From 8f38147e145c66ebd27f5d9fcc6f00172c25872f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 26 Oct 2016 23:18:20 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/transform_odeparms.html | 78 +++++++++++++++++++++------------- 1 file changed, 49 insertions(+), 29 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 66253bba..a07be0a0 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,14 +6,14 @@ -transform_odeparms. mkin + + — transform_odeparms • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be - negative, the ilr transformation is used.

+ negative, the ilr transformation is used.

The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. - This is no problem for the internal use in mkinfit.

+ This is no problem for the internal use in mkinfit.

transform_odeparms(parms, mkinmod,
@@ -95,7 +97,7 @@
 backtransform_odeparms(transparms, mkinmod,
                        transform_rates = TRUE, transform_fractions = TRUE)
-

Arguments

+

Arguments

parms
@@ -107,9 +109,9 @@
mkinmod
- The kinetic model of class mkinmod, containing the names of + The kinetic model of class mkinmod, containing the names of the model variables that are needed for grouping the formation fractions - before ilr transformation, the parameter names and + before ilr transformation, the parameter names and the information if the pathway to sink is included in the model.
transform_rates
@@ -128,27 +130,29 @@ assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the ilr + transformation used for these transformations is the ilr transformation.
-
-

Value

+

Value

-

A vector of transformed or backtransformed parameters with the same names +

A vector of transformed or backtransformed parameters with the same names as the original parameters.

-
-

Examples

- 
SFO_SFO <- mkinmod(
+
+    

+      
+      Examples
+    

+    
SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 10:47:45 2016 
-#> Date of summary: Thu Oct  6 10:47:45 2016 
+#> Date of fit:     Wed Oct 26 23:16:59 2016 
+#> Date of summary: Wed Oct 26 23:16:59 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -156,7 +160,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.638 s
+#> Fitted with method Port using 153 model solutions performed in 0.721 s
 #> 
 #> Weighting: none
 #> 
@@ -259,7 +263,16 @@
 # summary(fit.ff.2, data = FALSE)
 ## ---------------------------------------------

   

-  

+  
 
       
    

 
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