From d34e5c053794a08cc73c9042ccccfb334ae0f62d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Apr 2015 09:53:58 +0200 Subject: Pending commit of an updated vignette --- vignettes/FOCUS_L.html | 153 ++++++++++++++++++++++++------------------------- 1 file changed, 76 insertions(+), 77 deletions(-) diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index b5228532..96ea70ce 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -214,7 +214,13 @@ 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,
@@ -236,17 +242,17 @@ given in the FOCUS report. 

 summary(m.L1.SFO)
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:49 2014 
-## Date of summary: Thu Dec 18 09:52:49 2014 
+## Date of fit:     Sat Feb 21 14:44:53 2015 
+## Date of summary: Sat Feb 21 14:44:53 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.214 s
+## Fitted with method Port using 37 model solutions performed in 0.098 s
 ## 
 ## Weighting: none
 ## 
@@ -323,43 +329,32 @@ summary(m.L1.SFO)
 
plot(m.L1.SFO)
 

 
-
plot of chunk unnamed-chunk-4 
+
plot of chunk unnamed-chunk-4 
 The residual plot can be easily obtained by

 
 
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
 

 
-
plot of chunk unnamed-chunk-5 

+
plot of chunk unnamed-chunk-5 

 
 
For comparison, the FOMC model is fitted as well, and the chi2 error level
 is checked.

 
 
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
+summary(m.L1.FOMC, data = FALSE)
 

 
-
## 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:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:50 2014 
-## Date of summary: Thu Dec 18 09:52:50 2014 
-## 
-## 
-## Warning: Optimisation by method Port did not converge.
-## Convergence code is 1 
-## 
+## Date of fit:     Sat Feb 21 14:44:55 2015 
+## Date of summary: Sat Feb 21 14:44:55 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.085 s
+## Fitted with method Port using 611 model solutions performed in 1.509 s
 ## 
 ## Weighting: none
 ## 
@@ -379,24 +374,28 @@ is checked.

 ## None
 ## 
 ## Optimised, transformed parameters:
-##           Estimate Std. Error  Lower Upper t value  Pr(>|t|)    Pr(>t)
-## parent_0     92.47      1.422  89.44 95.50  65.030 8.317e-20 4.158e-20
-## log_alpha    15.43     15.080 -16.71 47.58   1.023 3.224e-01 1.612e-01
-## log_beta     17.78     15.090 -14.37 49.93   1.179 2.569e-01 1.284e-01
+##           Estimate Std. Error    Lower   Upper  t value  Pr(>|t|)
+## parent_0     92.47      1.482    89.31   95.63 62.39000 1.546e-19
+## log_alpha    11.25    598.200 -1264.00 1286.00  0.01880 9.852e-01
+## log_beta     13.60    598.200 -1261.00 1289.00  0.02273 9.822e-01
+##              Pr(>t)
+## parent_0  7.730e-20
+## log_alpha 4.926e-01
+## log_beta  4.911e-01
 ## 
 ## Parameter correlation:
 ##           parent_0 log_alpha log_beta
-## parent_0    1.0000    0.1129   0.1112
-## log_alpha   0.1129    1.0000   1.0000
-## log_beta    0.1112    1.0000   1.0000
+## parent_0    1.0000   -0.3016  -0.3016
+## log_alpha  -0.3016    1.0000   1.0000
+## log_beta   -0.3016    1.0000   1.0000
 ## 
 ## Residual standard error: 3.045 on 15 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##           Estimate     Lower     Upper
-## parent_0 9.247e+01 8.944e+01 9.550e+01
-## alpha    5.044e+06 5.510e-08 4.618e+20
-## beta     5.276e+07 5.732e-07 4.857e+21
+##           Estimate Lower Upper
+## parent_0     92.47 89.31 95.63
+## alpha     76830.00  0.00   Inf
+## beta     803500.00  0.00   Inf
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -404,8 +403,8 @@ is checked.

 ## parent     3.619       3  6
 ## 
 ## Estimated disappearance times:
-##        DT50  DT90 DT50back
-## parent 7.25 24.08     7.25
+##         DT50  DT90 DT50back
+## parent 7.249 24.08    7.249
 

 
 
Due to the higher number of parameters, and the lower number of degrees of
@@ -443,17 +442,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:51 2014 
-## Date of summary: Thu Dec 18 09:52:51 2014 
+## Date of fit:     Sat Feb 21 14:44:55 2015 
+## Date of summary: Sat Feb 21 14:44:55 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.238 s
+## Fitted with method Port using 41 model solutions performed in 0.1 s
 ## 
 ## Weighting: none
 ## 
@@ -527,7 +526,7 @@ plot(m.L2.SFO)
 mkinresplot(m.L2.SFO)
 

 
-
plot of chunk unnamed-chunk-9 

+
plot of chunk unnamed-chunk-9 

 
 
In the FOCUS kinetics report, it is stated that there is no apparent systematic
 error observed from the residual plot up to the measured DT90 (approximately at
@@ -548,22 +547,22 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)
 

 
-
plot of chunk unnamed-chunk-10 

+
plot of chunk unnamed-chunk-10 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:51 2014 
-## Date of summary: Thu Dec 18 09:52:51 2014 
+## Date of fit:     Sat Feb 21 14:44:55 2015 
+## Date of summary: Sat Feb 21 14:44:55 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.464 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
 ## 
 ## Weighting: none
 ## 
@@ -622,7 +621,7 @@ experimental error has to be assumed in order to explain the data.

 plot(m.L2.DFOP)
 

 
-
plot of chunk unnamed-chunk-11 

+
plot of chunk unnamed-chunk-11 

 
 
Here, the default starting parameters for the DFOP model obviously do not lead
 to a reasonable solution. Therefore the fit is repeated with different starting
@@ -634,15 +633,15 @@ parameters.

 plot(m.L2.DFOP)
 

 
-
plot of chunk unnamed-chunk-12 

+
plot of chunk unnamed-chunk-12 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:56 2014 
-## Date of summary: Thu Dec 18 09:52:56 2014 
+## Date of fit:     Sat Feb 21 14:44:57 2015 
+## Date of summary: Sat Feb 21 14:44:57 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -651,7 +650,7 @@ plot(m.L2.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 1.986 s
+## Fitted with method Port using 336 model solutions performed in 0.856 s
 ## 
 ## Weighting: none
 ## 
@@ -723,22 +722,22 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
 plot(m.L3.SFO)
 

 
-
plot of chunk unnamed-chunk-14 

+
plot of chunk unnamed-chunk-14 

 
 
summary(m.L3.SFO)
 

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:56 2014 
-## Date of summary: Thu Dec 18 09:52:56 2014 
+## Date of fit:     Sat Feb 21 14:44:57 2015 
+## Date of summary: Sat Feb 21 14:44:57 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.246 s
+## Fitted with method Port using 43 model solutions performed in 0.109 s
 ## 
 ## Weighting: none
 ## 
@@ -809,22 +808,22 @@ does not fit very well. 

 plot(m.L3.FOMC)
 

 
-
plot of chunk unnamed-chunk-15 

+
plot of chunk unnamed-chunk-15 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:57 2014 
-## Date of summary: Thu Dec 18 09:52:57 2014 
+## Date of fit:     Sat Feb 21 14:44:58 2015 
+## Date of summary: Sat Feb 21 14:44:58 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.475 s
+## Fitted with method Port using 83 model solutions performed in 0.203 s
 ## 
 ## Weighting: none
 ## 
@@ -882,15 +881,15 @@ considerably:

 plot(m.L3.DFOP)
 

 
-
plot of chunk unnamed-chunk-16 

+
plot of chunk unnamed-chunk-16 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:58 2014 
-## Date of summary: Thu Dec 18 09:52:58 2014 
+## Date of fit:     Sat Feb 21 14:44:58 2015 
+## Date of summary: Sat Feb 21 14:44:58 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -899,7 +898,7 @@ plot(m.L3.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.813 s
+## Fitted with method Port using 137 model solutions performed in 0.346 s
 ## 
 ## Weighting: none
 ## 
@@ -980,22 +979,22 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
 plot(m.L4.SFO)
 

 
-
plot of chunk unnamed-chunk-18 

+
plot of chunk unnamed-chunk-18 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:58 2014 
-## Date of summary: Thu Dec 18 09:52:58 2014 
+## Date of fit:     Sat Feb 21 14:44:58 2015 
+## Date of summary: Sat Feb 21 14:44:58 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.264 s
+## Fitted with method Port using 46 model solutions performed in 0.109 s
 ## 
 ## Weighting: none
 ## 
@@ -1055,22 +1054,22 @@ fits very well. 

 plot(m.L4.FOMC)
 

 
-
plot of chunk unnamed-chunk-19 

+
plot of chunk unnamed-chunk-19 

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

 
-
## mkin version:    0.9.34 
+
## mkin version:    0.9.35 
 ## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:59 2014 
-## Date of summary: Thu Dec 18 09:52:59 2014 
+## Date of fit:     Sat Feb 21 14:44:58 2015 
+## Date of summary: Sat Feb 21 14:44:58 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.375 s
+## Fitted with method Port using 66 model solutions performed in 0.161 s
 ## 
 ## Weighting: none
 ## 
-- 
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