From 6733555d7a9315c55001770bacc4c61c4d4f39d5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 21 Jun 2015 01:46:51 +0200 Subject: Do the t-test for untransformed parameters --- vignettes/FOCUS_D.html | 50 +++++++++++++++++++++----------------------------- 1 file changed, 21 insertions(+), 29 deletions(-) (limited to 'vignettes/FOCUS_D.html') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 6573cc7a..b1ea64ea 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -215,13 +215,7 @@ library we look a the data. We have observed concentrations in the column named named parent and m1.

library("mkin")
-
- -
## Loading required package: minpack.lm
-## Loading required package: rootSolve
-
- -
print(FOCUS_2006_D)
+print(FOCUS_2006_D)
 
##      name time  value
@@ -276,7 +270,7 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics
 
 
The call to mkinmod returns a degradation model. The differential equations represented in 
 R code can be found in the character vector $diffs of the mkinmod object. If
-the ccSolve package is installed and functional, the differential equation model
+the gcc compiler is installed and functional, the differential equation model
 will be compiled from auto-generated C code.

 
 
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
@@ -312,7 +306,7 @@ using the plot method for mkinfit objects.

 
mkinparplot(fit)
 

 
-
plot of chunk unnamed-chunk-6 

+
plot of chunk unnamed-chunk-6 

 
 
A comprehensive report of the results is obtained using the summary method for mkinfit
 objects.

@@ -321,9 +315,9 @@ objects.

 

 
 
## mkin version:    0.9.36 
-## R version:       3.2.0 
-## Date of fit:     Fri Jun  5 14:20:31 2015 
-## Date of summary: Fri Jun  5 14:20:31 2015 
+## R version:       3.2.1 
+## Date of fit:     Sun Jun 21 01:47:59 2015 
+## Date of summary: Sun Jun 21 01:47:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -331,7 +325,7 @@ objects.

 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.621 s
+## Fitted with method Port using 153 model solutions performed in 0.698 s
 ## 
 ## Weighting: none
 ## 
@@ -353,17 +347,12 @@ objects.

 ##      value  type
 ## m1_0     0 state
 ## 
-## Optimised, transformed parameters:
-##                   Estimate Std. Error  Lower   Upper t value  Pr(>|t|)
-## parent_0            99.600    1.61400 96.330 102.900   61.72 4.048e-38
-## log_k_parent_sink   -3.038    0.07826 -3.197  -2.879  -38.82 5.601e-31
-## log_k_parent_m1     -2.980    0.04124 -3.064  -2.897  -72.27 1.446e-40
-## log_k_m1_sink       -5.248    0.13610 -5.523  -4.972  -38.56 7.087e-31
-##                      Pr(>t)
-## parent_0          2.024e-38
-## log_k_parent_sink 2.800e-31
-## log_k_parent_m1   7.228e-41
-## log_k_m1_sink     3.543e-31
+## Optimised, transformed parameters with symmetric confidence intervals:
+##                   Estimate Std. Error  Lower   Upper
+## parent_0            99.600    1.61400 96.330 102.900
+## log_k_parent_sink   -3.038    0.07826 -3.197  -2.879
+## log_k_parent_m1     -2.980    0.04124 -3.064  -2.897
+## log_k_m1_sink       -5.248    0.13610 -5.523  -4.972
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
@@ -375,11 +364,14 @@ objects.

 ## Residual standard error: 3.211 on 36 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##                Estimate     Lower     Upper
-## parent_0      99.600000 96.330000 1.029e+02
-## k_parent_sink  0.047920  0.040890 5.616e-02
-## k_parent_m1    0.050780  0.046700 5.521e-02
-## k_m1_sink      0.005261  0.003992 6.933e-03
+##   Confidence intervals for internally transformed parameters are asymmetric.
+##   t-test (unrealistically) based on the assumption of normal distribution
+##   for estimators of untransformed parameters.
+##                Estimate t value    Pr(>t)     Lower     Upper
+## parent_0      99.600000  61.720 2.024e-38 96.330000 1.029e+02
+## k_parent_sink  0.047920  12.780 3.050e-15  0.040890 5.616e-02
+## k_parent_m1    0.050780  24.250 3.407e-24  0.046700 5.521e-02
+## k_m1_sink      0.005261   7.349 5.758e-09  0.003992 6.933e-03
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-- 
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