From a7600ca6d4e5dfa62a16102f5a965f5e9891cf28 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 10:32:31 +0200 Subject: Bump version for new release, rebuild static docs The test test_FOMC_ill-defined leads to errors on several architectures/distributions, as apparent from CRAN checks, so we need a new release. Static documentation rebuilt by staticdocs::build_site() --- vignettes/FOCUS_D.html | 8 +++--- vignettes/FOCUS_L.html | 56 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 238788 -> 238789 bytes vignettes/compiled_models.html | 38 ++++++++++++++-------------- 4 files changed, 51 insertions(+), 51 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index c7e2047f..d60d1c7f 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -190,10 +190,10 @@ print(FOCUS_2006_D)

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

summary(fit)
-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:31 2016 
-## Date of summary: Tue Jun 28 08:19:31 2016 
+## Date of fit:     Tue Jun 28 10:30:09 2016 
+## Date of summary: Tue Jun 28 10:30:09 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -201,7 +201,7 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.706 s
+## Fitted with method Port using 153 model solutions performed in 1.707 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 05b9bdbd..4c509eb2 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -233,17 +233,17 @@ 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:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:32 2016 
-## Date of summary: Tue Jun 28 08:19:32 2016 
+## Date of fit:     Tue Jun 28 10:30:10 2016 
+## Date of summary: Tue Jun 28 10:30:10 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.245 s
+## Fitted with method Port using 37 model solutions performed in 0.249 s
 ## 
 ## Weighting: none
 ## 
@@ -326,10 +326,10 @@ summary(m.L1.SFO)

 
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

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

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:34 2016 
-## Date of summary: Tue Jun 28 08:19:34 2016 
+## Date of fit:     Tue Jun 28 10:30:12 2016 
+## Date of summary: Tue Jun 28 10:30:12 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -341,7 +341,7 @@ summary(m.L1.SFO)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.216 s
+## Fitted with method Port using 188 model solutions performed in 1.227 s
 ## 
 ## Weighting: none
 ## 
@@ -423,17 +423,17 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:36 2016 
-## Date of summary: Tue Jun 28 08:19:36 2016 
+## Date of fit:     Tue Jun 28 10:30:14 2016 
+## Date of summary: Tue Jun 28 10:30:14 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 0.537 s
+## Fitted with method Port using 81 model solutions performed in 0.543 s
 ## 
 ## Weighting: none
 ## 
@@ -493,10 +493,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

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

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:39 2016 
-## Date of summary: Tue Jun 28 08:19:39 2016 
+## Date of fit:     Tue Jun 28 10:30:17 2016 
+## Date of summary: Tue Jun 28 10:30:17 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -505,7 +505,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 2.267 s
+## Fitted with method Port using 336 model solutions performed in 2.274 s
 ## 
 ## Weighting: none
 ## 
@@ -582,10 +582,10 @@ plot(mm.L3)

 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:41 2016 
-## Date of summary: Tue Jun 28 08:19:42 2016 
+## Date of fit:     Tue Jun 28 10:30:19 2016 
+## Date of summary: Tue Jun 28 10:30:20 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -594,7 +594,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.924 s
+## Fitted with method Port using 137 model solutions performed in 0.898 s
 ## 
 ## Weighting: none
 ## 
@@ -682,17 +682,17 @@ plot(mm.L4)

 

 
The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:42 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:20 2016 
+## Date of summary: Tue Jun 28 10:30:21 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.307 s
+## Fitted with method Port using 46 model solutions performed in 0.302 s
 ## 
 ## Weighting: none
 ## 
@@ -742,17 +742,17 @@ plot(mm.L4)

 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version:    0.9.43.9000 
+
## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:43 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:21 2016 
+## Date of summary: Tue Jun 28 10:30:21 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 0.414 s
+## Fitted with method Port using 66 model solutions performed in 0.425 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 1f9560b0..af86c965 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 cec76ef9..12289676 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -250,21 +250,21 @@ mb.1 <- microbenchmark(
 print(mb.1)

 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 25.422123 25.889685 26.065978 26.357247 26.387905
-##       Eigenvalue based  2.243667  2.254539  2.277770  2.265412  2.294821
-##      deSolve, compiled  1.849468  1.865343  1.871339  1.881219  1.882274
-##       max neval cld
-##  26.41856     3   b
-##   2.32423     3  a 
-##   1.88333     3  a

+##  deSolve, not compiled 25.120822 25.185794 25.345704 25.250766 25.458146
+##       Eigenvalue based  2.246793  2.255533  2.258865  2.264274  2.264901
+##      deSolve, compiled  1.861661  1.893380  1.930436  1.925098  1.964823
+##        max neval cld
+##  25.665525     3   b
+##   2.265527     3  a 
+##   2.004547     3  a

 
autoplot(mb.1)

-

-
We see that using the compiled model is by a factor of 14 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:

+

+
We see that using the compiled model is by a factor of 13.1 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:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                          median
-## deSolve, not compiled 14.010730
-## Eigenvalue based       1.204226
+## deSolve, not compiled 13.116611
+## Eigenvalue based       1.176186
 ## deSolve, compiled      1.000000

 
 

@@ -285,20 +285,20 @@ smb.1["median"]/smb.1["deSolve, compiled", "median"
 
smb.2 <- summary(mb.2)
 print(mb.2)

 
## Unit: seconds
-##                   expr       min       lq      mean    median        uq
-##  deSolve, not compiled 54.386189 54.39423 54.477986 54.402271 54.523884
-##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 54.536624 54.617928 54.690830 54.699231 54.767933
+##      deSolve, compiled  3.690661  3.693247  3.720722  3.695833  3.735753
 ##        max neval cld
-##  54.645498     3   b
-##   3.653319     3  a

+##  54.836635     3   b
+##   3.775673     3  a

 
smb.2["median"]/smb.2["deSolve, compiled", "median"]

 
##   median
 ## 1     NA
 ## 2     NA

 
autoplot(mb.2)

-

-
Here we get a performance benefit of a factor of 14.9 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.43.9000 on

+

+
Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code!

+
This vignette was built with mkin 0.9.44 on

 
## R version 3.3.1 (2016-06-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)

-- 
cgit v1.2.1