From d2c1ab854491ff047135fa8377400a68499e72de Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Jul 2014 12:53:30 +0200 Subject: Handle non-convergence and maximum number of iterations For details see NEWS.md --- vignettes/FOCUS_L.html | 118 ++++++++++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 212996 -> 214130 bytes vignettes/mkin.pdf | Bin 160326 -> 160326 bytes 3 files changed, 67 insertions(+), 51 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index bb02ec3e..85fadbfe 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -193,7 +193,13 @@ hr { report, p. 284

library("mkin")
-FOCUS_2006_L1 = data.frame(
+
+ +
## Loading required package: minpack.lm
+## Loading required package: rootSolve
+
+ +
FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
   parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
@@ -223,16 +229,17 @@ FOCUS report.

 summary(m.L1.SFO)
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:20 2014 
-## Date of summary: Mon Jul 14 20:32:20 2014 
+## Date of fit:     Thu Jul 17 12:37:41 2014 
+## Date of summary: Thu Jul 17 12:37:41 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 14 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -325,16 +332,17 @@ is checked.

 summary(m.L1.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:20 2014 
-## Date of summary: Mon Jul 14 20:32:20 2014 
+## Date of fit:     Thu Jul 17 12:37:42 2014 
+## Date of summary: Thu Jul 17 12:37:42 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 45 model solutions performed in 0.266 s
 ## 
 ## Weighting: none
 ## 
@@ -417,16 +425,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:20 2014 
-## Date of summary: Mon Jul 14 20:32:20 2014 
+## Date of fit:     Thu Jul 17 12:37:42 2014 
+## Date of summary: Thu Jul 17 12:37:42 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 32 model solutions performed in 0.357 s
 ## 
 ## Weighting: none
 ## 
@@ -526,16 +535,17 @@ mkinresplot(m.L2.FOMC)
 
summary(m.L2.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:21 2014 
-## Date of summary: Mon Jul 14 20:32:21 2014 
+## Date of fit:     Thu Jul 17 12:37:43 2014 
+## Date of summary: Thu Jul 17 12:37:43 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 39 model solutions performed in 0.235 s
 ## 
 ## Weighting: none
 ## 
@@ -611,16 +621,17 @@ plot(m.L2.DFOP)
 
summary(m.L2.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:23 2014 
-## Date of summary: Mon Jul 14 20:32:23 2014 
+## Date of fit:     Thu Jul 17 12:37:44 2014 
+## Date of summary: Thu Jul 17 12:37:44 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 54 model solutions performed in 0.423 s
 ## 
 ## Weighting: none
 ## 
@@ -697,16 +708,17 @@ plot(m.L3.SFO)
 
summary(m.L3.SFO)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:23 2014 
-## Date of summary: Mon Jul 14 20:32:23 2014 
+## Date of fit:     Thu Jul 17 12:37:45 2014 
+## Date of summary: Thu Jul 17 12:37:45 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 44 model solutions performed in 0.241 s
 ## 
 ## Weighting: none
 ## 
@@ -782,16 +794,17 @@ plot(m.L3.FOMC)
 
summary(m.L3.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:24 2014 
-## Date of summary: Mon Jul 14 20:32:24 2014 
+## Date of fit:     Thu Jul 17 12:37:45 2014 
+## Date of summary: Thu Jul 17 12:37:45 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 26 model solutions performed in 0.208 s
 ## 
 ## Weighting: none
 ## 
@@ -854,16 +867,17 @@ plot(m.L3.DFOP)
 
summary(m.L3.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:24 2014 
-## Date of summary: Mon Jul 14 20:32:24 2014 
+## Date of fit:     Thu Jul 17 12:37:46 2014 
+## Date of summary: Thu Jul 17 12:37:46 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 37 model solutions performed in 0.338 s
 ## 
 ## Weighting: none
 ## 
@@ -944,16 +958,17 @@ plot(m.L4.SFO)
 
summary(m.L4.SFO, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:27 2014 
-## Date of summary: Mon Jul 14 20:32:27 2014 
+## Date of fit:     Thu Jul 17 12:37:46 2014 
+## Date of summary: Thu Jul 17 12:37:46 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 20 model solutions performed in 0.127 s
 ## 
 ## Weighting: none
 ## 
@@ -1018,16 +1033,17 @@ plot(m.L4.FOMC)
 
summary(m.L4.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.31 
+
## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 14 20:32:28 2014 
-## Date of summary: Mon Jul 14 20:32:28 2014 
+## Date of fit:     Thu Jul 17 12:37:46 2014 
+## Date of summary: Thu Jul 17 12:37:46 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
-## Method used for solution of differential equation system:
-## analytical 
+## Model predictions using solution type analytical 
+## 
+## Fitted with method Marq using 53 model solutions performed in 0.355 s
 ## 
 ## Weighting: none
 ## 
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