From 19997986f7ee5b6274c9a06796b97a5610c4f888 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 26 Jun 2015 14:52:22 +0200 Subject: Pass R CMD check --as-cran, vignette rebuild --- vignettes/FOCUS_L.html | 93 ++++++++++++++++++++++++++------------------------ 1 file changed, 49 insertions(+), 44 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 095c0ec0..7e0ef4dd 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -65,7 +65,7 @@ img {
@@ -80,8 +80,13 @@ img {

Laboratory Data L1

The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:

-
library("mkin")
-FOCUS_2006_L1 = data.frame(
+
library("mkin")

+
## Loading required package: minpack.lm
+## Loading required package: rootSolve
+## Loading required package: inline
+## Loading required package: methods
+## Loading required package: parallel

+
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,
@@ -91,17 +96,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

 
Since mkin version 0.9-32 (July 2014), we can use shorthand notation like SFO for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet=TRUE)
 summary(m.L1.SFO)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:14 2015 
-## Date of summary: Tue Jun 23 15:18:14 2015 
+## Date of fit:     Fri Jun 26 14:41:41 2015 
+## Date of summary: Fri Jun 26 14:41:41 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.101 s
+## Fitted with method Port using 37 model solutions performed in 0.08 s
 ## 
 ## Weighting: none
 ## 
@@ -181,10 +186,10 @@ summary(m.L1.SFO)

 
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1

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

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:15 2015 
-## Date of summary: Tue Jun 23 15:18:15 2015 
+## Date of fit:     Fri Jun 26 14:41:41 2015 
+## Date of summary: Fri Jun 26 14:41:41 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +201,7 @@ summary(m.L1.SFO)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.484 s
+## Fitted with method Port using 188 model solutions performed in 0.397 s
 ## 
 ## Weighting: none
 ## 
@@ -261,17 +266,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)

 
Again, the SFO model is fitted and a summary is obtained:

 
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 summary(m.L2.SFO)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:15 2015 
-## Date of summary: Tue Jun 23 15:18:15 2015 
+## Date of fit:     Fri Jun 26 14:41:42 2015 
+## Date of summary: Fri Jun 26 14:41:42 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.109 s
+## Fitted with method Port using 41 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -349,17 +354,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:16 2015 
-## Date of summary: Tue Jun 23 15:18:16 2015 
+## Date of fit:     Fri Jun 26 14:41:42 2015 
+## Date of summary: Fri Jun 26 14:41:42 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.227 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -421,10 +426,10 @@ plot(m.L2.DFOP)

 plot(m.L2.DFOP)

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:18 2015 
-## Date of summary: Tue Jun 23 15:18:18 2015 
+## Date of fit:     Fri Jun 26 14:41:44 2015 
+## Date of summary: Fri Jun 26 14:41:44 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +438,7 @@ plot(m.L2.DFOP)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.93 s
+## Fitted with method Port using 336 model solutions performed in 0.744 s
 ## 
 ## Weighting: none
 ## 
@@ -498,17 +503,17 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

 plot(m.L3.SFO)

 

 
summary(m.L3.SFO)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:19 2015 
-## Date of summary: Tue Jun 23 15:18:19 2015 
+## Date of fit:     Fri Jun 26 14:41:44 2015 
+## Date of summary: Fri Jun 26 14:41:44 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.111 s
+## Fitted with method Port using 43 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -574,17 +579,17 @@ plot(m.L3.SFO)

 plot(m.L3.FOMC)

 

 
summary(m.L3.FOMC, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:19 2015 
-## Date of summary: Tue Jun 23 15:18:19 2015 
+## Date of fit:     Fri Jun 26 14:41:44 2015 
+## Date of summary: Fri Jun 26 14:41:44 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.213 s
+## Fitted with method Port using 83 model solutions performed in 0.178 s
 ## 
 ## Weighting: none
 ## 
@@ -640,10 +645,10 @@ plot(m.L3.FOMC)

 plot(m.L3.DFOP)

 

 
summary(m.L3.DFOP, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:20 2015 
-## Date of summary: Tue Jun 23 15:18:20 2015 
+## Date of fit:     Fri Jun 26 14:41:45 2015 
+## Date of summary: Fri Jun 26 14:41:45 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +657,7 @@ plot(m.L3.DFOP)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.348 s
+## Fitted with method Port using 137 model solutions performed in 0.287 s
 ## 
 ## Weighting: none
 ## 
@@ -722,17 +727,17 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

 plot(m.L4.SFO)

 

 
summary(m.L4.SFO, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:20 2015 
-## Date of summary: Tue Jun 23 15:18:20 2015 
+## Date of fit:     Fri Jun 26 14:41:45 2015 
+## Date of summary: Fri Jun 26 14:41:45 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.115 s
+## Fitted with method Port using 46 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -787,17 +792,17 @@ plot(m.L4.SFO)

 plot(m.L4.FOMC)

 

 
summary(m.L4.FOMC, data = FALSE)

-
## mkin version:    0.9.38 
+
## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 15:18:20 2015 
-## Date of summary: Tue Jun 23 15:18:20 2015 
+## Date of fit:     Fri Jun 26 14:41:45 2015 
+## Date of summary: Fri Jun 26 14:41:45 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.169 s
+## Fitted with method Port using 66 model solutions performed in 0.143 s
 ## 
 ## Weighting: none
 ## 
-- 
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