From 4510a609159216041f10a33146534f5a8366ac76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 14 Oct 2014 22:04:54 +0200 Subject: Further formatting improvement for differential equations --- DESCRIPTION | 2 +- NEWS.md | 4 +++ R/mkinfit.R | 2 +- vignettes/FOCUS_L.html | 96 ++++++++++++++++++++++++++----------------------- vignettes/FOCUS_Z.pdf | Bin 213325 -> 220198 bytes 5 files changed, 57 insertions(+), 47 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6c4545c4..a984391c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-34 -Date: 2014-10-11 +Date: 2014-10-14 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), diff --git a/NEWS.md b/NEWS.md index 55a11818..4478be6b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ # CHANGES in mkin VERSION 0.9-34 +## MINOR CHANGES + +- The formatting of differential equations in the summary was further improved + # CHANGES in mkin VERSION 0.9-33 ## NEW FEATURES diff --git a/R/mkinfit.R b/R/mkinfit.R index 5c1de846..a966cea6 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -567,7 +567,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), . if (!is.null(x$warning)) cat("\n\nWarning:", x$warning, "\n\n") cat("\nEquations:\n") - cat(noquote(strwrap(x[["diffs"]], exdent = 11)), fill = TRUE) + writeLines(strwrap(x[["diffs"]], exdent = 11)) df <- x$df rdf <- df[2] diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index c0430358..60c5132a 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -214,7 +214,13 @@ hr { report, p. 284:

library("mkin")
-FOCUS_2006_L1 = data.frame(
+
+ +
## Loading required package: minpack.lm
+## Loading required package: rootSolve
+
+ +
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,
@@ -236,17 +242,17 @@ given in the FOCUS report. 

 summary(m.L1.SFO)
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:43 2014 
-## Date of summary: Sat Oct 11 11:06:43 2014 
+## Date of fit:     Tue Oct 14 22:03:33 2014 
+## Date of summary: Tue Oct 14 22:03:33 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 14 model solutions performed in 0.083 s
+## Fitted with method Marq using 14 model solutions performed in 0.081 s
 ## 
 ## Weighting: none
 ## 
@@ -338,17 +344,17 @@ is checked.

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

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:44 2014 
-## Date of summary: Sat Oct 11 11:06:44 2014 
+## Date of fit:     Tue Oct 14 22:03:34 2014 
+## Date of summary: Tue Oct 14 22:03:34 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 53 model solutions performed in 0.314 s
+## Fitted with method Marq using 53 model solutions performed in 0.289 s
 ## 
 ## Weighting: none
 ## 
@@ -432,17 +438,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:44 2014 
-## Date of summary: Sat Oct 11 11:06:44 2014 
+## Date of fit:     Tue Oct 14 22:03:35 2014 
+## Date of summary: Tue Oct 14 22:03:35 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 29 model solutions performed in 0.173 s
+## Fitted with method Marq using 29 model solutions performed in 0.154 s
 ## 
 ## Weighting: none
 ## 
@@ -542,17 +548,17 @@ mkinresplot(m.L2.FOMC)
 
summary(m.L2.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:46 2014 
-## Date of summary: Sat Oct 11 11:06:47 2014 
+## Date of fit:     Tue Oct 14 22:03:36 2014 
+## Date of summary: Tue Oct 14 22:03:36 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 35 model solutions performed in 0.206 s
+## Fitted with method Marq using 35 model solutions performed in 0.192 s
 ## 
 ## Weighting: none
 ## 
@@ -628,19 +634,19 @@ plot(m.L2.DFOP)
 
summary(m.L2.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:47 2014 
-## Date of summary: Sat Oct 11 11:06:47 2014 
+## Date of fit:     Tue Oct 14 22:03:36 2014 
+## Date of summary: Tue Oct 14 22:03:36 2014 
 ## 
 ## Equations:
-## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
-##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 *
 ##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 43 model solutions performed in 0.265 s
+## Fitted with method Marq using 43 model solutions performed in 0.24 s
 ## 
 ## Weighting: none
 ## 
@@ -717,17 +723,17 @@ plot(m.L3.SFO)
 
summary(m.L3.SFO)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:48 2014 
-## Date of summary: Sat Oct 11 11:06:48 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 44 model solutions performed in 0.261 s
+## Fitted with method Marq using 44 model solutions performed in 0.237 s
 ## 
 ## Weighting: none
 ## 
@@ -803,17 +809,17 @@ plot(m.L3.FOMC)
 
summary(m.L3.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:48 2014 
-## Date of summary: Sat Oct 11 11:06:48 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 26 model solutions performed in 0.159 s
+## Fitted with method Marq using 26 model solutions performed in 0.139 s
 ## 
 ## Weighting: none
 ## 
@@ -876,19 +882,19 @@ plot(m.L3.DFOP)
 
summary(m.L3.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:50 2014 
-## Date of summary: Sat Oct 11 11:06:50 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
-## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
-##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 *
 ##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 37 model solutions performed in 0.225 s
+## Fitted with method Marq using 37 model solutions performed in 0.207 s
 ## 
 ## Weighting: none
 ## 
@@ -974,17 +980,17 @@ plot(m.L4.SFO)
 
summary(m.L4.SFO, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:51 2014 
-## Date of summary: Sat Oct 11 11:06:51 2014 
+## Date of fit:     Tue Oct 14 22:03:38 2014 
+## Date of summary: Tue Oct 14 22:03:38 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 20 model solutions performed in 0.119 s
+## Fitted with method Marq using 20 model solutions performed in 0.106 s
 ## 
 ## Weighting: none
 ## 
@@ -1049,17 +1055,17 @@ plot(m.L4.FOMC)
 
summary(m.L4.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.33 
+
## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:51 2014 
-## Date of summary: Sat Oct 11 11:06:51 2014 
+## Date of fit:     Tue Oct 14 22:03:38 2014 
+## Date of summary: Tue Oct 14 22:03:38 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 48 model solutions performed in 0.283 s
+## Fitted with method Marq using 48 model solutions performed in 0.26 s
 ## 
 ## Weighting: none
 ## 
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