From 1c647363430e0db732c23feebe4293dc48978608 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 8 Nov 2020 02:59:07 +0100 Subject: Update static docs --- docs/dev/reference/endpoints.html | 14 +- docs/dev/reference/index.html | 6 + docs/dev/reference/saem.html | 44 +-- docs/dev/reference/summary.saem.mmkin.html | 436 +++++++++++++++++++++++++++++ 4 files changed, 477 insertions(+), 23 deletions(-) create mode 100644 docs/dev/reference/summary.saem.mmkin.html (limited to 'docs/dev/reference') diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index 5a20a34c..db702c2e 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -165,8 +165,11 @@ advantage that the SFORB model can also be used for metabolites.

fit -

An object of class mkinfit or -nlme.mmkin

+

An object of class mkinfit, nlme.mmkin or +saem.mmkin. Or another object that has list components +mkinmod containing an mkinmod degradation model, and two numeric vectors, +bparms.optim and bparms.fixed, that contain parameter values +for that model.

@@ -176,9 +179,14 @@ advantage that the SFORB model can also be used for metabolites.

and, if applicable, a vector of formation fractions named ff and, if the SFORB model was in use, a vector of eigenvalues of these SFORB models, equivalent to DFOP rate constants

+

Details

+ +

Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from +HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models

Note

-

The function is used internally by summary.mkinfit.

+

The function is used internally by summary.mkinfit, +summary.nlme.mmkin and summary.saem.mmkin.

Author

Johannes Ranke

diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index f1884d2b..825c4d27 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -342,6 +342,12 @@ of an mmkin object

Fit nonlinear mixed models with SAEM

+ +

summary(<saem.mmkin>) print(<summary.saem.mmkin>)

+ +

Summary method for class "saem.mmkin"

+ +

nlme_function() mean_degparms() nlme_data()

diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index f883eb11..06fcfaa7 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -41,8 +41,8 @@ +effects models created from mmkin row objects using the Stochastic Approximation +Expectation Maximisation algorithm (SAEM)." /> @@ -147,8 +147,8 @@ to the expectation maximisation algorithm (SAEM)." />

This function uses saemix::saemix() as a backend for fitting nonlinear mixed -effects models created from mmkin row objects using the stochastic approximation -to the expectation maximisation algorithm (SAEM).

+effects models created from mmkin row objects using the Stochastic Approximation +Expectation Maximisation algorithm (SAEM).

saem(object, control, ...)
@@ -205,7 +205,8 @@ by the saemix function?

 
     
Value

 
-    
An saemix::SaemixObject.

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

 
An saemix::SaemixModel object.

 
An saemix::SaemixData object.

     
Details

@@ -215,6 +216,9 @@ obtained by fitting the same model to a list of datasets using saemix::saemixModel() are the mean values of the parameters found
 using mmkin.

+    
See also

+
+    
summary.saem.mmkin

 
     
Examples

     
# \dontrun{
@@ -225,27 +229,27 @@ 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] "Sat Nov  7 13:14:50 2020"
+#> [1] "Sun Nov  8 02:44:42 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:52 2020"

+#> [1] "Sun Nov  8 02:44:43 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] "Sat Nov  7 13:14:53 2020"
+#> [1] "Sun Nov  8 02:44:45 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:55 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+#> [1] "Sun Nov  8 02:44:46 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:55 2020"
+#> [1] "Sun Nov  8 02:44:47 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:57 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+#> [1] "Sun Nov  8 02:44:49 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:57 2020"
+#> [1] "Sun Nov  8 02:44:49 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:15:00 2020"

+#> [1] "Sun Nov  8 02:44:52 2020"

 # The returned saem.mmkin object contains an SaemixObject, we can use
 # functions from saemix
 library(saemix)
@@ -258,10 +262,10 @@ 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] "Sat Nov  7 13:15:02 2020"
+#> [1] "Sun Nov  8 02:44:54 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:15:07 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
+#> [1] "Sun Nov  8 02:44:59 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

@@ -271,20 +275,20 @@ using mmkin.

 # This takes about 4 minutes on my system
 f_saem <- saem(f_mmkin)
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:15:08 2020"
+#> [1] "Sun Nov  8 02:45:00 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:19:07 2020"

+#> [1] "Sun Nov  8 02:49:01 2020"
#> Error in exp(trans_k): non-numeric argument to mathematical function
#> Timing stopped at: 317.7 169.9 258.9

 f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve")
 # Using a single core, the following takes about 6 minutes, using 10 cores
 # it is slower instead of faster
 f_saem_des <- saem(f_mmkin_des, cores = 1)
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:19:26 2020"
+#> [1] "Sun Nov  8 02:49:20 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:27:33 2020"
compare.saemix(list(f_saemix$so, f_saemix_des$so))
-
#> Error in compare.saemix(list(f_saemix$so, f_saemix_des$so)): object 'f_saemix' not found
# }
+#> [1] "Sun Nov  8 02:57:30 2020"
#> Error in exp(trans_k): non-numeric argument to mathematical function
#> Timing stopped at: 591.7 205.6 521.4
compare.saemix(list(f_saem$so, f_saem_des$so))
+
#> Error in compare.saemix(list(f_saem$so, f_saem_des$so)): object 'f_saem' not found
# }