From 737fc7f352bbb853b01ff6e3c6ec21a528da901e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Jan 2021 14:45:04 +0100 Subject: Change default ylab in plot.mkinfit, explicit ylab for plot.mmkin See NEWS.md. Closes #12 --- docs/dev/reference/saem.html | 49 +++++++++++++++++--------------------------- 1 file changed, 19 insertions(+), 30 deletions(-) (limited to 'docs/dev/reference/saem.html') diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index a832e911..59589378 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -162,7 +162,6 @@ Expectation Maximisation algorithm (SAEM).

control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE), verbose = FALSE, - suppressPlot = TRUE, quiet = FALSE, ... ) @@ -219,11 +218,6 @@ automatic choice is not desired

verbose

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 @@ -267,36 +261,33 @@ 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 Jan 11 12:42:01 2021" +#> [1] "Mon Jan 25 14:41:42 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:03 2021"
+#> [1] "Mon Jan 25 14:41:43 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] "Mon Jan 11 12:42:04 2021" +#> [1] "Mon Jan 25 14:41:45 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:06 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Mon Jan 25 14:41:46 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:06 2021" +#> [1] "Mon Jan 25 14:41:47 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:08 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Mon Jan 25 14:41:49 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:09 2021" +#> [1] "Mon Jan 25 14:41:49 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:12 2021"
+#> [1] "Mon Jan 25 14:41:52 2021"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix)
#> Package saemix, version 3.1.9000 #> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) -
#> Likelihoods computed by importance sampling
#> AIC BIC -#> 1 624.2484 622.2956 -#> 2 467.7096 464.9757 -#> 3 495.4373 491.9222
plot(f_saem_fomc$so, plot.type = "convergence") +
#> Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.
plot(f_saem_fomc$so, plot.type = "convergence")
#> Plotting convergence plots
plot(f_saem_fomc$so, plot.type = "individual.fit")
#> Plotting individual fits
plot(f_saem_fomc$so, plot.type = "npde")
#> Simulating data using nsim = 1000 simulated datasets @@ -333,13 +324,11 @@ 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 Jan 11 12:42:14 2021" +#> [1] "Mon Jan 25 14:41:55 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:19 2021"
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
+#> [1] "Mon Jan 25 14:42:00 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +
#> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO"))
#> Temporary DLL for differentials generated and loaded
fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), @@ -357,15 +346,15 @@ using mmkin.

# four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:22 2021" +#> [1] "Mon Jan 25 14:42:02 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:27 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Mon Jan 25 14:42:07 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Mon Jan 11 12:42:28 2021" +#> [1] "Mon Jan 25 14:42:08 2021" #> .... #> Minimisation finished -#> [1] "Mon Jan 11 12:42:37 2021"
# We can use print, plot and summary methods to check the results +#> [1] "Mon Jan 25 14:42:17 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: @@ -408,8 +397,8 @@ 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: Mon Jan 11 12:42:38 2021 -#> Date of summary: Mon Jan 11 12:42:38 2021 +#> Date of fit: Mon Jan 25 14:42:18 2021 +#> Date of summary: Mon Jan 25 14:42:18 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -424,7 +413,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 10.092 s using 300, 100 iterations +#> Fitted in 9.954 s using 300, 100 iterations #> #> Variance model: Constant variance #> -- cgit v1.2.1