From 3ea655cdbefcf2056da456b7debc68ba7b535f55 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Mar 2016 08:35:26 +0100 Subject: Static documentation rebuilt by staticdocs::build_site() --- vignettes/FOCUS_L.html | 164 ++++++++++++++++++++++++------------------------- 1 file changed, 82 insertions(+), 82 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index a7564f72..25551855 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:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:06 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:54 2016 
+## Date of summary: Thu Mar 24 08:30:54 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -131,9 +131,9 @@ summary(m.L1.SFO)

 ## Residual standard error: 2.948 on 16 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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      92.47000   67.58 2.170e-21 89.57000 95.3700
 ## k_parent_sink  0.09561   24.65 1.867e-14  0.08773  0.1042
@@ -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:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## 
 ## 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 0.43 s
+## Fitted with method Port using 188 model solutions performed in 0.527 s
 ## 
 ## Weighting: none
 ## 
@@ -230,9 +230,9 @@ summary(m.L1.SFO)
## Residual standard error: 3.045 on 15 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## 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 9.247e+01 65.150 4.044e-20 8.944e+01 9.550e+01 ## alpha 5.044e+06 1.271 1.115e-01 5.510e-08 4.618e+20 @@ -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:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.094 s
+## Fitted with method Port using 41 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -301,9 +301,9 @@ summary(m.L2.SFO)

 ## Residual standard error: 5.51 on 10 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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       91.4700   24.03 1.773e-10 82.9800 99.9500
 ## k_parent_sink   0.6629    9.31 1.525e-06  0.5218  0.8421
@@ -349,17 +349,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

summary(m.L2.FOMC, data = FALSE)
-
## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:08 2015 
-## Date of summary: Mon Jul 20 14:51:08 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:56 2016 
+## Date of summary: Thu Mar 24 08:30:56 2016 
 ## 
 ## 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 0.18 s
+## Fitted with method Port using 81 model solutions performed in 0.2 s
 ## 
 ## Weighting: none
 ## 
@@ -393,9 +393,9 @@ mkinresplot(m.L2.FOMC)

 ## Residual standard error: 2.628 on 9 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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   93.770  50.510 1.173e-12 89.5700 97.970
 ## alpha       1.374   5.355 2.296e-04  0.9009  2.097
@@ -421,10 +421,10 @@ plot(m.L2.DFOP)
plot(m.L2.DFOP) 

summary(m.L2.DFOP, data = FALSE)
-
## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## 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 0.793 s
+## Fitted with method Port using 336 model solutions performed in 0.903 s
 ## 
 ## Weighting: none
 ## 
@@ -467,9 +467,9 @@ plot(m.L2.DFOP)
## Residual standard error: 1.732 on 8 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## 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 93.9500 NA NA NA NA ## k1 22.6700 NA NA NA NA @@ -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:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## 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 0.104 s
 ## 
 ## Weighting: none
 ## 
@@ -538,9 +538,9 @@ plot(m.L3.SFO)

 ## Residual standard error: 12.91 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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      74.87000   8.853 5.776e-05 54.18000 95.57000
 ## k_parent_sink  0.02527   3.067 1.102e-02  0.01138  0.05612
@@ -574,17 +574,17 @@ plot(m.L3.SFO)
plot(m.L3.FOMC) 

summary(m.L3.FOMC, data = FALSE)
-
## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## 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 0.187 s
+## Fitted with method Port using 83 model solutions performed in 0.208 s
 ## 
 ## Weighting: none
 ## 
@@ -618,9 +618,9 @@ plot(m.L3.FOMC)

 ## Residual standard error: 4.572 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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  96.9700  21.310 2.108e-06 85.2800 108.7000
 ## alpha      0.4224   5.867 1.020e-03  0.2725   0.6546
@@ -640,10 +640,10 @@ plot(m.L3.FOMC)
plot(m.L3.DFOP) 

summary(m.L3.DFOP, data = FALSE)
-
## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## 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 0.322 s
+## Fitted with method Port using 137 model solutions performed in 0.351 s
 ## 
 ## Weighting: none
 ## 
@@ -690,9 +690,9 @@ plot(m.L3.DFOP)
## Residual standard error: 1.439 on 4 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## 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 97.75000 67.970 1.404e-07 93.75000 101.70000 ## k1 0.51620 7.499 8.460e-04 0.35650 0.74750 @@ -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:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.116 s
 ## 
 ## Weighting: none
 ## 
@@ -762,9 +762,9 @@ plot(m.L4.SFO)

 ## Residual standard error: 3.651 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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      96.440000   49.49 2.283e-09 91.670000 1.012e+02
 ## k_parent_sink  0.006541   12.50 8.008e-06  0.005378 7.955e-03
@@ -787,17 +787,17 @@ plot(m.L4.SFO)
plot(m.L4.FOMC) 

summary(m.L4.FOMC, data = FALSE)
-
## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+
## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## 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 0.146 s
+## Fitted with method Port using 66 model solutions performed in 0.164 s
 ## 
 ## Weighting: none
 ## 
@@ -831,9 +831,9 @@ plot(m.L4.FOMC)

 ## Residual standard error: 2.315 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## 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  99.1400  59.020 1.322e-08 94.8200 103.500
 ## alpha      0.7042   2.685 2.178e-02  0.2703   1.835
-- 
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