Anova method for saem.mmkin objects — anova.saem.mmkin • mkin

From 630e657f1794ea441afc9ff10663309fec5e847e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 1 Nov 2022 14:16:21 +0100 Subject: Update online docs --- docs/dev/reference/Rplot001.png | Bin 20021 -> 1011 bytes docs/dev/reference/Rplot002.png | Bin 17243 -> 17010 bytes docs/dev/reference/anova.saem.mmkin.html | 14 +++++++---- docs/dev/reference/aw.html | 7 ++++-- docs/dev/reference/illparms.html | 21 +++++++++++++--- docs/dev/reference/index.html | 4 +-- docs/dev/reference/llhist.html | 2 +- docs/dev/reference/logLik.saem.mmkin.html | 2 +- docs/dev/reference/mhmkin.html | 14 ++++++++--- docs/dev/reference/mkinfit.html | 33 +++++++++++++----------- docs/dev/reference/multistart.html | 3 +-- docs/dev/reference/parms.html | 2 +- docs/dev/reference/parplot.html | 2 +- docs/dev/reference/plot.mixed.mmkin-4.png | Bin 175535 -> 175586 bytes docs/dev/reference/plot.mixed.mmkin.html | 14 +++++++++-- docs/dev/reference/saem.html | 18 ++++++++----- docs/dev/reference/set_nd_nq.html | 2 +- docs/dev/reference/status.html | 2 +- docs/dev/reference/summary.mkinfit.html | 15 ++++++----- docs/dev/reference/summary.mmkin.html | 8 +++--- docs/dev/reference/summary.saem.mmkin.html | 39 +++++++++++++++++------------ 21 files changed, 129 insertions(+), 73 deletions(-) (limited to 'docs/dev/reference') diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index 6841f086..17a35806 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png index 11f6a1cd..f06a860e 100644 Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index abe77c65..2c109cc2 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -1,6 +1,8 @@ -Anova method for saem.mmkin objects — anova.saem.mmkin • mkinAnova method for saem.mmkin objects — anova.saem.mmkin • mkin @@ -18,7 +20,7 @@ the saemix package. As in other prominent anova methods, models are sorted"> @@ -87,8 +89,10 @@ the saemix package. As in other prominent anova methods, models are sorted">

Generate an anova object. The method to calculate the BIC is that from -the saemix package. As in other prominent anova methods, models are sorted

Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line.

diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index 57dfa06c..e552cc62 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004).">

@@ -52,11 +52,14 @@ likelihood function.">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

@@ -378,17 +381,17 @@ Degradation Data. Environments 6(12) 124 # Use shorthand notation for parent only degradation fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) -#> mkin version used for fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Fri Sep 16 10:29:10 2022 -#> Date of summary: Fri Sep 16 10:29:10 2022 +#> mkin version used for fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:09:26 2022 +#> Date of summary: Tue Nov 1 14:09:26 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.045 s +#> Fitted using 222 model solutions performed in 0.049 s #> #> Error model: Constant variance #> @@ -530,9 +533,9 @@ Degradation Data. Environments 6(12) 124 } #> Loading required package: rbenchmark #> test relative elapsed -#> 3 analytical 1.000 0.577 -#> 1 deSolve_compiled 1.537 0.887 -#> 2 eigen 2.551 1.472 +#> 3 analytical 1.000 0.559 +#> 1 deSolve_compiled 1.556 0.870 +#> 2 eigen 2.603 1.455 # } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO @@ -559,10 +562,10 @@ Degradation Data. Environments 6(12) 124 #> Warning: NaNs produced #> Warning: NaNs produced #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful -#> mkin version used for fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Fri Sep 16 10:29:21 2022 -#> Date of summary: Fri Sep 16 10:29:21 2022 +#> mkin version used for fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:09:37 2022 +#> Date of summary: Tue Nov 1 14:09:37 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -571,7 +574,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.48 s +#> Fitted using 3729 model solutions performed in 2.43 s #> #> Error model: Two-component variance function #> diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 176d40c0..3f5c4b35 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."> - 1.1.2 + 1.2.0 @@ -202,7 +202,6 @@ doi: 10.1186/s12859-021-04373-4.

f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") illparms(f_saem_reduced) -#> character(0) # On Windows, we need to create a cluster first. When working with # such a cluster, we need to export the mmkin object to the cluster # nodes, as it is referred to when updating the saem object on the nodes. diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 949bb2f9..95db0593 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index 38a93e27..ffe93e6c 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."> diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png index d2fa1ae1..a849aaee 100644 Binary files a/docs/dev/reference/plot.mixed.mmkin-4.png and b/docs/dev/reference/plot.mixed.mmkin-4.png differ diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 83017908..b1c62721 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

@@ -96,6 +99,7 @@ xlab = "Time", xlim = range(x$data$time), resplot = c("predicted", "time"), + pop_curve = "auto", pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, @@ -149,6 +153,12 @@ variables in the model.

predicted values?

pop_curve

Per default, a population curve is drawn in case +population parameters are fitted by the model, e.g. for saem objects. +In case there is a covariate model, no population curve is currently shown.

+ +

pred_over

Named list of alternative predictions as obtained from mkinpredict with a compatible mkinmod.

diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index c8a7504f..8ea0ef6e 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."> - 1.1.2 + 1.2.0 @@ -100,6 +100,7 @@ Expectation Maximisation algorithm (SAEM).

saem( object, transformations = c("mkin", "saemix"), + error_model = "auto", degparms_start = numeric(), test_log_parms = TRUE, conf.level = 0.6, @@ -124,6 +125,7 @@ Expectation Maximisation algorithm (SAEM).

object, solution_type = "auto", transformations = c("mkin", "saemix"), + error_model = "auto", degparms_start = numeric(), covariance.model = "auto", no_random_effect = NULL, @@ -160,6 +162,10 @@ SFO, FOMC, DFOP and HS without fixing parent_0, and SFO or DFOP wit one SFO metabolite.

error_model

Possibility to override the error model used in the mmkin object

+ +

degparms_start

Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.

@@ -409,10 +415,10 @@ using mmkin.

summary(f_saem_dfop_sfo, data = TRUE) #> saemix version used for fitting: 3.2 -#> mkin version used for pre-fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Wed Oct 26 09:20:37 2022 -#> Date of summary: Wed Oct 26 09:20:37 2022 +#> mkin version used for pre-fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:12:07 2022 +#> Date of summary: Tue Nov 1 14:12:07 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -427,7 +433,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 8.902 s +#> Fitted in 8.45 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 26a28339..6c6a5d46 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."> diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index 778446b3..4c856100 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index c58fffbb..993544c7 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values.">