From 373d98038c514c5152478127a8a2b9b390ee1b58 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 14 Jan 2018 18:37:07 +0100 Subject: Load mkin quietly in vignettes Static documentation articles rebuilt by pkgdown::build_articles() --- docs/articles/FOCUS_D.R | 2 +- docs/articles/FOCUS_D.html | 11 ++---- docs/articles/FOCUS_L.html | 72 +++++++++++++++++++------------------- docs/articles/FOCUS_Z.R | 2 +- docs/articles/FOCUS_Z.html | 4 +-- docs/articles/compiled_models.R | 2 +- docs/articles/compiled_models.html | 18 +++++----- docs/articles/index.html | 2 +- docs/articles/mkin.R | 2 +- docs/articles/mkin.html | 11 ++---- docs/articles/twa.html | 2 +- 11 files changed, 59 insertions(+), 69 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.R b/docs/articles/FOCUS_D.R index 51723496..b831e14e 100644 --- a/docs/articles/FOCUS_D.R +++ b/docs/articles/FOCUS_D.R @@ -3,7 +3,7 @@ library(knitr) opts_chunk$set(tidy = FALSE, cache = TRUE) ## ----data---------------------------------------------------------------- -library("mkin") +library("mkin", quietly = TRUE) print(FOCUS_2006_D) ## ----model--------------------------------------------------------------- diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index d6941019..e3f87eae 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -77,20 +77,15 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2017-11-16

+

2018-01-14

This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look a the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

-
library("mkin")
-
## Lade nötiges Paket: minpack.lm
-
## Lade nötiges Paket: rootSolve
-
## Lade nötiges Paket: inline
-
## Lade nötiges Paket: methods
-
## Lade nötiges Paket: parallel
-
print(FOCUS_2006_D)
+
library("mkin", quietly = TRUE)
+print(FOCUS_2006_D)
##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 7cef7abd..bc2b9947 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -77,7 +77,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2017-11-16

+            
2018-01-14
@@ -98,17 +98,17 @@ FOCUS_2006_L1_mkin <- 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:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:46 2017 
-## Date of summary: Thu Nov 16 17:12:46 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:12 2018 
+## Date of summary: Sun Jan 14 18:36:12 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.253 s
+## Fitted with method Port using 37 model solutions performed in 0.258 s
 ## 
 ## Weighting: none
 ## 
@@ -191,10 +191,10 @@ FOCUS_2006_L1_mkin <- 
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

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

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:47 2017 
-## Date of summary: Thu Nov 16 17:12:47 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:13 2018 
+## Date of summary: Sun Jan 14 18:36:13 2018 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -206,7 +206,7 @@ FOCUS_2006_L1_mkin <-  main = "FOCUS L2 - FOMC")

 

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

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:48 2017 
-## Date of summary: Thu Nov 16 17:12:48 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:14 2018 
+## Date of summary: Sun Jan 14 18:36:14 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.183 s
+## Fitted with method Port using 81 model solutions performed in 0.177 s
 ## 
 ## Weighting: none
 ## 
@@ -362,10 +362,10 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - DFOP")

 

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

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:49 2017 
-## Date of summary: Thu Nov 16 17:12:49 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:15 2018 
+## Date of summary: Sun Jan 14 18:36:15 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -374,7 +374,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:50 2017 
-## Date of summary: Thu Nov 16 17:12:50 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:16 2018 
+## Date of summary: Sun Jan 14 18:36:16 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -466,7 +466,7 @@ mm.L3 <-  

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

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

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:50 2017 
-## Date of summary: Thu Nov 16 17:12:51 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:16 2018 
+## Date of summary: Sun Jan 14 18:36:17 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.098 s
+## Fitted with method Port using 46 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -615,17 +615,17 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version:    0.9.46.2 
-## R version:       3.4.2 
-## Date of fit:     Thu Nov 16 17:12:51 2017 
-## Date of summary: Thu Nov 16 17:12:51 2017 
+
## mkin version:    0.9.47.1 
+## R version:       3.4.3 
+## Date of fit:     Sun Jan 14 18:36:17 2018 
+## Date of summary: Sun Jan 14 18:36:17 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.136 s
+## Fitted with method Port using 66 model solutions performed in 0.138 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index a77441cf..65ddbeba 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -3,7 +3,7 @@ require(knitr)
 opts_chunk$set(engine='R', tidy = FALSE)
 
 ## ---- echo = TRUE, fig = TRUE, fig.width = 8, fig.height = 7-------------
-library(mkin, quiet = TRUE)
+library(mkin, quietly = TRUE)
 LOD = 0.5
 FOCUS_2006_Z = data.frame(
   t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index d16299ca..7a37c66d 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -77,7 +77,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2017-11-16

+            
2018-01-14

           
 
     
@@ -88,7 +88,7 @@
 

 The data

 
The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report (FOCUS Work Group on Degradation Kinetics 2014, 354).

-
library(mkin, quiet = TRUE)
+
library(mkin, quietly = TRUE)
 LOD = 0.5
 FOCUS_2006_Z = data.frame(
   t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R
index 25c39dac..c5b06c11 100644
--- a/docs/articles/compiled_models.R
+++ b/docs/articles/compiled_models.R
@@ -6,7 +6,7 @@ opts_chunk$set(tidy = FALSE, cache = FALSE)
 Sys.which("gcc")
 
 ## ----create_SFO_SFO------------------------------------------------------
-library("mkin")
+library("mkin", quietly = TRUE)
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 68aa1bac..4c850d14 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -77,7 +77,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2017-11-16

+            
2018-01-14

           

 
     
@@ -91,7 +91,7 @@
 
##            gcc 
 ## "/usr/bin/gcc"

 
First, we build a simple degradation model for a parent compound with one metabolite.

-
library("mkin")
+
library("mkin", quietly = TRUE)
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))

@@ -115,9 +115,9 @@ SFO_SFO <-  
-  
Articles version 0.9.46.3

+  
Articles version 0.9.47.1

 

 
 

diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R
index 67dc3623..19e80322 100644
--- a/docs/articles/mkin.R
+++ b/docs/articles/mkin.R
@@ -3,7 +3,7 @@ require(knitr)
 opts_chunk$set(engine='R', tidy=FALSE)
 
 ## ---- echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7----
-library(mkin)
+library("mkin", quietly = TRUE)
 # Define the kinetic model
 m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                          M1 = mkinsub("SFO", "M2"),
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 14349e53..13df8a5d 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -77,7 +77,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2017-11-16

+            
2018-01-14

           

 
     
@@ -88,13 +88,8 @@
 

 Abstract

 
In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The R add-on package mkin (Ranke 2016) implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.

-
library(mkin)

-
## Lade nötiges Paket: minpack.lm

-
## Lade nötiges Paket: rootSolve

-
## Lade nötiges Paket: inline

-
## Lade nötiges Paket: methods

-
## Lade nötiges Paket: parallel

-
# Define the kinetic model
+
library("mkin", quietly = TRUE)
+# Define the kinetic model
 m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                          M1 = mkinsub("SFO", "M2"),
                          M2 = mkinsub("SFO"),
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 0a4df0ff..f141ce63 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -77,7 +77,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2017-11-16

+            
2018-01-14

           

 
     
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