From aa74f5a30853fb0a15c99c283e072f08ee819149 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Nov 2020 17:24:53 +0100 Subject: saemix.mmkin and nlme.mmkin inherit from mixed.mmkin With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method. --- docs/dev/reference/saem.html | 39 ++++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 19 deletions(-) (limited to 'docs/dev/reference/saem.html') diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 26f4c3e3..f1b4c421 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -206,7 +206,8 @@ by the saemix function?

Value

An S3 object of class 'saem.mmkin', containing the fitted -saemix::SaemixObject as a list component named 'so'.

+saemix::SaemixObject as a list component named 'so'. The +object also inherits from 'mixed.mmkin'.

An saemix::SaemixModel object.

An saemix::SaemixData object.

Details

@@ -218,7 +219,7 @@ psi0 of saemix:: using mmkin.

See also

-

summary.saem.mmkin

+

summary.saem.mmkin plot.mixed.mmkin

Examples

# \dontrun{
@@ -229,27 +230,27 @@ using mmkin.

   state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
 f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:11 2020"
+#> [1] "Mon Nov  9 17:18:28 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:13 2020"

+#> [1] "Mon Nov  9 17:18:30 2020"

 f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
 f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:14 2020"
+#> [1] "Mon Nov  9 17:18:31 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:16 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+#> [1] "Mon Nov  9 17:18:33 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:16 2020"
+#> [1] "Mon Nov  9 17:18:33 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:18 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+#> [1] "Mon Nov  9 17:18:35 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:19 2020"
+#> [1] "Mon Nov  9 17:18:36 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:22 2020"

+#> [1] "Mon Nov  9 17:18:39 2020"

 # The returned saem.mmkin object contains an SaemixObject, therefore we can use
 # functions from saemix
 library(saemix)
@@ -295,10 +296,10 @@ using mmkin.

 f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
 f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:24 2020"
+#> [1] "Mon Nov  9 17:18:41 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:29 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
+#> [1] "Mon Nov  9 17:18:46 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
 
#> Likelihoods computed by importance sampling 
#>        AIC      BIC
 #> 1 467.7644 465.0305
 #> 2 469.4862 466.3617

@@ -318,20 +319,20 @@ using mmkin.

 # solutions written for mkin this took around four minutes
 f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:31 2020"
+#> [1] "Mon Nov  9 17:18:48 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:36 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
+#> [1] "Mon Nov  9 17:18:53 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
 
#> Running main SAEM algorithm
-#> [1] "Mon Nov  9 09:03:37 2020"
+#> [1] "Mon Nov  9 17:18:54 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Mon Nov  9 09:03:46 2020"
summary(f_saem_dfop_sfo, data = FALSE)
+#> [1] "Mon Nov  9 17:19:03 2020"
summary(f_saem_dfop_sfo, data = FALSE)
 
#> saemix version used for fitting:      3.1.9000 
 #> mkin version used for pre-fitting:  0.9.50.4 
 #> R version used for fitting:         4.0.3 
-#> Date of fit:     Mon Nov  9 09:03:47 2020 
-#> Date of summary: Mon Nov  9 09:03:47 2020 
+#> Date of fit:     Mon Nov  9 17:19:04 2020 
+#> Date of summary: Mon Nov  9 17:19:04 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -346,7 +347,7 @@ using mmkin.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 9.758 s using 300, 100 iterations
+#> Fitted in 9.941 s using 300, 100 iterations
 #> 
 #> Variance model: Constant variance 
 #> 
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