From c0c82d9523da8965f5fb7a5f8cf1410750885d30 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 11 Nov 2020 19:49:25 +0100 Subject: Update static docs --- docs/dev/reference/saem.html | 50 +++++++++++++++++++++++++------------------- 1 file changed, 28 insertions(+), 22 deletions(-) (limited to 'docs/dev/reference/saem.html') diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index bc54e1e1..d0c3495a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -141,7 +141,7 @@ Expectation Maximisation algorithm (SAEM)." />

Fit nonlinear mixed models with SAEM

- Source: R/saemix.R + Source: R/saem.R
@@ -161,6 +161,7 @@ Expectation Maximisation algorithm (SAEM).

cores = 1, verbose = FALSE, suppressPlot = TRUE, + quiet = FALSE, ... ) @@ -185,24 +186,29 @@ Expectation Maximisation algorithm (SAEM).

... -

Further parameters passed to saemix::saemixData -and saemix::saemixModel.

+

Further parameters passed to saemix::saemixModel.

cores

The number of cores to be used for multicore processing using parallel::mclapply(). Using more than 1 core is experimental and may -lead to uncontrolled forking, apparently depending on the BLAS version +lead to excessive forking, apparently depending on the BLAS version used.

verbose -

Should we print information about created objects?

+

Should we print information about created objects of +type saemix::SaemixModel and saemix::SaemixData?

suppressPlot

Should we suppress any plotting that is done by the saemix function?

+ + + quiet +

Should we suppress the messages saemix prints at the beginning +and the end of the optimisation process?

x @@ -241,27 +247,27 @@ 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] "Wed Nov 11 09:36:41 2020" +#> [1] "Wed Nov 11 19:47:58 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:43 2020"
+#> [1] "Wed Nov 11 19:48:00 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] "Wed Nov 11 09:36:44 2020" +#> [1] "Wed Nov 11 19:48:01 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:45 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Wed Nov 11 19:48:03 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:36:46 2020" +#> [1] "Wed Nov 11 19:48:03 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:48 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Wed Nov 11 19:48:05 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:36:48 2020" +#> [1] "Wed Nov 11 19:48:06 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:51 2020"
+#> [1] "Wed Nov 11 19:48:08 2020"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -307,10 +313,10 @@ 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] "Wed Nov 11 09:36:54 2020" +#> [1] "Wed Nov 11 19:48:11 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:36:59 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Wed Nov 11 19:48:16 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
#> Likelihoods computed by importance sampling
#> AIC BIC #> 1 467.7096 464.9757 #> 2 469.5208 466.3963
@@ -330,15 +336,15 @@ 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] "Wed Nov 11 09:37:01 2020" +#> [1] "Wed Nov 11 19:48:18 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:06 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Wed Nov 11 19:48:23 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Wed Nov 11 09:37:06 2020" +#> [1] "Wed Nov 11 19:48:23 2020" #> .... #> Minimisation finished -#> [1] "Wed Nov 11 09:37:15 2020"
# We can use print, plot and summary methods to check the results +#> [1] "Wed Nov 11 19:48:32 2020"
# We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -384,8 +390,8 @@ using mmkin.

#> LL by is "-407.78 (df=13)"
#> 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: Wed Nov 11 09:37:16 2020 -#> Date of summary: Wed Nov 11 09:37:16 2020 +#> Date of fit: Wed Nov 11 19:48:33 2020 +#> Date of summary: Wed Nov 11 19:48:33 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -400,7 +406,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 9.691 s using 300, 100 iterations +#> Fitted in 9.564 s using 300, 100 iterations #> #> Variance model: Constant variance #> -- cgit v1.2.1