Fit nonlinear mixed models with SAEM

@@ -87,7 +74,7 @@ Expectation Maximisation algorithm (SAEM).
Usage

saem(object, ...)
 
-# S3 method for mmkin
+# S3 method for class 'mmkin'
 saem(
   object,
   transformations = c("mkin", "saemix"),
@@ -110,7 +97,7 @@ Expectation Maximisation algorithm (SAEM).
   ...
 )
 
-# S3 method for saem.mmkin
+# S3 method for class 'saem.mmkin'
 print(x, digits = max(3, getOption("digits") - 3), ...)
 
 saemix_model(
@@ -136,16 +123,18 @@ Expectation Maximisation algorithm (SAEM).
 
     
     Arguments
-    object
+
+
+object
 An mmkin row object containing several fits of the same
 mkinmod model to different datasets
 
 
-...
+...
 Further parameters passed to saemix::saemixModel.
 
 
-transformations
+transformations
 Per default, all parameter transformations are done
 in mkin. If this argument is set to 'saemix', parameter transformations
 are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2)
@@ -153,39 +142,39 @@ SFO, FOMC, DFOP and HS without fixing parent_0, and SFO or DFOP wit
 one SFO metabolite.
 
 
-error_model
+error_model
 Possibility to override the error model used in the mmkin object
 
 
-degparms_start
+degparms_start
 Parameter values given as a named numeric vector will
 be used to override the starting values obtained from the 'mmkin' object.
 
 
-test_log_parms
+test_log_parms
 If TRUE, an attempt is made to use more robust starting
 values for population parameters fitted as log parameters in mkin (like
 rate constants) by only considering rate constants that pass the t-test
 when calculating mean degradation parameters using mean_degparms.
 
 
-conf.level
+conf.level
 Possibility to adjust the required confidence level
 for parameter that are tested if requested by 'test_log_parms'.
 
 
-solution_type
+solution_type
 Possibility to specify the solution type in case the
 automatic choice is not desired
 
 
-covariance.model
+covariance.model
 Will be passed to saemix::saemixModel(). Per
 default, uncorrelated random effects are specified for all degradation
 parameters.
 
 
-omega.init
+omega.init
 Will be passed to saemix::saemixModel(). If using
 mkin transformations and the default covariance model with optionally
 excluded random effects, the variances of the degradation parameters
@@ -195,66 +184,60 @@ mkin transformations or a custom covariance model, the default
 initialisation of saemix::saemixModel is used for omega.init.
 
 
-covariates
+covariates
 A data frame with covariate data for use in
 'covariate_models', with dataset names as row names.
 
 
-covariate_models
+covariate_models
 A list containing linear model formulas with one explanatory
 variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available
 in the 'covariates' data frame.
 
 
-no_random_effect
+no_random_effect
 Character vector of degradation parameters for
 which there should be no variability over the groups. Only used
 if the covariance model is not explicitly specified.
 
 
-error.init
+error.init
 Will be passed to saemix::saemixModel().
 
 
-nbiter.saemix
+nbiter.saemix
 Convenience option to increase the number of
 iterations
 
 
-control
+control
 Passed to saemix::saemix.
 
 
-verbose
+verbose
 Should we print information about created objects of
 type saemix::SaemixModel and saemix::SaemixData?
 
 
-quiet
+quiet
 Should we suppress the messages saemix prints at the beginning
 and the end of the optimisation process?
 
 
-x
+x
 An saem.mmkin object to print
 
 
-digits
+digits
 Number of digits to use for printing
 
 
     
     Value
-    
-
-An S3 object of class 'saem.mmkin', containing the fitted
+    
An S3 object of class 'saem.mmkin', containing the fitted
 saemix::SaemixObject as a list component named 'so'. The
 object also inherits from 'mixed.mmkin'.
-
-
 An saemix::SaemixModel object.
-
-
 An saemix::SaemixData object.
     
     
@@ -320,7 +303,7 @@ using mmkin.
 # functions from saemix
 library(saemix)
 #> Loading required package: npde
-#> Package saemix, version 3.2
+#> Package saemix, version 3.3, March 2024
 #>   please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
 #> 
 #> Attaching package: ‘saemix’
@@ -411,11 +394,11 @@ using mmkin.
 plot(f_saem_dfop_sfo)
 
 summary(f_saem_dfop_sfo, data = TRUE)
-#> saemix version used for fitting:      3.2 
-#> mkin version used for pre-fitting:  1.2.6 
-#> R version used for fitting:         4.3.2 
-#> Date of fit:     Thu Nov 16 04:17:34 2023 
-#> Date of summary: Thu Nov 16 04:17:34 2023 
+#> saemix version used for fitting:      3.3 
+#> mkin version used for pre-fitting:  1.2.9 
+#> R version used for fitting:         4.4.2 
+#> Date of fit:     Thu Feb 13 14:59:07 2025 
+#> Date of summary: Thu Feb 13 14:59:07 2025 
 #> 
 #> Equations:
 #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -430,7 +413,7 @@ using mmkin.
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 3.385 s
+#> Fitted in 3.96 s
 #> Using 300, 100 iterations and 10 chains
 #> 
 #> Variance model: Constant variance 
@@ -726,23 +709,23 @@ using mmkin.
 # }