From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 15:31:13 +0200 Subject: Adapt and improve the dimethenamid vignette Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs --- docs/dev/reference/saem.html | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) (limited to 'docs/dev/reference/saem.html') diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 620173b2..8d986126 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> mkin - 1.0.5 + 1.1.0 @@ -288,27 +288,27 @@ 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 Aug 4 16:22:05 2021" +#> [1] "Thu Sep 16 14:34:42 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:06 2021"
+#> [1] "Thu Sep 16 14:34:43 2021"
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 Aug 4 16:22:08 2021" +#> [1] "Thu Sep 16 14:34:45 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:10 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Thu Sep 16 14:34:47 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:22:10 2021" +#> [1] "Thu Sep 16 14:34:47 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:12 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Thu Sep 16 14:34:49 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:22:12 2021" +#> [1] "Thu Sep 16 14:34:49 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:16 2021"
+#> [1] "Thu Sep 16 14:34:52 2021"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -357,10 +357,10 @@ 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 Aug 4 16:22:19 2021" +#> [1] "Thu Sep 16 14:34:55 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:24 2021"
compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so) +#> [1] "Thu Sep 16 14:35:00 2021"
compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so)
#> Likelihoods calculated by importance sampling
#> AIC BIC #> 1 467.7096 464.9757 #> 2 469.6831 466.5586
@@ -381,15 +381,15 @@ using mmkin.

# four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:22:27 2021" +#> [1] "Thu Sep 16 14:35:03 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:32 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Thu Sep 16 14:35:08 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Wed Aug 4 16:22:33 2021" +#> [1] "Thu Sep 16 14:35:08 2021" #> .... #> Minimisation finished -#> [1] "Wed Aug 4 16:22:42 2021"
# We can use print, plot and summary methods to check the results +#> [1] "Thu Sep 16 14:35:17 2021"
# 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: @@ -430,10 +430,10 @@ using mmkin.

#> SD.g_qlogis 0.44816 -1.25437 2.1507
plot(f_saem_dfop_sfo)
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.5 -#> R version used for fitting: 4.1.0 -#> Date of fit: Wed Aug 4 16:22:43 2021 -#> Date of summary: Wed Aug 4 16:22:43 2021 +#> mkin version used for pre-fitting: 1.1.0 +#> R version used for fitting: 4.1.1 +#> Date of fit: Thu Sep 16 14:35:18 2021 +#> Date of summary: Thu Sep 16 14:35:18 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -448,7 +448,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 10.143 s using 300, 100 iterations +#> Fitted in 9.349 s using 300, 100 iterations #> #> Variance model: Constant variance #> -- cgit v1.2.1