From 17af45b984d348505527140470c7fff204748ea6 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Fri, 12 Sep 2025 22:16:13 +0200
Subject: Facilitate centering covariates
The motivation for this is to obtain confidence intervals for
covariate dependent parameters that are valid for a median/mean
value of the covariate.
Implementation by adding an argument to the 'saem' function, and
adapting the relevant functions working with 'saem' objects.
Vignettes, the template and tests were updated to use the new functionality.
---
docs/reference/index.html | 6 +++---
docs/reference/saem-3.png | Bin 128590 -> 128574 bytes
docs/reference/saem.html | 29 ++++++++++++++++++-----------
3 files changed, 21 insertions(+), 14 deletions(-)
(limited to 'docs/reference')
diff --git a/docs/reference/index.html b/docs/reference/index.html
index f8fc6615..57af6079 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Package index • mkin
+Package index • mkinSkip to contents
@@ -7,7 +7,7 @@
mkin
- 1.2.10
+ 1.2.11
omega.init ="auto", covariates =NULL, covariate_models =NULL,
+ center_covariates =c(NA, "median", "mean"), no_random_effect =NULL, error.init =c(1, 1), nbiter.saemix =c(300, 100),
@@ -195,6 +196,12 @@ variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available
in the 'covariates' data frame.
+
center_covariates
+
Either NA, for no centering, or your
+preferred function for calculating the center, currently either
+median or mean.
+
+
no_random_effect
Character vector of degradation parameters for
which there should be no variability over the groups. Only used
@@ -303,7 +310,7 @@ using mmkin.
# functions from saemixlibrary(saemix)#> Loading required package: npde
-#> Package saemix, version 3.3, March 2024
+#> Package saemix, version 3.4, March 2024#> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr#>#> Attaching package: ‘saemix’
@@ -394,11 +401,11 @@ using mmkin.
plot(f_saem_dfop_sfo)summary(f_saem_dfop_sfo, data =TRUE)
-#> saemix version used for fitting: 3.3
-#> mkin version used for pre-fitting: 1.2.10
-#> R version used for fitting: 4.5.0
-#> Date of fit: Mon May 12 20:24:36 2025
-#> Date of summary: Mon May 12 20:24:36 2025
+#> saemix version used for fitting: 3.4
+#> mkin version used for pre-fitting: 1.2.11
+#> R version used for fitting: 4.5.1
+#> Date of fit: Fri Sep 12 20:34:55 2025
+#> Date of summary: Fri Sep 12 20:34:55 2025 #>#> Equations:#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +420,7 @@ using mmkin.
#>#> Model predictions using solution type analytical #>
-#> Fitted in 3.747 s
+#> Fitted in 4.017 s#> Using 300, 100 iterations and 10 chains#>#> Variance model: Constant variance
@@ -718,7 +725,7 @@ using mmkin.
--
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