$TASKS$populationParameters
#> list()
#>
#> $MONOLIX$TASKS$TASKS$individualParameters
#> $MONOLIX$TASKS$TASKS$individualParameters$method
#> $MONOLIX$TASKS$TASKS$individualParameters$method[[1]]
#> [1] "conditionalMean"
#>
#> $MONOLIX$TASKS$TASKS$individualParameters$method[[2]]
#> [1] "conditionalMode"
#>
#>
#>
#> $MONOLIX$TASKS$TASKS$fim
#> $MONOLIX$TASKS$TASKS$fim$method
#> [1] "Linearization"
#>
#>
#> $MONOLIX$TASKS$TASKS$logLikelihood
#> $MONOLIX$TASKS$TASKS$logLikelihood$method
#> [1] "Linearization"
#>
#>
#> $MONOLIX$TASKS$TASKS$plotResult
#> $MONOLIX$TASKS$TASKS$plotResult$method
#> $MONOLIX$TASKS$TASKS$plotResult$method[[1]]
#> [1] "indfits"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[2]]
#> [1] "obspred"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[3]]
#> [1] "vpc"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[4]]
#> [1] "residualsscatter"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[5]]
#> [1] "residualsdistribution"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[6]]
#> [1] "parameterdistribution"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[7]]
#> [1] "covariatemodeldiagnosis"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[8]]
#> [1] "randomeffects"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[9]]
#> [1] "covariancemodeldiagnosis"
#>
#> $MONOLIX$TASKS$TASKS$plotResult$method[[10]]
#> [1] "saemresults"
#>
#>
#>
#>
#>
#> $MONOLIX$SETTINGS
#> $MONOLIX$SETTINGS$SETTINGS
#> $MONOLIX$SETTINGS$SETTINGS[[1]]
#> [1] ""
#>
#>
#> $MONOLIX$SETTINGS$GLOBAL
#> $MONOLIX$SETTINGS$GLOBAL$exportpath
#> [1] "tp"
```

## Translating models from the Monolix model library
Expand Down Expand Up @@ -554,6 +270,15 @@ to `rxode2`:

``` r
monolix2rx("lib:bolus_1cpt_TlagVCl.txt")
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> In file included from /usr/share/R/include/R.h:71,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2parse.h:33,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2/include/rxode2.h:9,
#> from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2_model_shared.h:3,
#> from rx_006529352ac819b40b322c71010f90c5_.c:117:
#> /usr/share/R/include/R_ext/Complex.h:80:6: warning: ISO C99 doesn’t support unnamed structs/unions [-Wpedantic]
#> 80 | };
#> | ^
#> ℹ cannot find individual parameter estimates
#> ── rxode2-based free-form 1-cmt ODE model ──────────────────────────────────────
#>
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