From 524a8bba89b95840b4e9215c403947a8bb76d7b2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Nov 2020 16:05:10 +0100 Subject: Complete rebuild of static docs of dev version --- docs/dev/reference/saem.html | 52 ++++++++++++++++++++++---------------------- 1 file changed, 26 insertions(+), 26 deletions(-) (limited to 'docs/dev/reference/saem.html') diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 948e1378..e4ebf5d9 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -247,27 +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] "Thu Nov 19 14:51:31 2020" +#> [1] "Mon Nov 30 15:53:02 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:33 2020"
+#> [1] "Mon Nov 30 15:53:04 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] "Thu Nov 19 14:51:34 2020" +#> [1] "Mon Nov 30 15:53:05 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:36 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Mon Nov 30 15:53:07 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:36 2020" +#> [1] "Mon Nov 30 15:53:07 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:38 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Mon Nov 30 15:53:09 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:39 2020" +#> [1] "Mon Nov 30 15:53:10 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:42 2020"
+#> [1] "Mon Nov 30 15:53:13 2020"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -313,20 +313,20 @@ 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] "Thu Nov 19 14:51:44 2020" +#> [1] "Mon Nov 30 15:53:15 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:49 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Mon Nov 30 15:53:20 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
-sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), - A1 = mkinsub("SFO")) -
#> Successfully compiled differential equation model from auto-generated C code.
fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), - A1 = mkinsub("SFO")) -
#> Successfully compiled differential equation model from auto-generated C code.
dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), - A1 = mkinsub("SFO")) -
#> Successfully compiled differential equation model from auto-generated C code.
# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, +sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), + A1 = mkinsub("SFO")) +
#> Temporary DLL for differentials generated and loaded
fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), + A1 = mkinsub("SFO")) +
#> Temporary DLL for differentials generated and loaded
dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO")) +
#> Temporary DLL for differentials generated and loaded
# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, # and compiled ODEs for FOMC that are much slower f_mmkin <- mmkin(list( "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), @@ -336,15 +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] "Thu Nov 19 14:51:52 2020" +#> [1] "Mon Nov 30 15:53:23 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:57 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Mon Nov 30 15:53:28 2020"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:57 2020" +#> [1] "Mon Nov 30 15:53:29 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:52:06 2020"
# We can use print, plot and summary methods to check the results +#> [1] "Mon Nov 30 15:53:38 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: @@ -387,8 +387,8 @@ using mmkin.

#> 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: Thu Nov 19 14:52:07 2020 -#> Date of summary: Thu Nov 19 14:52:07 2020 +#> Date of fit: Mon Nov 30 15:53:38 2020 +#> Date of summary: Mon Nov 30 15:53:39 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -403,7 +403,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 10.034 s using 300, 100 iterations +#> Fitted in 9.963 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -647,7 +647,7 @@ using mmkin.

# analytical solution. Using 10 cores it is slower instead of faster f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
#> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:52:08 2020" +#> [1] "Mon Nov 30 15:53:39 2020" #> DLSODA- At current T (=R1), MXSTEP (=I1) steps #> taken on this call before reaching TOUT #> In above message, I1 = 5000 @@ -667,7 +667,7 @@ using mmkin.

#> #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:59:05 2020"
plot(f_saem_fomc) +#> [1] "Mon Nov 30 16:00:45 2020"
plot(f_saem_fomc)
# }
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