From c9e245f88fc8c6b7776353e3b2fc2dd7451bd97b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 20 Jul 2015 09:22:03 +0200 Subject: Avoid error message for SFORB in endpoints, updates --- vignettes/FOCUS_D.html | 12 +++---- vignettes/FOCUS_L.html | 88 ++++++++++++++++++++++++------------------------- vignettes/FOCUS_Z.pdf | Bin 219834 -> 226064 bytes vignettes/mkin.pdf | Bin 160260 -> 160258 bytes 4 files changed, 50 insertions(+), 50 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index b8264c22..f5b8f22a 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -10,7 +10,7 @@ - + Example evaluation of FOCUS Example Dataset D @@ -64,7 +64,7 @@ img { @@ -135,10 +135,10 @@ print(FOCUS_2006_D)

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

summary(fit)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:35:59 2015 
-## Date of summary: Fri Jun 26 16:35:59 2015 
+## Date of fit:     Sat Jul 18 16:50:58 2015 
+## Date of summary: Sat Jul 18 16:50:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.71 s
+## Fitted with method Port using 153 model solutions performed in 0.604 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index d1a10e6a..963dff0c 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 {
 
 
 

@@ -91,17 +91,17 @@ 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:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:00 2015 
-## Date of summary: Fri Jun 26 16:36:00 2015 
+## Date of fit:     Sat Jul 18 16:50:59 2015 
+## Date of summary: Sat Jul 18 16:50:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.083 s
 ## 
 ## Weighting: none
 ## 
@@ -181,10 +181,10 @@ 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:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:00 2015 
-## Date of summary: Fri Jun 26 16:36:00 2015 
+## Date of fit:     Sat Jul 18 16:51:00 2015 
+## Date of summary: Sat Jul 18 16:51:00 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.48 s
+## Fitted with method Port using 188 model solutions performed in 0.414 s
 ## 
 ## Weighting: none
 ## 
@@ -261,17 +261,17 @@ 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:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:01 2015 
-## Date of summary: Fri Jun 26 16:36:01 2015 
+## Date of fit:     Sat Jul 18 16:51:00 2015 
+## Date of summary: Sat Jul 18 16:51:00 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.103 s
+## Fitted with method Port using 41 model solutions performed in 0.089 s
 ## 
 ## Weighting: none
 ## 
@@ -349,17 +349,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

 

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

-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:01 2015 
-## Date of summary: Fri Jun 26 16:36:01 2015 
+## Date of fit:     Sat Jul 18 16:51:01 2015 
+## Date of summary: Sat Jul 18 16:51:01 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 0.212 s
+## Fitted with method Port using 81 model solutions performed in 0.177 s
 ## 
 ## Weighting: none
 ## 
@@ -421,10 +421,10 @@ plot(m.L2.DFOP)

 plot(m.L2.DFOP)

 

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

-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:03 2015 
-## Date of summary: Fri Jun 26 16:36:03 2015 
+## Date of fit:     Sat Jul 18 16:51:03 2015 
+## Date of summary: Sat Jul 18 16:51:03 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.862 s
+## Fitted with method Port using 336 model solutions performed in 0.791 s
 ## 
 ## Weighting: none
 ## 
@@ -482,8 +482,8 @@ plot(m.L2.DFOP)

 ## parent      2.53       4  2
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90 DT50_k1 DT50_k2
-## parent   NA   NA 0.03058   2.058

+##          DT50  DT90 DT50_k1 DT50_k2
+## parent 0.5335 5.311 0.03058   2.058

Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.

@@ -498,17 +498,17 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3) plot(m.L3.SFO) 

summary(m.L3.SFO)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:04 2015 
-## Date of summary: Fri Jun 26 16:36:04 2015 
+## Date of fit:     Sat Jul 18 16:51:03 2015 
+## Date of summary: Sat Jul 18 16:51:03 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.103 s
+## Fitted with method Port using 43 model solutions performed in 0.093 s
 ## 
 ## Weighting: none
 ## 
@@ -574,17 +574,17 @@ plot(m.L3.SFO)

 plot(m.L3.FOMC)

summary(m.L3.FOMC, data = FALSE)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:04 2015 
-## Date of summary: Fri Jun 26 16:36:04 2015 
+## Date of fit:     Sat Jul 18 16:51:03 2015 
+## Date of summary: Sat Jul 18 16:51:03 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 0.205 s
+## Fitted with method Port using 83 model solutions performed in 0.173 s
 ## 
 ## Weighting: none
 ## 
@@ -640,10 +640,10 @@ plot(m.L3.FOMC)

 plot(m.L3.DFOP)

summary(m.L3.DFOP, data = FALSE)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:05 2015 
-## Date of summary: Fri Jun 26 16:36:05 2015 
+## Date of fit:     Sat Jul 18 16:51:04 2015 
+## Date of summary: Sat Jul 18 16:51:04 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.361 s
+## Fitted with method Port using 137 model solutions performed in 0.303 s
 ## 
 ## Weighting: none
 ## 
@@ -722,17 +722,17 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
plot(m.L4.SFO) 

summary(m.L4.SFO, data = FALSE)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:05 2015 
-## Date of summary: Fri Jun 26 16:36:05 2015 
+## Date of fit:     Sat Jul 18 16:51:04 2015 
+## Date of summary: Sat Jul 18 16:51:04 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.11 s
+## Fitted with method Port using 46 model solutions performed in 0.104 s
 ## 
 ## Weighting: none
 ## 
@@ -787,17 +787,17 @@ plot(m.L4.SFO)

 plot(m.L4.FOMC)

summary(m.L4.FOMC, data = FALSE)
-
## mkin version:    0.9.39 
+
## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 16:36:05 2015 
-## Date of summary: Fri Jun 26 16:36:05 2015 
+## Date of fit:     Sat Jul 18 16:51:04 2015 
+## Date of summary: Sat Jul 18 16:51:04 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 0.174 s
+## Fitted with method Port using 66 model solutions performed in 0.148 s
 ## 
 ## Weighting: none
 ## 
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