From f39815aa87272849f8e0c808099c4cee780c2a81 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Nov 2016 14:33:05 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() Using pkgdown with PR hadley/pkgdown#212 --- docs/reference/transform_odeparms.html | 39 +++++++++++++++++----------------- 1 file changed, 19 insertions(+), 20 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index ab5ce062..ccd56ca4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -61,7 +61,12 @@ @@ -83,7 +88,7 @@ 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. @@ -109,7 +114,7 @@

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
@@ -128,7 +133,7 @@ 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. @@ -139,18 +144,15 @@ as the original parameters.

-

- - Examples -

+

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
+  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)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.44.9000 
-#> R version:       3.3.1 
-#> Date of fit:     Wed Oct 26 23:50:51 2016 
-#> Date of summary: Wed Oct 26 23:50:51 2016 
+#> R version:       3.3.2 
+#> Date of fit:     Thu Nov  3 17:46:36 2016 
+#> Date of summary: Thu Nov  3 17:46:36 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +160,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.629 s
+#> Fitted with method Port using 153 model solutions performed in 0.657 s
 #> 
 #> Weighting: none
 #> 
@@ -221,8 +223,7 @@
 #> Estimated disappearance times:
 #>           DT50   DT90
 #> parent   7.023  23.33
-#> m1     131.761 437.70
-#> 

+#> m1     131.761 437.70

 ## Not run: ------------------------------------
 # fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)
 # summary(fit.2, data=FALSE) 
@@ -233,10 +234,8 @@
 transformed <- fit$start_transformed$value
 names(transformed) <- rownames(fit$start_transformed)
 transform_odeparms(initials, SFO_SFO)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
-#>        100.750000         -2.302585         -2.301586         -2.300587 
-#> 
backtransform_odeparms(transformed, SFO_SFO)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
-#>      100.7500        0.1000        0.1001        0.1002 
-#> 

+#>        100.750000         -2.302585         -2.301586         -2.300587 
backtransform_odeparms(transformed, SFO_SFO)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
+#>      100.7500        0.1000        0.1001        0.1002 

 ## Not run: ------------------------------------
 # # The case of formation fractions
 # SFO_SFO.ff <- mkinmod(
@@ -280,7 +279,7 @@