From 005a39e3f4413ae27d8334b8000abd1d25108a7a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 23 Jun 2015 15:19:21 +0200 Subject: Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge --- vignettes/FOCUS_D.html | 8 ++--- vignettes/FOCUS_L.html | 78 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 225008 -> 225020 bytes vignettes/compiled_models.html | 34 +++++++++--------- vignettes/mkin.pdf | Bin 160260 -> 160260 bytes 5 files changed, 60 insertions(+), 60 deletions(-) diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 0ec2542c..01d5d4f3 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:52 2015 
-## Date of summary: Tue Jun 23 13:14:52 2015 
+## Date of fit:     Tue Jun 23 15:18:13 2015 
+## Date of summary: Tue Jun 23 15:18:14 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 0.682 s
+## Fitted with method Port using 153 model solutions performed in 0.749 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index bb012d65..095c0ec0 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:53 2015 
-## Date of summary: Tue Jun 23 13:14:53 2015 
+## Date of fit:     Tue Jun 23 15:18:14 2015 
+## Date of summary: Tue Jun 23 15:18:14 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.1 s
+## Fitted with method Port using 37 model solutions performed in 0.101 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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:54 2015 
-## Date of summary: Tue Jun 23 13:14:54 2015 
+## Date of fit:     Tue Jun 23 15:18:15 2015 
+## Date of summary: Tue Jun 23 15:18:15 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 0.539 s
+## Fitted with method Port using 188 model solutions performed in 0.484 s
 ## 
 ## Weighting: none
 ## 
@@ -261,10 +261,10 @@ 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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:54 2015 
-## Date of summary: Tue Jun 23 13:14:54 2015 
+## Date of fit:     Tue Jun 23 15:18:15 2015 
+## Date of summary: Tue Jun 23 15:18:15 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
@@ -349,17 +349,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

 

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

-
## mkin version:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:54 2015 
-## Date of summary: Tue Jun 23 13:14:54 2015 
+## Date of fit:     Tue Jun 23 15:18:16 2015 
+## Date of summary: Tue Jun 23 15:18:16 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 0.228 s
+## Fitted with method Port using 81 model solutions performed in 0.227 s
 ## 
 ## Weighting: none
 ## 
@@ -421,10 +421,10 @@ plot(m.L2.DFOP)

 plot(m.L2.DFOP)

 

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

-
## mkin version:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:57 2015 
-## Date of summary: Tue Jun 23 13:14:57 2015 
+## Date of fit:     Tue Jun 23 15:18:18 2015 
+## Date of summary: Tue Jun 23 15:18:18 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 0.907 s
+## Fitted with method Port using 336 model solutions performed in 0.93 s
 ## 
 ## Weighting: none
 ## 
@@ -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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:57 2015 
-## Date of summary: Tue Jun 23 13:14:57 2015 
+## Date of fit:     Tue Jun 23 15:18:19 2015 
+## Date of summary: Tue Jun 23 15:18:19 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.112 s
+## Fitted with method Port using 43 model solutions performed in 0.111 s
 ## 
 ## Weighting: none
 ## 
@@ -574,17 +574,17 @@ plot(m.L3.SFO)

 plot(m.L3.FOMC)

 

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

-
## mkin version:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:58 2015 
-## Date of summary: Tue Jun 23 13:14:58 2015 
+## Date of fit:     Tue Jun 23 15:18:19 2015 
+## Date of summary: Tue Jun 23 15:18:19 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 0.204 s
+## Fitted with method Port using 83 model solutions performed in 0.213 s
 ## 
 ## Weighting: none
 ## 
@@ -640,10 +640,10 @@ plot(m.L3.FOMC)

 plot(m.L3.DFOP)

 

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

-
## mkin version:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:58 2015 
-## Date of summary: Tue Jun 23 13:14:58 2015 
+## Date of fit:     Tue Jun 23 15:18:20 2015 
+## Date of summary: Tue Jun 23 15:18:20 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 0.359 s
+## Fitted with method Port using 137 model solutions performed in 0.348 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:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:59 2015 
-## Date of summary: Tue Jun 23 13:14:59 2015 
+## Date of fit:     Tue Jun 23 15:18:20 2015 
+## Date of summary: Tue Jun 23 15:18:20 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.12 s
+## Fitted with method Port using 46 model solutions performed in 0.115 s
 ## 
 ## Weighting: none
 ## 
@@ -787,17 +787,17 @@ plot(m.L4.SFO)

 plot(m.L4.FOMC)

summary(m.L4.FOMC, data = FALSE)
-
## mkin version:    0.9.37 
+
## mkin version:    0.9.38 
 ## R version:       3.2.1 
-## Date of fit:     Tue Jun 23 13:14:59 2015 
-## Date of summary: Tue Jun 23 13:14:59 2015 
+## Date of fit:     Tue Jun 23 15:18:20 2015 
+## Date of summary: Tue Jun 23 15:18:20 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 0.163 s
+## Fitted with method Port using 66 model solutions performed in 0.169 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 43592d51..146e9b23 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index a415c735..8d4c36a4 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -99,18 +99,18 @@ smb.1 <- summary(mb.1)[-1]
 rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
 print(smb.1)

 
##                             min        lq      mean    median        uq
-## deSolve, not compiled 6958.1752 7034.5639 7074.0173 7110.9526 7131.9383
-## Eigenvalue based       978.8821  988.5741 1012.6283  998.2660 1029.5014
-## deSolve, compiled      756.0280  767.9740  800.3639  779.9199  822.5318
+## deSolve, not compiled 6555.9044 6654.5464 6693.6732 6753.1885 6762.5577
+## Eigenvalue based       941.4496  949.4094  972.3045  957.3693  987.7320
+## deSolve, compiled      743.6684  756.3411  761.1512  769.0139  769.8926
 ##                             max neval
-## deSolve, not compiled 7152.9240     3
-## Eigenvalue based      1060.7367     3
-## deSolve, compiled      865.1437     3

-
We see that using the compiled model is by a factor of 9.1 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+## deSolve, not compiled 6771.9268     3
+## Eigenvalue based      1018.0946     3
+## deSolve, compiled      770.7713     3
+

We see that using the compiled model is by a factor of 8.8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 9.117542
-## Eigenvalue based      1.279960
+## deSolve, not compiled 8.781621
+## Eigenvalue based      1.244931
 ## deSolve, compiled     1.000000
@@ -128,17 +128,17 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2) 
##                             min        lq      mean    median        uq
-## deSolve, not compiled 14.586587 14.604167 14.614147 14.621747 14.627927
-## deSolve, compiled      1.428573  1.449463  1.459828  1.470352  1.475455
+## deSolve, not compiled 14.202106 14.342265 14.430352 14.482424 14.544475
+## deSolve, compiled      1.363102  1.367979  1.377016  1.372857  1.383973
 ##                             max neval
-## deSolve, not compiled 14.634107     3
-## deSolve, compiled      1.480558     3
+## deSolve, not compiled 14.606526 3 +## deSolve, compiled 1.395088 3 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 9.944383
-## deSolve, compiled     1.000000
-

Here we get a performance benefit of a factor of 9.9 using the version of the differential equation model compiled from C code using the inline package!

-

This vignette was built with mkin 0.9.37 on

+## deSolve, not compiled 10.54912 +## deSolve, compiled 1.00000 +

Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code using the inline package!

+

This vignette was built with mkin 0.9.38 on

## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf index fe600666..88566e24 100644 Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ -- cgit v1.2.1