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() --- inst/web/vignettes/FOCUS_L.html | 56 ++++++++++++++++++++--------------------- 1 file changed, 28 insertions(+), 28 deletions(-) (limited to 'inst/web/vignettes/FOCUS_L.html') diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html index 05b9bdbd..4c509eb2 100644 --- a/inst/web/vignettes/FOCUS_L.html +++ b/inst/web/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
 ## 
-- 
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