From d185c26e4909efbae9dc4210ed9eac4b2600910e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 11 Mar 2018 22:12:51 +0100 Subject: Static docs rebuilt again, with current pkgdown --- docs/articles/FOCUS_D.html | 13 +++--- docs/articles/FOCUS_L.R | 86 -------------------------------------- docs/articles/FOCUS_L.html | 49 ++++++++++++---------- docs/articles/FOCUS_Z.html | 7 +++- docs/articles/compiled_models.html | 19 +++++---- docs/articles/index.html | 2 + docs/articles/mkin.html | 7 +++- docs/articles/twa.html | 7 +++- 8 files changed, 62 insertions(+), 128 deletions(-) delete mode 100644 docs/articles/FOCUS_L.R (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index d85246f8..a8002acd 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,7 +9,10 @@ - @@ -77,7 +80,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-09

+

2018-03-11

@@ -152,8 +155,8 @@ 
summary(fit)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:48 2018 
-## Date of summary: Fri Mar  9 23:09:48 2018 
+## Date of fit:     Sun Mar 11 22:11:56 2018 
+## Date of summary: Sun Mar 11 22:11:57 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -161,7 +164,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.99 s
+## Fitted with method Port using 153 model solutions performed in 0.984 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.R b/docs/articles/FOCUS_L.R
deleted file mode 100644
index 063e3d57..00000000
--- a/docs/articles/FOCUS_L.R
+++ /dev/null
@@ -1,86 +0,0 @@
-## ---- include = FALSE----------------------------------------------------
-library(knitr)
-opts_chunk$set(tidy = FALSE, cache = FALSE)
-
-## ------------------------------------------------------------------------
-library("mkin", quietly = TRUE)
-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,
-             27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
-FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
-
-## ------------------------------------------------------------------------
-m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.SFO)
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
-plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
-summary(m.L1.FOMC, data = FALSE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L2 = data.frame(
-  t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
-  parent = c(96.1, 91.8, 41.4, 38.7,
-             19.3, 22.3, 4.6, 4.6,
-             2.6, 1.2, 0.3, 0.6))
-FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - SFO")
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.FOMC, show_residuals = TRUE,
-     main = "FOCUS L2 - FOMC")
-summary(m.L2.FOMC, data = FALSE)
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - DFOP")
-summary(m.L2.DFOP, data = FALSE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L3 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
-
-## ----fig.height = 8------------------------------------------------------
-# Only use one core here, not to offend the CRAN checks
-mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
-               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
-plot(mm.L3)
-
-## ----fig.height = 5------------------------------------------------------
-summary(mm.L3[["DFOP", 1]])
-plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L4 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
-
-## ----fig.height = 6------------------------------------------------------
-# Only use one core here, not to offend the CRAN checks
-mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin),
-               quiet = TRUE)
-plot(mm.L4)
-
-## ----fig.height = 8------------------------------------------------------
-summary(mm.L4[["SFO", 1]], data = FALSE)
-summary(mm.L4[["FOMC", 1]], data = FALSE)
-
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 196a0c4f..a23876ec 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
@@ -100,15 +103,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:50 2018 
-## Date of summary: Fri Mar  9 23:09:50 2018 
+## Date of fit:     Sun Mar 11 22:11:58 2018 
+## Date of summary: Sun Mar 11 22:11:58 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 0.264 s
+## Fitted with method Port using 37 model solutions performed in 0.235 s
 ## 
 ## Weighting: none
 ## 
@@ -191,15 +194,15 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:52 2018 
-## Date of summary: Fri Mar  9 23:09:52 2018 
+## Date of fit:     Sun Mar 11 22:12:01 2018 
+## Date of summary: Sun Mar 11 22:12:01 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.451 s
+## Fitted with method Port using 611 model solutions performed in 1.458 s
 ## 
 ## Weighting: none
 ## 
@@ -286,15 +289,15 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:53 2018 
-## Date of summary: Fri Mar  9 23:09:53 2018 
+## Date of fit:     Sun Mar 11 22:12:01 2018 
+## Date of summary: Sun Mar 11 22:12:01 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 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.158 s
 ## 
 ## Weighting: none
 ## 
@@ -357,8 +360,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:54 2018 
-## Date of summary: Fri Mar  9 23:09:54 2018 
+## Date of fit:     Sun Mar 11 22:12:02 2018 
+## Date of summary: Sun Mar 11 22:12:02 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -367,7 +370,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:55 2018 
-## Date of summary: Fri Mar  9 23:09:55 2018 
+## Date of fit:     Sun Mar 11 22:12:03 2018 
+## Date of summary: Sun Mar 11 22:12:03 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -459,7 +462,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:55 2018 
-## Date of summary: Fri Mar  9 23:09:56 2018 
+## Date of fit:     Sun Mar 11 22:12:04 2018 
+## Date of summary: Sun Mar 11 22:12:04 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 0.09 s
+## Fitted with method Port using 46 model solutions performed in 0.092 s
 ## 
 ## Weighting: none
 ## 
@@ -610,15 +613,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:56 2018 
-## Date of summary: Fri Mar  9 23:09:56 2018 
+## Date of fit:     Sun Mar 11 22:12:04 2018 
+## Date of summary: Sun Mar 11 22:12:04 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 0.134 s
+## Fitted with method Port using 66 model solutions performed in 0.13 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 606121ff..78a00062 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 915e5474..8923acac 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
@@ -115,9 +118,9 @@ SFO_SFO <-  
   
   
+
 
 
 
@@ -134,3 +135,4 @@
 
   
 
+
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index f668b500..7b26b3f1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index e5b68cfe..7f4c941e 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
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