Executes an NLME simple estimation

Usage

fitmodel(
  model,
  hostPlatform = NULL,
  params,
  simpleTables,
  runInBackground = FALSE,
  filesToReturn = "*",
  ...
)

Arguments

model: PK/PD model class object.
hostPlatform: Host definition for model execution. See hostParams. If missing, PhoenixMPIDir64 is given and MPI is installed, MPI local host with 4 threads is used. If MPI is not found, local host without parallelization is used.
params: Engine parameters. See engineParams. If missing, default parameters generated by engineParams(model) are used.
simpleTables: Optional list of simple tables. See tableParams. By default a table named 'posthoc.csv' is returned with structural parameters values for all source data rows.
runInBackground: Set to TRUE to run in background and return prompt.
filesToReturn: Used to specify which files to be outputted to the model directory and loaded as returned value. By default, all the applicable files listed in the Value section will be outputted to the model directory and loaded as returned value. Only those files listed in the Value section can be specified. Simple regex patterns are supported for the specification.
...: Additional arguments for hostParams or arguments available inside engineParams functions. If engineParams arguments are supplied through both params argument and additional argument (i.e., ellipsis), then the arguments in params will be ignored and only the additional arguments will be used with warning. If hostParams arguments are supplied through both the hostPlatform argument and the ellipses, values supplied to hostPlatform will be overridden by additional arguments supplied via the ellipses e.g., ....

Value

if runInBackground is FALSE, a list with main resulted dataframes is returned:

Overall
ConvergenceData
residuals
Secondary
StrCovariate - if continuous covariates presented
StrCovariateCat - if categorical covariates presented
theta
posthoc table
posthocStacked table
Requested tables

nlme7engine.log textual output is returned and loaded with the main information related to fitting. dmp.txt structure with the results of fitting (including LL by subject information) is returned and loaded. These 2 files are returned and loaded irrespective of filesToReturn argument value.

For individual models, additional dataframe with partial derivatives is returned:

ParDer

For population models and the method specified is NOT Naive-Pooled, additional dataframes are returned:

omega
Eta
EtaStacked
EtaEta
EtaCov
EtaCovariate - if continuous covariates presented
EtaCovariateCat - if categorical covariates presented
bluptable.dat

If standard error computation was requested and it was successful, additional dataframes are returned:

thetaCorrelation
thetaCovariance
Covariance
omega_stderr

If nonparametric method was requested (numIterNonParametric > 0) and the method specified in engineParams is NOT Naive-Pooled, additional dataframes are returned:

nonParSupportResult
nonParStackedResult
nonParEtaResult
nonParOverallResult

if runInBackground is TRUE, only current status of job is returned.

`filesToReturn` with `Certara.Xpose.NLME`

If filesToReturn is used and "ConvergenceData.csv" and "residuals.csv" are not in the patterns, these files won't be returned and loaded. These files are essential for Certara.Xpose.NLME::xposeNlmeModel and Certara.Xpose.NLME::xposeNlme functions. This makes impossible to use the resulted object in Certara.Xpose.NLME functions.

Non-loaded but returned files

The non-loaded but returned files in the model working directory are:

err1.txt - concatenated for all runs detailed logs for all steps of optimization,
out.txt - general pivoted information about results,
doses.csv - information about doses given for all subjects,
iniest.csv - information about initial estimates

Examples

# \donttest{

 # Define the host
 host <- hostParams(parallelMethod = "None",
                    hostName = "local",
                    numCores = 1)
 # Define the model
 model <- pkmodel(numComp = 2,
                  absorption = "FirstOrder",
                  ID = "Subject",
                  Time = "Act_Time",
                  CObs = "Conc",
                  Aa = "Amount",
                  data = pkData,
                  modelName = "PkModel")

 Table01 <- tableParams(name = "SimTableObs.csv",
                        timesList = "0,1,2,4,4.9,55.1,56,57,59,60",
                        variablesList = "C, CObs",
                        timeAfterDose = FALSE,
                        forSimulation = FALSE)

 # Update fixed effects
 model <- fixedEffect(model,
                     effect = c("tvV", "tvCl", "tvV2", "tvCl2"),
                     value = c(16, 41, 7, 14))

 # Define the engine parameters
 params <- engineParams(model)

 # Fit model
 res <- fitmodel(model = model,
                 hostPlatform = host,
                 params = params,
                 simpleTables = Table01)
#> 
#> NLME Job
#> 
#> Compiling 1 of 1 NLME models
#> TDL5 version: 24.9.1.1
#> 
#> Status: OK
#> License expires: 2026-04-08
#> Refresh until: 2025-05-07 20:38:27
#> Current Date: 2025-04-07
#> The model compiled
#> 
#> 
#>  Iteration         -2LL tvKa tvV tvCl tvV2 tvCl2 nSubj nObs
#>          1 6.799441e+20    1  16   41    7    14    16  112
#>          2 6.799441e+20    1  16   41    7    14    16  112
#> 
#> Trying to generate job results...
#> 
#> Generating Overall.csv
#> Generating EtaEta.csv
#> Generating Eta.csv
#> Generating EtaStacked.csv
#> Generating bluptable.dat
#> Generating ConvergenceData.csv
#> Generating initest.csv
#> Generating doses.csv
#> Generating omega.csv
#> Generating theta.csv
#> Generating thetaCorrelation.csv
#> Generating thetaCovariance.csv
#> Generating Covariance.csv
#> Generating Residuals.csv
#> Generating posthoc.csv
#> Generating SimTableObs.csv
#> 
#> Finished summarizing results. Transferring data and loading the results...
#> Done generating job results.
# }