From 39b2c2c762b03922a2648b1b226d0f308600cc87 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 01:24:15 +0200 Subject: Static documentation rebuilt by pkgdown 1.1.0 --- DESCRIPTION | 1 + docs/articles/FOCUS_D.html | 120 ++-- docs/articles/FOCUS_L.html | 102 ++-- .../figure-html/unnamed-chunk-12-1.png | Bin 54520 -> 55024 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 21712 -> 22098 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 38347 -> 38740 bytes docs/articles/FOCUS_Z.html | 52 +- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 85456 -> 86312 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 128546 -> 129920 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 128162 -> 129452 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 101891 -> 97933 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22697 -> 22321 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 86036 -> 86923 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 85658 -> 86529 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 101516 -> 102872 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 129164 -> 130096 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 128994 -> 130164 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 108244 -> 109280 bytes docs/articles/compiled_models.html | 42 +- docs/articles/index.html | 35 +- docs/articles/mkin.html | 26 +- docs/articles/twa.html | 26 +- docs/authors.html | 27 +- docs/docsearch.css | 148 +++++ docs/docsearch.js | 85 +++ docs/index.html | 33 +- docs/news/index.html | 170 +++--- docs/pkgdown.css | 50 +- docs/pkgdown.js | 160 ++--- docs/pkgdown.yml | 11 +- docs/reference/DFOP.solution-1.png | Bin 18578 -> 19459 bytes docs/reference/DFOP.solution.html | 31 +- docs/reference/Extract.mmkin.html | 47 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 27 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 27 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 27 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 27 +- docs/reference/FOCUS_2006_datasets.html | 27 +- docs/reference/FOMC.solution-1.png | Bin 18068 -> 18710 bytes docs/reference/FOMC.solution.html | 31 +- docs/reference/HS.solution-1.png | Bin 17999 -> 18994 bytes docs/reference/HS.solution.html | 31 +- docs/reference/IORE.solution-1.png | Bin 17721 -> 18751 bytes docs/reference/IORE.solution.html | 31 +- docs/reference/SFO.solution.html | 29 +- docs/reference/SFORB.solution.html | 29 +- docs/reference/add_err-1.png | Bin 85947 -> 89876 bytes docs/reference/add_err-2.png | Bin 48008 -> 51188 bytes docs/reference/add_err-3.png | Bin 49035 -> 52612 bytes docs/reference/add_err.html | 35 +- docs/reference/endpoints.html | 29 +- docs/reference/geometric_mean.html | 29 +- docs/reference/ilr.html | 31 +- docs/reference/index.html | 655 +++++++++++---------- docs/reference/max_twa_parent.html | 29 +- docs/reference/mccall81_245T.html | 35 +- docs/reference/mkin_long_to_wide.html | 29 +- docs/reference/mkin_wide_to_long.html | 29 +- docs/reference/mkinds.html | 27 +- docs/reference/mkinerrmin.html | 29 +- docs/reference/mkinfit.html | 47 +- docs/reference/mkinmod.html | 29 +- docs/reference/mkinparplot-1.png | Bin 15645 -> 16495 bytes docs/reference/mkinparplot.html | 31 +- docs/reference/mkinplot.html | 29 +- docs/reference/mkinpredict.html | 41 +- docs/reference/mkinresplot-1.png | Bin 14009 -> 15020 bytes docs/reference/mkinresplot.html | 35 +- docs/reference/mkinsub.html | 29 +- docs/reference/mmkin.html | 31 +- docs/reference/plot.mkinfit-1.png | Bin 43100 -> 45512 bytes docs/reference/plot.mkinfit-2.png | Bin 51815 -> 53185 bytes docs/reference/plot.mkinfit-3.png | Bin 42604 -> 43963 bytes docs/reference/plot.mkinfit-4.png | Bin 57866 -> 60143 bytes docs/reference/plot.mkinfit.html | 35 +- docs/reference/plot.mmkin-1.png | Bin 32597 -> 34395 bytes docs/reference/plot.mmkin-2.png | Bin 32965 -> 34836 bytes docs/reference/plot.mmkin-3.png | Bin 24581 -> 25453 bytes docs/reference/plot.mmkin.html | 33 +- docs/reference/print.mkinds.html | 29 +- docs/reference/print.mkinmod.html | 29 +- docs/reference/schaefer07_complex_case.html | 27 +- docs/reference/sigma_rl.html | 29 +- docs/reference/summary.mkinfit.html | 37 +- docs/reference/synthetic_data_for_UBA.html | 27 +- docs/reference/test_data_from_UBA_2014.html | 27 +- docs/reference/transform_odeparms.html | 37 +- 87 files changed, 2042 insertions(+), 949 deletions(-) create mode 100644 docs/docsearch.css create mode 100644 docs/docsearch.js diff --git a/DESCRIPTION b/DESCRIPTION index e3c7de4e..7158f2e0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,3 +27,4 @@ Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues URL: https://cgit.jrwb.de/mkin/about +RoxygenNote: 6.0.1 diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a83c2f44..8a1f51d1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -8,8 +8,8 @@ Example evaluation of FOCUS Example Dataset D • mkin - - + + -
+
-
+

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-21

-
+

2018-06-06

+ + + + +
-

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", quietly = TRUE)
 print(FOCUS_2006_D)
@@ -153,10 +160,10 @@

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

summary(fit)
-
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:11:56 2018 
-## Date of summary: Sun Mar 11 22:11:57 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:49 2018 
+## Date of summary: Wed Jun  6 01:21:50 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -164,7 +171,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.984 s
+## Fitted with method Port using 153 model solutions performed in 0.633 s
 ## 
 ## Weighting: none
 ## 
@@ -231,51 +238,46 @@
 ## 
 ## Data:
 ##  time variable observed predicted   residual
-##     0   parent    99.46 9.960e+01 -1.385e-01
-##     0   parent   102.04 9.960e+01  2.442e+00
-##     1   parent    93.50 9.024e+01  3.262e+00
-##     1   parent    92.50 9.024e+01  2.262e+00
-##     3   parent    63.23 7.407e+01 -1.084e+01
-##     3   parent    68.99 7.407e+01 -5.083e+00
-##     7   parent    52.32 4.991e+01  2.408e+00
-##     7   parent    55.13 4.991e+01  5.218e+00
-##    14   parent    27.27 2.501e+01  2.257e+00
-##    14   parent    26.64 2.501e+01  1.627e+00
-##    21   parent    11.50 1.253e+01 -1.035e+00
-##    21   parent    11.64 1.253e+01 -8.946e-01
-##    35   parent     2.85 3.148e+00 -2.979e-01
-##    35   parent     2.91 3.148e+00 -2.379e-01
-##    50   parent     0.69 7.162e-01 -2.624e-02
-##    50   parent     0.63 7.162e-01 -8.624e-02
-##    75   parent     0.05 6.074e-02 -1.074e-02
-##    75   parent     0.06 6.074e-02 -7.382e-04
-##   100   parent       NA 5.151e-03         NA
-##   100   parent       NA 5.151e-03         NA
-##   120   parent       NA 7.155e-04         NA
-##   120   parent       NA 7.155e-04         NA
-##     0       m1     0.00 0.000e+00  0.000e+00
-##     0       m1     0.00 0.000e+00  0.000e+00
-##     1       m1     4.84 4.803e+00  3.704e-02
-##     1       m1     5.64 4.803e+00  8.370e-01
-##     3       m1    12.91 1.302e+01 -1.140e-01
-##     3       m1    12.96 1.302e+01 -6.400e-02
-##     7       m1    22.97 2.504e+01 -2.075e+00
-##     7       m1    24.47 2.504e+01 -5.748e-01
-##    14       m1    41.69 3.669e+01  5.000e+00
-##    14       m1    33.21 3.669e+01 -3.480e+00
-##    21       m1    44.37 4.165e+01  2.717e+00
-##    21       m1    46.44 4.165e+01  4.787e+00
-##    35       m1    41.22 4.331e+01 -2.093e+00
-##    35       m1    37.95 4.331e+01 -5.363e+00
-##    50       m1    41.19 4.122e+01 -2.831e-02
-##    50       m1    40.01 4.122e+01 -1.208e+00
-##    75       m1    40.09 3.645e+01  3.643e+00
-##    75       m1    33.85 3.645e+01 -2.597e+00
-##   100       m1    31.04 3.198e+01 -9.416e-01
-##   100       m1    33.13 3.198e+01  1.148e+00
-##   120       m1    25.15 2.879e+01 -3.640e+00
-##   120       m1    33.31 2.879e+01  4.520e+00

-
+## 0 parent 99.46 99.59848 -1.385e-01 +## 0 parent 102.04 99.59848 2.442e+00 +## 1 parent 93.50 90.23787 3.262e+00 +## 1 parent 92.50 90.23787 2.262e+00 +## 3 parent 63.23 74.07320 -1.084e+01 +## 3 parent 68.99 74.07320 -5.083e+00 +## 7 parent 52.32 49.91207 2.408e+00 +## 7 parent 55.13 49.91207 5.218e+00 +## 14 parent 27.27 25.01257 2.257e+00 +## 14 parent 26.64 25.01257 1.627e+00 +## 21 parent 11.50 12.53462 -1.035e+00 +## 21 parent 11.64 12.53462 -8.946e-01 +## 35 parent 2.85 3.14787 -2.979e-01 +## 35 parent 2.91 3.14787 -2.379e-01 +## 50 parent 0.69 0.71624 -2.624e-02 +## 50 parent 0.63 0.71624 -8.624e-02 +## 75 parent 0.05 0.06074 -1.074e-02 +## 75 parent 0.06 0.06074 -7.382e-04 +## 0 m1 0.00 0.00000 0.000e+00 +## 0 m1 0.00 0.00000 0.000e+00 +## 1 m1 4.84 4.80296 3.704e-02 +## 1 m1 5.64 4.80296 8.370e-01 +## 3 m1 12.91 13.02400 -1.140e-01 +## 3 m1 12.96 13.02400 -6.400e-02 +## 7 m1 22.97 25.04476 -2.075e+00 +## 7 m1 24.47 25.04476 -5.748e-01 +## 14 m1 41.69 36.69002 5.000e+00 +## 14 m1 33.21 36.69002 -3.480e+00 +## 21 m1 44.37 41.65310 2.717e+00 +## 21 m1 46.44 41.65310 4.787e+00 +## 35 m1 41.22 43.31312 -2.093e+00 +## 35 m1 37.95 43.31312 -5.363e+00 +## 50 m1 41.19 41.21831 -2.831e-02 +## 50 m1 40.01 41.21831 -1.208e+00 +## 75 m1 40.09 36.44704 3.643e+00 +## 75 m1 33.85 36.44704 -2.597e+00 +## 100 m1 31.04 31.98163 -9.416e-01 +## 100 m1 33.13 31.98163 1.148e+00 +## 120 m1 25.15 28.78984 -3.640e+00 +## 120 m1 33.31 28.78984 4.520e+00
+ + diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 08e144bd..fcd0719d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -8,8 +8,8 @@ Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - + + -
+
-
+

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-03-21

-
+

2018-06-06

+ + + + +
-

Laboratory Data L1

@@ -101,17 +108,17 @@ FOCUS_2006_L1_mkin <- 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:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:03 2018 
-## Date of summary: Wed Mar 21 18:16:03 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:52 2018 
+## Date of summary: Wed Jun  6 01:21:52 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 0.257 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
 ## 
 ## Weighting: none
 ## 
@@ -192,17 +199,17 @@ FOCUS_2006_L1_mkin <- plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

summary(m.L1.FOMC, data = FALSE)
-
## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:05 2018 
-## Date of summary: Wed Mar 21 18:16:05 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:53 2018 
+## Date of summary: Wed Jun  6 01:21:53 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 1.404 s
+## Fitted with method Port using 611 model solutions performed in 1.369 s
 ## 
 ## Weighting: none
 ## 
@@ -287,17 +294,17 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - FOMC")

summary(m.L2.FOMC, data = FALSE)
-
## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:06 2018 
-## Date of summary: Wed Mar 21 18:16:06 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:54 2018 
+## Date of summary: Wed Jun  6 01:21:54 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 0.168 s
+## Fitted with method Port using 81 model solutions performed in 0.173 s
 ## 
 ## Weighting: none
 ## 
@@ -358,10 +365,10 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - DFOP")

summary(m.L2.DFOP, data = FALSE)
-
## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:06 2018 
-## Date of summary: Wed Mar 21 18:16:06 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:55 2018 
+## Date of summary: Wed Jun  6 01:21:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +377,7 @@ FOCUS_2006_L2_mkin <- 2006_L3_mkin <-  mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
                list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)
-

+

The \(\chi^2\) error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the \(\chi^2\) test passes of 7%. Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level considerably.

@@ -450,10 +457,10 @@ mm.L3 <- 
summary(mm.L3[["DFOP", 1]])
-
## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:07 2018 
-## Date of summary: Wed Mar 21 18:16:07 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:56 2018 
+## Date of summary: Wed Jun  6 01:21:56 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +469,7 @@ mm.L3 <-  
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)
-

+

Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the \(\chi^2\) error level criterion for laboratory data L3.

This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

@@ -548,20 +555,20 @@ mm.L4 <- list("FOCUS L4" = FOCUS_2006_L4_mkin), quiet = TRUE) plot(mm.L4)
-

+

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:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:08 2018 
-## Date of summary: Wed Mar 21 18:16:08 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:56 2018 
+## Date of summary: Wed Jun  6 01:21:57 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 0.092 s
+## Fitted with method Port using 46 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -611,17 +618,17 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)
-
## mkin version:    0.9.46.3 
-## R version:       3.4.4 
-## Date of fit:     Wed Mar 21 18:16:08 2018 
-## Date of summary: Wed Mar 21 18:16:08 2018 
+
## mkin version used for fitting:    0.9.47.1 
+## R version used for fitting:       3.5.0 
+## Date of fit:     Wed Jun  6 01:21:57 2018 
+## Date of summary: Wed Jun  6 01:21:57 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 0.138 s
+## Fitted with method Port using 66 model solutions performed in 0.146 s
 ## 
 ## Weighting: none
 ## 
@@ -680,7 +687,6 @@ mm.L4 <-  
 
-
-
+
+
 
 
 
 
 
-    

+    

       

-  

+  

     

       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-21

-          

+            
2018-06-06

+      
+      
+      
+
+    

 
     
     
-

 
Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany
Privatdozent at the University of Bremen

 

 

@@ -116,7 +123,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.

 
m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.2a)

-

+

 
summary(m.Z.2a, data = FALSE)$bpar

 
##             Estimate se_notrans    t value     Pr(>t) Lower Upper
 ## Z0_0      9.7015e+01   3.553140 2.7304e+01 1.6793e-21    NA    NA
@@ -131,7 +138,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.

 
m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.2a.ff)

-

+

 
summary(m.Z.2a.ff, data = FALSE)$bpar

 
##            Estimate se_notrans t value     Pr(>t) Lower Upper
 ## Z0_0       97.01488   3.553145 27.3039 1.6793e-21    NA    NA
@@ -146,7 +153,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.

 
m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.3)

-

+

 
summary(m.Z.3, data = FALSE)$bpar

 
##      Estimate se_notrans t value     Pr(>t)    Lower   Upper
 ## Z0_0 97.01488   2.681772  36.176 2.3636e-25 91.52152 102.508
@@ -164,7 +171,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.

 
m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.5)

-

+

 
Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.

 
Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
@@ -175,10 +182,10 @@ FOCUS_2006_Z_mkin <- 
m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
                      parms.ini = m.Z.5$bparms.ode,
                      quiet = TRUE)

-
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge.
-## Convergence code is 1

+
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge:
+## false convergence (8)

 
plot_sep(m.Z.FOCUS)

-

+

 
summary(m.Z.FOCUS, data = FALSE)$bpar

 
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
 ## Z0_0       96.837112   2.058861 47.0343 5.5877e-44 92.703779 100.970445
@@ -215,7 +222,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.

 
m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.mkin.1)

-

+

 
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled

 
## NULL

 
Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.

@@ -225,7 +232,7 @@ FOCUS_2006_Z_mkin <- ## Successfully compiled differential equation model from auto-generated C code.
m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.mkin.3)
-

+

This results in a much better representation of the behaviour of the parent compound Z0.

Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.

Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
@@ -237,7 +244,7 @@ FOCUS_2006_Z_mkin <- parms.ini = m.Z.mkin.3$bparms.ode,
                       quiet = TRUE)
 plot_sep(m.Z.mkin.4)
-

+

The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.

Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
@@ -248,7 +255,7 @@ FOCUS_2006_Z_mkin <- parms.ini = m.Z.mkin.4$bparms.ode[1:4],
                       quiet = TRUE)
 plot_sep(m.Z.mkin.5)
-

+

The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.

m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                        parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
@@ -256,11 +263,11 @@ FOCUS_2006_Z_mkin <- fixed_parms = "k_Z3_bound_free",
                        quiet = TRUE)
 plot_sep(m.Z.mkin.5a)
-

+

As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.

A graphical representation of the confidence intervals can finally be obtained.

mkinparplot(m.Z.mkin.5a)
-

+

The endpoints obtained with this model are

endpoints(m.Z.mkin.5a)
## $ff
@@ -288,7 +295,6 @@ FOCUS_2006_Z_mkin <- FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 
 
-
 
   
 
@@ -320,5 +326,7 @@ FOCUS_2006_Z_mkin <- 
 
 
+  
+
   
 
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
index cb32b3c6..53f2ce85 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
index 7ce8a39c..90eab945 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
index 7a8f3fad..f44737ad 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
index b61de1fc..98562168 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
index 1e4c541d..27e7eb52 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
index dfe447ed..236cdbfe 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
index 8f7102aa..693c9c2c 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
index a0a00abb..180f44f9 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
index 783f7954..a67e9c1d 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
index 29824228..80452f9f 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
index 8eb7e968..e6ce97cd 100644
Binary files a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png and b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png differ
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 19cb806b..379176bf 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -8,8 +8,8 @@
 Performance benefit by using compiled model definitions in mkin • mkin
 
 
-
-
+
+
 
 
 
 
 
-    

+    

       

-  

+  

     

       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-21

-          

+            
2018-06-06

+      
+      
+      
+
+    

 
     
     
-

 

 

 Model that can also be solved with Eigenvalues

@@ -118,9 +125,9 @@ SFO_SFO <-   
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
+
+
+
 
 
 
@@ -40,7 +46,7 @@
   
 
   
-    

+    

       

       
 

@@ -99,21 +110,21 @@
       
       
 
-      

-  
Articles version 0.9.47.1

-

-
 

-  

+  

+    

+      
Articles

+    

+
     

       
All vignettes

       

 
       
@@ -133,6 +144,8 @@
       
    

 
+  
+
   
 
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 12ff2e98..28186062 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -8,8 +8,8 @@
 Introduction to mkin • mkin
 
 
-
-
+
+
 
 
 
 
 
-    

+    

       

-  

+  

     

       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-03-21

-          

+            
2018-06-06

+      
+      
+      
+
+    

 
     
     
-

 
Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany
Privatdozent at the University of Bremen

 

 

@@ -205,7 +212,6 @@ f_SFO_SFO_SFO <- http://www.jstatsoft.org/v33/i03/.

 

 

-

 

   

 
@@ -246,5 +252,7 @@ f_SFO_SFO_SFO <- 
 
-
-
+
+
 
 
 
 
 
-    

+    

       

-  

+  

     

       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-21

-          

+            
2018-06-06

+      
+      
+      
+
+    

 
     
     
-

 
Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (i.e. only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, i.e. the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.

 
Time weighted average concentrations for the SFO, FOMC and the DFOMP model are calculated using the formulas given in the FOCUS kinetics guidance (FOCUS Work Group on Degradation Kinetics 2014, 251):

 
SFO:

@@ -114,7 +121,6 @@
 

 
FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

 

-

 

   

 
@@ -135,5 +141,7 @@
       
 

 
+  
+
   
 
diff --git a/docs/authors.html b/docs/authors.html
index a9712678..492c3a18 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -21,13 +21,19 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
+
+
+
 
 
 
@@ -50,8 +56,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     

+
     
   

 

@@ -99,15 +110,15 @@
       
       
 
-      

-  

+

+  

     

       
Authors

     

 
     
    
       
  • 
-        
    Johannes Ranke. Author, maintainer, copyright holder. 
+        
    Johannes Ranke. Author, maintainer, copyright holder. 
         
    
       
    • 
       
  • 
@@ -141,6 +152,8 @@
       
    

 
+  
+
   
 
 
diff --git a/docs/docsearch.css b/docs/docsearch.css
new file mode 100644
index 00000000..e5f1fe1d
--- /dev/null
+++ b/docs/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+  Source: https://github.com/algolia/docsearch/
+  License: MIT
+*/
+
+.algolia-autocomplete {
+  display: block;
+  -webkit-box-flex: 1;
+  -ms-flex: 1;
+  flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+  width: 100%;
+  min-width: none;
+  max-width: none;
+  padding: .75rem 0;
+  background-color: #fff;
+  background-clip: padding-box;
+  border: 1px solid rgba(0, 0, 0, .1);
+  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+  .algolia-autocomplete .ds-dropdown-menu {
+      width: 175%
+  }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+  padding: 0;
+  background-color: rgb(255,255,255);
+  border: 0;
+  max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+  margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+  padding: 0;
+  overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+  padding: .125rem 1rem;
+  margin-top: 0;
+  font-size: 1.3em;
+  font-weight: 500;
+  color: #00008B;
+  border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+    float: none;
+    padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+  float: none;
+  width: auto;
+  padding: 0;
+  text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+  float: none;
+  width: auto;
+  padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+  padding-top: .75rem;
+  margin-top: .75rem;
+  border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+  display: block;
+  padding: .1rem 1rem;
+  margin-bottom: 0.1;
+  font-size: 1.0em;
+  font-weight: 400
+  /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+  display: block;
+  padding: .25rem 1rem;
+  margin-bottom: 0;
+  font-size: 0.9em;
+  font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+  padding: 0 1rem .5rem;
+  margin-top: -.25rem;
+  font-size: 0.8em;
+  font-weight: 400;
+  line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+  width: 110px;
+  height: 20px;
+  z-index: 3;
+  margin-top: 10.66667px;
+  float: right;
+  font-size: 0;
+  line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
+  background-image: url("data:image/svg+xml;utf8,");
+  background-repeat: no-repeat;
+  background-position: 50%;
+  background-size: 100%;
+  overflow: hidden;
+  text-indent: -9000px;
+  width: 100%;
+  height: 100%;
+  display: block;
+  transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+  color: #FF8C00;
+  background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 00000000..b35504cd
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+  // register a handler to move the focus to the search bar
+  // upon pressing shift + "/" (i.e. "?")
+  $(document).on('keydown', function(e) {
+    if (e.shiftKey && e.keyCode == 191) {
+      e.preventDefault();
+      $("#search-input").focus();
+    }
+  });
+
+  $(document).ready(function() {
+    // do keyword highlighting
+    /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+    var mark = function() {
+
+      var referrer = document.URL ;
+      var paramKey = "q" ;
+
+      if (referrer.indexOf("?") !== -1) {
+        var qs = referrer.substr(referrer.indexOf('?') + 1);
+        var qs_noanchor = qs.split('#')[0];
+        var qsa = qs_noanchor.split('&');
+        var keyword = "";
+
+        for (var i = 0; i < qsa.length; i++) {
+          var currentParam = qsa[i].split('=');
+
+          if (currentParam.length !== 2) {
+            continue;
+          }
+
+          if (currentParam[0] == paramKey) {
+            keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+          }
+        }
+
+        if (keyword !== "") {
+          $(".contents").unmark({
+            done: function() {
+              $(".contents").mark(keyword);
+            }
+          });
+        }
+      }
+    };
+
+    mark();
+  });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+  var words = [];
+
+  var hierarchy = hit._highlightResult.hierarchy;
+  // loop to fetch from lvl0, lvl1, etc.
+  for (var idx in hierarchy) {
+    words = words.concat(hierarchy[idx].matchedWords);
+  }
+
+  var content = hit._highlightResult.content;
+  if (content) {
+    words = words.concat(content.matchedWords);
+  }
+
+  // return unique words
+  var words_uniq = [...new Set(words)];
+  return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+  var words = matchedWords(hit);
+  var url = "";
+
+  if (hit.anchor) {
+    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+  } else {
+    url = hit.url + '?q=' + escape(words.join(" "));
+  }
+
+  return url;
+}
diff --git a/docs/index.html b/docs/index.html
index 9caba262..2a5f5107 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,8 @@
 Kinetic Evaluation of Chemical Degradation Data • mkin
 
 
-
-
+
+
 
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     

+
     
 
 
@@ -191,5 +206,7 @@
       
 

 
+  
+
   
 
diff --git a/docs/news/index.html b/docs/news/index.html
index c4605ae1..cc837f1e 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -6,7 +6,7 @@
 
 
 
-All news • mkin
+Changelog • mkin
 
 
 
@@ -21,13 +21,19 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
-
+
+
+
+
+
+
+
 
 
 
@@ -50,8 +56,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     

+
     
   

 

@@ -99,17 +110,17 @@
       
       
 
-      

-
-  

+

+  

     

-      
Change log All releases

+      
Changelog 

+      
     

 
-    

     

-

-mkin 0.9.47.1 (2018-02-06)

+

+mkin 0.9.47.1 (2018-02-06) 2018-02-06 
+

 
    
 
  • Skip some test on CRAN and winbuilder to avoid timeouts
    • 
 
  • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014
    • 
@@ -120,24 +131,27 @@
 

 

     

-

-mkin 0.9.46.3 (2017-11-16)

+

+mkin 0.9.46.3 (2017-11-16) 2017-11-16 
+

 
    
 
  • README.md, vignettes/mkin.Rmd: URLs were updated
    • 
 
  • synthetic_data_for_UBA: Add the code used to generate the data in the interest of reproducibility
    • 
 

 

     

-

-mkin 0.9.46.2 (2017-10-10)

+

+mkin 0.9.46.2 (2017-10-10) 2017-10-10 
+

 
    
 
  • Converted the vignette FOCUS_Z from tex/pdf to markdown/html
    • 
 
  • DESCRIPTION: Add ORCID
    • 
 

 

     

-

-mkin 0.9.46.1 (2017-09-14)

+

+mkin 0.9.46.1 (2017-09-14) 2017-09-14 
+

 
    
 
  • plot.mkinfit: Fix scaling of residual plots for the case of separate plots for each observed variable
    • 
 
  • plot.mkinfit: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable
    • 
@@ -145,15 +159,17 @@
 

 

     

-

-mkin 0.9.46 (2017-07-24)

+

+mkin 0.9.46 (2017-07-24) 2017-07-29 
+

 
    
 
  • Remove test_FOMC_ill-defined.R as it is too platform dependent
    • 
 

 

     

-

-mkin 0.9.45.2 (2017-07-24)

+

+mkin 0.9.45.2 (2017-07-24) 2017-07-22 
+

 
    
 
  • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package
    • 
 
  • Update URLs in documentation
    • 
@@ -162,8 +178,9 @@
 

 

     

-

-mkin 0.9.45.1 (2016-12-20)

+

+mkin 0.9.45.1 (2016-12-20) Unreleased 
+

 

 

 New features

@@ -173,8 +190,9 @@
 

 

     

-

-mkin 0.9.45 (2016-12-08)

+

+mkin 0.9.45 (2016-12-08) 2016-12-08 
+

 

 

 Minor changes

@@ -186,8 +204,9 @@
 

 

     

-

-mkin 0.9.44 (2016-06-29)

+

+mkin 0.9.44 (2016-06-29) 2016-06-29 
+

 

 

 Bug fixes

@@ -197,8 +216,9 @@
 

 

     

-

-mkin 0.9.43 (2016-06-28)

+

+mkin 0.9.43 (2016-06-28) 2016-06-28 
+

 

 

 Major changes

@@ -235,8 +255,9 @@
 

 

     

-

-mkin 0.9.42 (2016-03-25)

+

+mkin 0.9.42 (2016-03-25) 2016-03-25 
+

 

 

 Major changes

@@ -255,8 +276,9 @@
 

 

     

-

-mkin 0.9-41 (2015-11-09)

+

+mkin 0.9-41 (2015-11-09) 2015-11-09 
+

 

 

 Minor changes

@@ -277,8 +299,9 @@
 

 

     

-

-mkin 0.9-40 (2015-07-21)

+

+mkin 0.9-40 (2015-07-21) 2015-07-21 
+

 

 

 Bug fixes

@@ -297,8 +320,9 @@
 

 

     

-

-mkin 0.9-39 (2015-06-26)

+

+mkin 0.9-39 (2015-06-26) 2015-06-26 
+

 

 

 Major changes

@@ -317,8 +341,9 @@
 

 

     

-

-mkin 0.9-38 (2015-06-24)

+

+mkin 0.9-38 (2015-06-24) 2015-06-23 
+

 

 

 Minor changes

@@ -337,8 +362,9 @@
 

 

     

-

-mkin 0.9-36 (2015-06-21)

+

+mkin 0.9-36 (2015-06-21) 2015-06-21 
+

 

 

 Major changes

@@ -358,8 +384,9 @@
 

 

     

-

-mkin 0.9-35 (2015-05-15)

+

+mkin 0.9-35 (2015-05-15) 2015-05-15 
+

 

 

 Major changes

@@ -389,8 +416,9 @@
 

 

     

-

-mkin 0.9-34 (2014-11-22)

+

+mkin 0.9-34 (2014-11-22) 2014-11-22 
+

 

 

 New features

@@ -410,8 +438,9 @@
 

 

     

-

-mkin 0.9-33 (2014-10-22)

+

+mkin 0.9-33 (2014-10-22) 2014-10-12 
+

 

 

 New features

@@ -442,8 +471,9 @@
 

 

     

-

-mkin 0.9-32 (2014-07-24)

+

+mkin 0.9-32 (2014-07-24) 2014-07-24 
+

 

 

 New features

@@ -478,8 +508,9 @@
 

 

     

-

-mkin 0.9-31 (2014-07-14)

+

+mkin 0.9-31 (2014-07-14) 2014-07-14 
+

 

 

 Bug fixes

@@ -489,8 +520,9 @@
 

 

     

-

-mkin 0.9-30 (2014-07-11)

+

+mkin 0.9-30 (2014-07-11) 2014-07-11 
+

 

 

 New features

@@ -520,8 +552,9 @@
 

 

     

-

-mkin 0.9-29 (2014-06-27)

+

+mkin 0.9-29 (2014-06-27) 2014-06-27 
+

 
    
 
  • R/mkinresplot.R: Make it possible to specify xlim
    • 
 
  • R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function
    • 
@@ -529,8 +562,9 @@
 

 

     

-

-mkin 0.9-28 (2014-05-20)

+

+mkin 0.9-28 (2014-05-20) 2014-05-20 
+

 
    
 
  • Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set
    • 
 
  • Add historical remarks and some background to the main package vignette
    • 
@@ -538,8 +572,9 @@
 

 

     

-

-mkin 0.9-27 (2014-05-10)

+

+mkin 0.9-27 (2014-05-10) 2014-05-10 
+

 
    
 
  • Fork the GUI into a separate package gmkin
    • 
 
  • DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information
    • 
@@ -561,8 +596,9 @@
 

 

     

-

-mkin 0.9-24 (2013-11-06)

+

+mkin 0.9-24 (2013-11-06) 2013-11-06 
+

 
    
 
  • Bugfix re-enabling the fixing of any combination of initial values for state variables
    • 
 
  • Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions
    • 
@@ -570,8 +606,9 @@
 

 

     

-

-mkin 0.9-22 (2013-10-26)

+

+mkin 0.9-22 (2013-10-26) 2013-10-26 
+

 
    
 
  • Get rid of the optimisation step in mkinerrmin - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally
    • 
 
  • Fix plot.mkinfit as it passed graphical arguments like main to the solver
    • 
@@ -587,7 +624,6 @@
 

 
For a detailed list of changes to the mkin source please consult the commit history on http://github.com/jranke/mkin

 

-    

   

 
   
 
+  
+
   
 
 
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 181fe639..6ca2f37a 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -1,13 +1,32 @@
-/* Sticker footer */
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+  height: 100%;
+}
+
 body > .container {
   display: flex;
-  padding-top: 60px;
-  min-height: calc(100vh);
+  height: 100%;
   flex-direction: column;
+
+  padding-top: 60px;
 }
 
 body > .container .row {
-  flex: 1;
+  flex: 1 0 auto;
 }
 
 footer {
@@ -16,6 +35,7 @@ footer {
   border-top: 1px solid #e5e5e5;
   color: #666;
   display: flex;
+  flex-shrink: 0;
 }
 footer p {
   margin-bottom: 0;
@@ -38,6 +58,12 @@ img {
   max-width: 100%;
 }
 
+/* Typographic tweaking ---------------------------------*/
+
+.contents h1.page-header {
+  margin-top: calc(-60px + 1em);
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -68,7 +94,7 @@ a.anchor {
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
   padding-top: 60px;
-  margin-top: -60px;
+  margin-top: -40px;
 }
 
 /* Static header placement on mobile devices */
@@ -108,7 +134,6 @@ a.anchor {
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
-.ref-index h2 {font-size: 20px;}
 
 .ref-index td {vertical-align: top;}
 .ref-index .alias {width: 40%;}
@@ -192,3 +217,16 @@ a.sourceLine:hover {
 .hasCopyButton:hover button.btn-copy-ex {
   visibility: visible;
 }
+
+/* mark.js ----------------------------*/
+
+mark {
+  background-color: rgba(255, 255, 51, 0.5);
+  border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+  padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+  margin-bottom: 10px;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 64b20df4..de9bd724 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,94 +1,110 @@
-$(function() {
-
-  $("#sidebar")
-    .stick_in_parent({offset_top: 40})
-    .on('sticky_kit:bottom', function(e) {
-      $(this).parent().css('position', 'static');
-    })
-    .on('sticky_kit:unbottom', function(e) {
-      $(this).parent().css('position', 'relative');
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+  $(function() {
+
+    $("#sidebar")
+      .stick_in_parent({offset_top: 40})
+      .on('sticky_kit:bottom', function(e) {
+        $(this).parent().css('position', 'static');
+      })
+      .on('sticky_kit:unbottom', function(e) {
+        $(this).parent().css('position', 'relative');
+      });
+
+    $('body').scrollspy({
+      target: '#sidebar',
+      offset: 60
     });
 
-  $('body').scrollspy({
-    target: '#sidebar',
-    offset: 60
-  });
+    $('[data-toggle="tooltip"]').tooltip();
+
+    var cur_path = paths(location.pathname);
+    var links = $("#navbar ul li a");
+    var max_length = -1;
+    var pos = -1;
+    for (var i = 0; i < links.length; i++) {
+      if (links[i].getAttribute("href") === "#")
+        continue;
+      var path = paths(links[i].pathname);
+
+      var length = prefix_length(cur_path, path);
+      if (length > max_length) {
+        max_length = length;
+        pos = i;
+      }
+    }
 
-  var cur_path = paths(location.pathname);
-  $("#navbar ul li a").each(function(index, value) {
-    if (value.text == "Home")
-      return;
-    if (value.getAttribute("href") === "#")
-      return;
-
-    var path = paths(value.pathname);
-    if (is_prefix(cur_path, path)) {
-      // Add class to parent 
  • , and enclosing 
  •  if in dropdown
-      var menu_anchor = $(value);
+    // Add class to parent 
  • , and enclosing 
  •  if in dropdown
+    if (pos >= 0) {
+      var menu_anchor = $(links[pos]);
       menu_anchor.parent().addClass("active");
       menu_anchor.closest("li.dropdown").addClass("active");
     }
   });
-});
 
-function paths(pathname) {
-  var pieces = pathname.split("/");
-  pieces.shift(); // always starts with /
+  function paths(pathname) {
+    var pieces = pathname.split("/");
+    pieces.shift(); // always starts with /
+
+    var end = pieces[pieces.length - 1];
+    if (end === "index.html" || end === "")
+      pieces.pop();
+    return(pieces);
+  }
 
-  var end = pieces[pieces.length - 1];
-  if (end === "index.html" || end === "")
-    pieces.pop();
-  return(pieces);
-}
+  function prefix_length(needle, haystack) {
+    if (needle.length > haystack.length)
+      return(0);
 
-function is_prefix(needle, haystack) {
-  if (needle.length > haystack.lengh)
-    return(false);
+    // Special case for length-0 haystack, since for loop won't run
+    if (haystack.length === 0) {
+      return(needle.length === 0 ? 1 : 0);
+    }
 
-  for (var i = 0; i < haystack.length; i++) {
-    if (needle[i] != haystack[i])
-      return(false);
-  }
+    for (var i = 0; i < haystack.length; i++) {
+      if (needle[i] != haystack[i])
+        return(i);
+    }
 
-  return(true);
-}
+    return(haystack.length);
+  }
 
-/* Clipboard --------------------------*/
+  /* Clipboard --------------------------*/
 
-function changeTooltipMessage(element, msg) {
-  var tooltipOriginalTitle=element.getAttribute('data-original-title');
-  element.setAttribute('data-original-title', msg);
-  $(element).tooltip('show');
-  element.setAttribute('data-original-title', tooltipOriginalTitle);
-}
+  function changeTooltipMessage(element, msg) {
+    var tooltipOriginalTitle=element.getAttribute('data-original-title');
+    element.setAttribute('data-original-title', msg);
+    $(element).tooltip('show');
+    element.setAttribute('data-original-title', tooltipOriginalTitle);
+  }
 
-if(Clipboard.isSupported()) {
-  $(document).ready(function() {
-    var copyButton = "";
+  if(Clipboard.isSupported()) {
+    $(document).ready(function() {
+      var copyButton = "";
 
-    $(".examples").addClass("hasCopyButton");
+      $(".examples, div.sourceCode").addClass("hasCopyButton");
 
-    // Insert copy buttons:
-    $(copyButton).prependTo(".hasCopyButton");
+      // Insert copy buttons:
+      $(copyButton).prependTo(".hasCopyButton");
 
-    // Initialize tooltips:
-    $('.btn-copy-ex').tooltip({container: 'body'});
+      // Initialize tooltips:
+      $('.btn-copy-ex').tooltip({container: 'body'});
 
-    // Initialize clipboard:
-    var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
-      text: function(trigger) {
-        return trigger.parentNode.textContent;
-      }
-    });
+      // Initialize clipboard:
+      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+        text: function(trigger) {
+          return trigger.parentNode.textContent;
+        }
+      });
 
-    clipboardBtnCopies.on('success', function(e) {
-      changeTooltipMessage(e.trigger, 'Copied!');
-      e.clearSelection();
-    });
+      clipboardBtnCopies.on('success', function(e) {
+        changeTooltipMessage(e.trigger, 'Copied!');
+        e.clearSelection();
+      });
 
-    clipboardBtnCopies.on('error', function() {
-      changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on('error', function() {
+        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      });
     });
-  });
-}
-
+  }
+})(window.jQuery || window.$)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 974e3585..485b80de 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,20 +1,11 @@
 pandoc: 1.19.2.4
-pkgdown: 0.1.0.9000
+pkgdown: 1.1.0
 pkgdown_sha: ~
 articles:
   FOCUS_D: FOCUS_D.html
-  FOCUS_D.html: FOCUS_D.html
   FOCUS_L: FOCUS_L.html
-  FOCUS_L.html: FOCUS_L.html
   FOCUS_Z: FOCUS_Z.html
-  FOCUS_Z.html: FOCUS_Z.html
-  FOCUS_Z.pdf: FOCUS_Z.pdf
   compiled_models: compiled_models.html
-  compiled_models.html: compiled_models.html
   mkin: mkin.html
-  mkin.html: mkin.html
-  mkin_vignettes.css: mkin_vignettes.css
-  references.bib: references.bib
   twa: twa.html
-  twa.html: twa.html
 
diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png
index e9268f94..0fbc1da1 100644
Binary files a/docs/reference/DFOP.solution-1.png and b/docs/reference/DFOP.solution-1.png differ
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index b1b3cf50..cd8f29e9 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -21,17 +21,23 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -54,8 +60,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    • 
+
     
   
    
 
    
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Double First-Order in Parallel kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing decline from a defined starting value using the sum
   of two exponential decline functions.
    
     
+    
    
 
     
    DFOP.solution(t, parent.0, k1, k2, g)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
@@ -156,7 +171,7 @@
     
 
     
    Examples
    
-    
      plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
    
+    
      plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
    
 
+  
+
   
 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 2a3b1c78..deb418c2 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,20 +113,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Subsetting method for mmkin objects
    
+    
+    
     
    
 
+    
    
     
     
    Subsetting method for mmkin objects.
    
     
+    
    
 
     
    # S3 method for mmkin
 [(x, i, j, ..., drop = FALSE)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -262,8 +277,8 @@
 #> [1] 29
 #> 
 #> $time
-#>    user  system elapsed 
-#>   0.242   0.000   0.244 
+#>        User      System verstrichen 
+#>       0.179       0.000       0.184 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -452,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x5555578ff9d0>
-#> <environment: 0x555559a0da40>
+#> <bytecode: 0x55555b9b9d58>
+#> <environment: 0x55555be59518>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -475,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559b90d60>
-#> <environment: 0x555559a0da40>
+#> <bytecode: 0x55555c2673f8>
+#> <environment: 0x55555be59518>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -495,7 +510,7 @@
 #> 
 #> $fixed
 #> [1] value type 
-#> <0 rows> (or 0-length row.names)
+#> <0 Zeilen> (oder row.names mit Länge 0)
 #> 
 #> $data
 #>   time variable observed   predicted    residual
@@ -543,13 +558,13 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Wed Mar 21 18:14:20 2018"
+#> [1] "Wed Jun  6 01:21:24 2018"
 #> 
 #> $version
 #> [1] "0.9.47.1"
 #> 
 #> $Rversion
-#> [1] "3.4.4"
+#> [1] "3.5.0"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
@@ -584,6 +599,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index f392bf64..78caf48d 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -57,8 +63,12 @@ in this fit." />
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -106,12 +117,15 @@ in this fit." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
    
+    
+    
     
    
 
+    
    
     
     
    A table with the fitted parameters and the resulting DT50 and DT90 values
 generated with different software packages. Taken directly from FOCUS (2006).
@@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as
 the initial concentration of the parent compound was fixed to a value of 100
 in this fit.
    
     
+    
    
 
     
    FOCUS_2006_DFOP_ref_A_to_B
    
         
@@ -173,6 +188,8 @@ in this fit.
    
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 6e4c8d64..c854c11c 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -57,8 +63,12 @@ in this fit." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -106,12 +117,15 @@ in this fit." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
    
+    
+    
     
    
 
+    
    
     
     
    A table with the fitted parameters and the resulting DT50 and DT90 values
 generated with different software packages. Taken directly from FOCUS (2006).
@@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as
 the initial concentration of the parent compound was fixed to a value of 100
 in this fit.
    
     
+    
    
 
     
    FOCUS_2006_FOMC_ref_A_to_F
    
         
@@ -172,6 +187,8 @@ in this fit.
    
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index ed38ccae..89ee9ae9 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -57,8 +63,12 @@ in this fit." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -106,12 +117,15 @@ in this fit." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Results of fitting the HS model to Datasets A to F of FOCUS (2006)
    
+    
+    
     
    
 
+    
    
     
     
    A table with the fitted parameters and the resulting DT50 and DT90 values
 generated with different software packages. Taken directly from FOCUS (2006).
@@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as
 the initial concentration of the parent compound was fixed to a value of 100
 in this fit.
    
     
+    
    
 
     
    FOCUS_2006_HS_ref_A_to_F
    
         
@@ -173,6 +188,8 @@ in this fit.
    
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 107f3e5f..182c7003 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -57,8 +63,12 @@ in this fit." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -106,12 +117,15 @@ in this fit." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
    
+    
+    
     
    
 
+    
    
     
     
    A table with the fitted parameters and the resulting DT50 and DT90 values
 generated with different software packages. Taken directly from FOCUS (2006).
@@ -119,6 +133,7 @@ The results from fitting the data with the Topfit software was removed, as
 the initial concentration of the parent compound was fixed to a value of 100
 in this fit.
    
     
+    
    
 
     
    FOCUS_2006_SFO_ref_A_to_F
    
         
@@ -171,6 +186,8 @@ in this fit.
    
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index cc310ee3..aa84e14b 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -21,16 +21,22 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -53,8 +59,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -102,15 +113,19 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Datasets A to F from the FOCUS Kinetics report from 2006
    
+    
+    
     
    
 
+    
    
     
     
    Data taken from FOCUS (2006), p. 258.
    
     
+    
    
 
     
    FOCUS_2006_datasets
    
         
@@ -169,6 +184,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png
index f10cff4e..127f3085 100644
Binary files a/docs/reference/FOMC.solution-1.png and b/docs/reference/FOMC.solution-1.png differ
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 397dc82d..4b8f1c92 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -57,8 +63,12 @@ The form given here differs slightly from the original reference by Gustafson
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -106,12 +117,15 @@ The form given here differs slightly from the original reference by Gustafson
       
       
 
-      
    
+
    
   
    
     
    
     
    First-Order Multi-Compartment kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing exponential decline from a defined starting value, with 
   a decreasing rate constant.
    
@@ -119,10 +133,11 @@ The form given here differs slightly from the original reference by Gustafson
   and Holden (1990). The parameter beta corresponds to 1/beta in the
   original equation.
    
     
+    
    
 
     
    FOMC.solution(t, parent.0, alpha, beta)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
 
 
 
 
 
    
@@ -168,7 +183,7 @@ The form given here differs slightly from the original reference by Gustafson
     
 
     
    Examples
    
-    
      plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
    
+    
      plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
    
 
+  
+
   
 
diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png
index 5e04d343..4dc42c31 100644
Binary files a/docs/reference/HS.solution-1.png and b/docs/reference/HS.solution-1.png differ
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index f633aa67..d06a839e 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Hockey-Stick kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing two exponential decline functions with a break point
   between them.
    
     
+    
    
 
     
    HS.solution(t, parent.0, k1, k2, tb)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -157,7 +172,7 @@
     
 
     
    Examples
    
-    
      plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
    
+    
      plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
    
 
+  
+
   
 
diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png
index e421d562..d8b6e8e3 100644
Binary files a/docs/reference/IORE.solution-1.png and b/docs/reference/IORE.solution-1.png differ
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 687dee5a..c037a8d2 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Indeterminate order rate equation kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing exponential decline from a defined starting value, with 
   a concentration dependent rate constant.
    
     
+    
    
 
     
    IORE.solution(t, parent.0, k__iore, N)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -157,7 +172,7 @@
 
     
    Examples
      plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
-                                       ylim = c(0, 100))
      fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+                                       ylim = c(0, 100))
      fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
   fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
   fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
 
@@ -200,6 +215,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 1156c16f..32ef9f29 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -21,16 +21,22 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -53,8 +59,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
+
     
   
 
@@ -102,19 +113,23 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Single First-Order kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing exponential decline from a defined starting value.
    
     
+    
    
 
     
    SFO.solution(t, parent.0, k)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
     
    
@@ -176,6 +191,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 6901c435..aee32558 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -57,8 +63,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -106,12 +117,15 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Single First-Order Reversible Binding kinetics
    
+    
+    
     
    
 
+    
    
     
     
    Function describing the solution of the differential equations describing
   the kinetic model with first-order terms for a two-way transfer from a free
@@ -119,10 +133,11 @@
   fraction.  The initial condition is a defined amount in the free fraction and
   no substance in the bound fraction.
    
     
+    
    
 
     
    SFORB.solution(t, parent.0, k_12, k_21, k_1output)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -193,6 +208,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
index fecfc52d..d099898c 100644
Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ
diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png
index 907001ed..f6de95a0 100644
Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ
diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png
index 3786d934..13f54e65 100644
Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 6d830113..063234b3 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -21,18 +21,24 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -55,8 +61,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -104,23 +115,27 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Add normally distributed errors to simulated kinetic degradation data
    
+    
+    
     
    
 
+    
    
     
     
    Normally distributed errors are added to data predicted for a specific
   degradation model using mkinpredict. The variance of the error
   may depend on the predicted value and is specified as a standard deviation.
    
     
+    
    
 
     
    add_err(prediction, sdfunc, secondary = c("M1", "M2"),
           n = 1000, LOD = 0.1, reps = 2,
           digits = 1, seed = NA)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -204,14 +219,14 @@
                    d_SFO_SFO_err, cores=1,
                    quiet=TRUE, method.modFit="Marq")
 
-plot(f_SFO_SFO)
    
+plot(f_SFO_SFO)
    
 # We would like to inspect the fit for dataset 3 more closely
 # Using double brackets makes the returned object an mkinfit object
 # instead of a list of mkinfit objects, so plot.mkinfit is used
-plot(f_SFO_SFO[[3]], show_residuals = TRUE)
    
+plot(f_SFO_SFO[[3]], show_residuals = TRUE)
    
 # If we use single brackets, we should give two indices (model and dataset),
 # and plot.mmkin is used
-plot(f_SFO_SFO[1, 3])
    
+plot(f_SFO_SFO[1, 3])
    
 
    
 
+  
+
   
 
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 0f5ba0a4..b10998fb 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -56,8 +62,12 @@ with the advantage that the SFORB model can also be used for metabolites." />
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -105,22 +116,26 @@ with the advantage that the SFORB model can also be used for metabolites." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to calculate endpoints for further use from kinetic models fitted with mkinfit
    
+    
+    
     
    
 
+    
    
     
     
    This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
 fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
 the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
 with the advantage that the SFORB model can also be used for metabolites.
    
     
+    
    
 
     
    endpoints(fit)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
          
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -182,6 +197,8 @@ with the advantage that the SFORB model can also be used for metabolites.
    
 
+  
+
   
 
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 9d91b5a8..90b6fd9d 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,19 +113,23 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Calculate the geometric mean
    
+    
+    
     
    
 
+    
    
     
     
    Function calculating the geometric mean of numeric vectors
    
     
+    
    
 
     
    geometric_mean(x, na.rm = FALSE)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
       
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -160,6 +175,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 33d749ce..8f337595 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,20 +113,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to perform isometric log-ratio transformation
    
+    
+    
     
    
 
+    
    
     
     
    This implementation is a special case of the class of isometric log-ratio transformations.
    
     
+    
    
 
     
    ilr(x)
   invilr(x)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -136,7 +151,7 @@
     
     
    See also
    
 
-    
    Another implementation can be found in R package robCompositions.
    
+    
    Another implementation can be found in R package robCompositions.
    Examples
    
@@ -184,6 +199,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6c05941d..5785b5aa 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -21,13 +21,19 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -50,8 +56,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -99,330 +110,326 @@
       
       
 
-      
    
-  
    
+
    
+  
    
     
    
-      
    
-        Reference
-        version 0.9.47.1
-      
    
+      
    Reference
    
     
    
 
-    
    
-      
    
     
     
    
     
 
     
    
 
 
 
 
 
         
       
     
   
 
    
+    
    
 
-      -        -        -      
+    +      
+      +      +    
 
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-      
-        
-          
-        
-        
-          
-          
-          
-        
-      
-      
    






    
-            
    Main functions
    
-            
    Essential functionality
    
-          
    
-            
    mkinmod 
    
-          
    Function to set up a kinetic model with one or more state variables
    
-            
    mkinfit 
    
-          
    Fit a kinetic model to data with one or more state variables
    
-            
    mmkin 
    
-          
    Fit one or more kinetic models with one or more state variables to one or more datasets
    
-            
    Show results
    
-            
    Functions working with mkinfit objects
    
-          
    
-            
    plot.mkinfit 
    
-          
    Plot the observed data and the fitted model of an mkinfit object
    
-            
    summary print 
    
-          
    Summary method for class "mkinfit"
    
-            
    mkinresplot 
    
-          
    Function to plot residuals stored in an mkin object
    
-            
    mkinparplot 
    
-          
    Function to plot the confidence intervals obtained using mkinfit
    
-            
    endpoints 
    
-          
    Function to calculate endpoints for further use from kinetic models fitted with mkinfit
    
-            
    mkinerrmin 
    
-          
    Calculate the minimum error to assume in order to pass the variance test
    
-            
    Work with mmkin objects
    
-            
    Functions working with aggregated results
    
-          
    
-            
    [.mmkin 
    
-          
    Subsetting method for mmkin objects
    
-            
    plot 
    
-          
    Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
    
-            
    Datasets and known results
    
-            
    
-          
    
-            
    FOCUS_2006_datasets 
    
-          
    Datasets A to F from the FOCUS Kinetics report from 2006
    
-            
    FOCUS_2006_SFO_ref_A_to_F 
    
-          
    Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
    
-            
    FOCUS_2006_FOMC_ref_A_to_F 
    
-          
    Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
    
-            
    FOCUS_2006_HS_ref_A_to_F 
    
-          
    Results of fitting the HS model to Datasets A to F of FOCUS (2006)
    
-            
    FOCUS_2006_DFOP_ref_A_to_B 
    
-          
    Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
    
-            
    mccall81_245T 
    
-          
    Datasets on aerobic soil metabolism of 2,4,5-T in six soils
    
-            
    schaefer07_complex_case 
    
-          
    Metabolism data set used for checking the software quality of KinGUI
    
-            
    synthetic_data_for_UBA_2014 
    
-          
    Synthetic datasets for one parent compound with two metabolites
    
-            
    test_data_from_UBA_2014 
    
-          
    Three experimental datasets from two water sediment systems and one soil
    
-            
    mkinds 
    
-          
    A dataset class for mkin
    
-            
    print 
    
-          
    Print mkinds objects
    
-            
    Helper functions
    
-            
    
-          
    
-            
    geometric_mean 
    
-          
    Calculate the geometric mean
    
-            
    mkinsub 
    
-          
    Function to set up a kinetic submodel for one state variable
    
-            
    max_twa_parent 
    
-          
    Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
    
-            
    mkinpredict 
    
-          
    Produce predictions from a kinetic model using specific parameters
    
-            
    mkin_wide_to_long 
    
-          
    Convert a dataframe with observations over time into long format
    
-            
    mkin_long_to_wide 
    
-          
    Convert a dataframe from long to wide format
    
-            
    print 
    
-          
    Print mkinmod objects
    
-            
    transform_odeparms backtransform_odeparms 
    
-          
    Functions to transform and backtransform kinetic parameters for fitting
    
-            
    ilr invilr 
    
-          
    Function to perform isometric log-ratio transformation
    
-            
    sigma_rl 
    
-          
    Two component error model of Rocke and Lorenzato
    
-            
    Analytical solutions
    
-            
    Parent only model solutions
    
-          
    
-            
    SFO.solution 
    
-          
    Single First-Order kinetics
    
-            
    FOMC.solution 
    
-          
    First-Order Multi-Compartment kinetics
    
-            
    DFOP.solution 
    
-          
    Double First-Order in Parallel kinetics
    
-            
    SFORB.solution 
    
-          
    Single First-Order Reversible Binding kinetics
    
-            
    HS.solution 
    
-          
    Hockey-Stick kinetics
    
-            
    IORE.solution 
    
-          
    Indeterminate order rate equation kinetics
    
-            
    Generate synthetic datasets
    
-            
    
-          
    
-            
    add_err 
    
-          
    Add normally distributed errors to simulated kinetic degradation data
    
-            
    Deprecated functions
    
-            
    Functions that have been superseeded
    
-          
    
-            
    mkinplot 
    
-          
    Plot the observed data and the fitted model of an mkinfit object
    
-    
    
+    
+      
+        
+          
    Main functions
    
+          
    Essential functionality
    
+        
+      
+      
+        
+        
+          
    mkinmod() 
    
+        
+        
    Function to set up a kinetic model with one or more state variables
    
+      
+        
+        
+          
    mkinfit() 
    
+        
+        
    Fit a kinetic model to data with one or more state variables
    
+      
+        
+        
+          
    mmkin() 
    
+        
+        
    Fit one or more kinetic models with one or more state variables to one or more datasets
    
+      
+    
+      
+        
+          
    Show results
    
+          
    Functions working with mkinfit objects
    
+        
+      
+      
+        
+        
+          
    plot(<mkinfit>) plot_sep() 
    
+        
+        
    Plot the observed data and the fitted model of an mkinfit object
    
+      
+        
+        
+          
    summary(<mkinfit>) print(<summary.mkinfit>) 
    
+        
+        
    Summary method for class "mkinfit"
    
+      
+        
+        
+          
    mkinresplot() 
    
+        
+        
    Function to plot residuals stored in an mkin object
    
+      
+        
+        
+          
    mkinparplot() 
    
+        
+        
    Function to plot the confidence intervals obtained using mkinfit
    
+      
+        
+        
+          
    endpoints() 
    
+        
+        
    Function to calculate endpoints for further use from kinetic models fitted with mkinfit
    
+      
+        
+        
+          
    mkinerrmin() 
    
+        
+        
    Calculate the minimum error to assume in order to pass the variance test
    
+      
+    
+      
+        
+          
    Work with mmkin objects
    
+          
    Functions working with aggregated results
    
+        
+      
+      
+        
+        
+          
    `[`(<mmkin>) 
    
+        
+        
    Subsetting method for mmkin objects
    
+      
+        
+        
+          
    plot(<mmkin>) 
    
+        
+        
    Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
    
+      
+    
+      
+        
+          
    Datasets and known results
    
+          
    
+        
+      
+      
+        
+        
+          
    FOCUS_2006_datasets 
    
+        
+        
    Datasets A to F from the FOCUS Kinetics report from 2006
    
+      
+        
+        
+          
    FOCUS_2006_SFO_ref_A_to_F 
    
+        
+        
    Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
    
+      
+        
+        
+          
    FOCUS_2006_FOMC_ref_A_to_F 
    
+        
+        
    Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
    
+      
+        
+        
+          
    FOCUS_2006_HS_ref_A_to_F 
    
+        
+        
    Results of fitting the HS model to Datasets A to F of FOCUS (2006)
    
+      
+        
+        
+          
    FOCUS_2006_DFOP_ref_A_to_B 
    
+        
+        
    Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
    
+      
+        
+        
+          
    mccall81_245T 
    
+        
+        
    Datasets on aerobic soil metabolism of 2,4,5-T in six soils
    
+      
+        
+        
+          
    schaefer07_complex_case 
    
+        
+        
    Metabolism data set used for checking the software quality of KinGUI
    
+      
+        
+        
+          
    synthetic_data_for_UBA_2014 
    
+        
+        
    Synthetic datasets for one parent compound with two metabolites
    
+      
+        
+        
+          
    test_data_from_UBA_2014 
    
+        
+        
    Three experimental datasets from two water sediment systems and one soil
    
+      
+        
+        
+          
    mkinds 
    
+        
+        
    A dataset class for mkin
    
+      
+        
+        
+          
    print(<mkinds>) 
    
+        
+        
    Print mkinds objects
    
+      
+    
+      
+        
+          
    Helper functions
    
+          
    
+        
+      
+      
+        
+        
+          
    geometric_mean() 
    
+        
+        
    Calculate the geometric mean
    
+      
+        
+        
+          
    mkinsub() 
    
+        
+        
    Function to set up a kinetic submodel for one state variable
    
+      
+        
+        
+          
    max_twa_parent() 
    
+        
+        
    Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
    
+      
+        
+        
+          
    mkinpredict() 
    
+        
+        
    Produce predictions from a kinetic model using specific parameters
    
+      
+        
+        
+          
    mkin_wide_to_long() 
    
+        
+        
    Convert a dataframe with observations over time into long format
    
+      
+        
+        
+          
    mkin_long_to_wide() 
    
+        
+        
    Convert a dataframe from long to wide format
    
+      
+        
+        
+          
    print(<mkinmod>) 
    
+        
+        
    Print mkinmod objects
    
+      
+        
+        
+          
    transform_odeparms() backtransform_odeparms() 
    
+        
+        
    Functions to transform and backtransform kinetic parameters for fitting
    
+      
+        
+        
+          
    ilr() invilr() 
    
+        
+        
    Function to perform isometric log-ratio transformation
    
+      
+        
+        
+          
    sigma_rl() 
    
+        
+        
    Two component error model of Rocke and Lorenzato
    
+      
+    
+      
+        
+          
    Analytical solutions
    
+          
    Parent only model solutions
    
+        
+      
+      
+        
+        
+          
    SFO.solution() 
    
+        
+        
    Single First-Order kinetics
    
+      
+        
+        
+          
    FOMC.solution() 
    
+        
+        
    First-Order Multi-Compartment kinetics
    
+      
+        
+        
+          
    DFOP.solution() 
    
+        
+        
    Double First-Order in Parallel kinetics
    
+      
+        
+        
+          
    SFORB.solution() 
    
+        
+        
    Single First-Order Reversible Binding kinetics
    
+      
+        
+        
+          
    HS.solution() 
    
+        
+        
    Hockey-Stick kinetics
    
+      
+        
+        
+          
    IORE.solution() 
    
+        
+        
    Indeterminate order rate equation kinetics
    
+      
+    
+      
+        
+          
    Generate synthetic datasets
    
+          
    
+        
+      
+      
+        
+        
+          
    add_err() 
    
+        
+        
    Add normally distributed errors to simulated kinetic degradation data
    
+      
+    
+      
+        
+          
    Deprecated functions
    
+          
    Functions that have been superseeded
    
+        
+      
+      
+        
+        
+          
    mkinplot() 
    
+        
+        
    Plot the observed data and the fitted model of an mkinfit object
    
+      
+    
+    
   
    
 
   
 
+  
+
   
 
 
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 696ca729..7b3ef8ea 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -57,8 +63,12 @@ guidance." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
 
    
@@ -106,12 +117,15 @@ guidance." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
    
+    
+    
     
    
 
+    
    
     
     
    This function calculates maximum moving window time weighted average concentrations
 (TWAs) for kinetic models fitted with mkinfit. Currently, only
@@ -119,10 +133,11 @@ calculations for the parent are implemented for the SFO, FOMC and DFOP models,
 using the analytical formulas given in the PEC soil section of the FOCUS
 guidance.
    
     
+    
    
 
     
    max_twa_parent(fit, windows)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
@@ -184,6 +199,8 @@ guidance.
    
 
+  
+
   
 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cb70e68c..3326a225 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -21,18 +21,24 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -55,8 +61,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -104,17 +115,21 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Datasets on aerobic soil metabolism of 2,4,5-T in six soils
    
+    
+    
     
    
 
+    
    
     
     
    Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
  2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
  extracts.
    
     
+    
    
 
     
    mccall81_245T
    
         
@@ -150,9 +165,9 @@
                  parms.ini = c(k_phenol_sink = 0),
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.4 
-#> Date of fit:     Wed Mar 21 18:14:30 2018 
-#> Date of summary: Wed Mar 21 18:14:30 2018 
+#> R version used for fitting:       3.5.0 
+#> Date of fit:     Wed Jun  6 01:21:34 2018 
+#> Date of summary: Wed Jun  6 01:21:34 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -162,7 +177,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.403 s
+#> Fitted with method Port using 246 model solutions performed in 1.452 s
 #> 
 #> Weighting: none
 #> 
@@ -270,6 +285,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 3c498a76..7f4431f5 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -21,18 +21,24 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -55,8 +61,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -104,21 +115,25 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Convert a dataframe from long to wide format
    
+    
+    
     
    
 
+    
    
     
     
    This function takes a dataframe in the long form as required by modCost
   and converts it into a dataframe with one independent variable and several
   dependent variables as columns.
    
     
+    
    
 
     
    mkin_long_to_wide(long_data, time = "time", outtime = "time")
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
       
    
 
 
 
 
 
 
 
 
         
       
     
   
 
 
    
@@ -196,6 +211,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index f40cb7cf..d52f582b 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Convert a dataframe with observations over time into long format
    
+    
+    
     
    
 
+    
    
     
     
    This function simply takes a dataframe with one independent variable and several
   dependent variable and converts it into the long form as required by modCost.
    
     
+    
    
 
     
    mkin_wide_to_long(wide_data, time = "t")
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -174,6 +189,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 7f5ec78e..43cd51f7 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,15 +113,19 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    A dataset class for mkin
    
+    
+    
     
    
 
+    
    
     
     
    A dataset class for mkin
    
     
+    
    
 
     
    mkinds
    
         
@@ -162,6 +177,8 @@ in order to be compatible with mkinfit
    
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index f172cba1..e6fd8807 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -21,17 +21,23 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -54,8 +60,12 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -103,20 +114,24 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Calculate the minimum error to assume in order to pass the variance test
    
+    
+    
     
    
 
+    
    
     
     
    This function finds the smallest relative error still resulting in passing the
 chi-squared test as defined in the FOCUS kinetics report from 2006.
    
     
+    
    
 
     
    mkinerrmin(fit, alpha = 0.05)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
 
    
@@ -198,6 +213,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.
    
 
+  
+
   
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8ac8295f..d0b54098 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+  using the argument reweight.method = "obs"." />
 
+
+
+
 
 
@@ -63,8 +69,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -112,12 +123,15 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Fit a kinetic model to data with one or more state variables
    
+    
+    
     
    
 
+    
    
     
     
    This function uses the Flexible Modelling Environment package
   FME to create a function calculating the model cost, i.e. the
@@ -131,6 +145,7 @@
   observed variable can optionally be iteratively reweighted until convergence
   using the argument reweight.method = "obs".
    
     
+    
    
 
     
    mkinfit(mkinmod, observed,
   parms.ini = "auto",
@@ -154,7 +169,7 @@
   reweight.tol = 1e-8, reweight.max.iter = 10,
   trace_parms = FALSE, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
       
    
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -384,10 +399,10 @@
     
     
    See also
    
 
-    
    Plotting methods plot.mkinfit and
+    
    Plotting methods plot.mkinfit and
   mkinparplot.
    
 
    Fitting of several models to several datasets in a single call to
-  mmkin.
    
+  mmkin.
    Note
    
 
@@ -413,16 +428,16 @@
     
    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.4 
-#> Date of fit:     Wed Mar 21 18:14:33 2018 
-#> Date of summary: Wed Mar 21 18:14:33 2018 
+#> R version used for fitting:       3.5.0 
+#> Date of fit:     Wed Jun  6 01:21:36 2018 
+#> Date of summary: Wed Jun  6 01:21:36 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.14 s
+#> Fitted with method Port using 64 model solutions performed in 0.143 s
 #> 
 #> Weighting: none
 #> 
@@ -490,8 +505,8 @@
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
-                           solution_type = "eigen", quiet = TRUE)))
    #>    user  system elapsed 
-#>   0.834   0.000   0.835 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+                           solution_type = "eigen", quiet = TRUE)))
    #>        User      System verstrichen 
+#>       0.927       0.000       0.929 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
    endpoints(fit)
    #> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -597,6 +612,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 7d3c0f94..04050367 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -58,8 +64,12 @@ For the definition of model types and their parameters, the equations given
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
+
     
   
 
@@ -107,12 +118,15 @@ For the definition of model types and their parameters, the equations given
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to set up a kinetic model with one or more state variables
    
+    
+    
     
    
 
+    
    
     
     
    The function usually takes several expressions, each assigning a compound name to 
   a list, specifying the kinetic model type and reaction or transfer to other
@@ -121,10 +135,11 @@ For the definition of model types and their parameters, the equations given
 
    For the definition of model types and their parameters, the equations given
   in the FOCUS and NAFTA guidance documents are used.
    
     
+    
    
 
     
    mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
     
     
    
@@ -262,6 +277,8 @@ For the definition of model types and their parameters, the equations given
       
 
+  
+
   
 
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index 1e7603d7..ba7212c5 100644
Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 81f52fc3..5a843c0e 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to plot the confidence intervals obtained using mkinfit
    
+    
+    
     
    
 
+    
    
     
     
    This function plots the confidence intervals for the parameters
   fitted using mkinfit.
    
     
+    
    
 
     
    mkinparplot(object)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -135,7 +150,7 @@
   T245=mkinsub("SFO", to=c("phenol"), sink=FALSE),
   phenol=mkinsub("SFO", to=c("anisole")),
   anisole=mkinsub("SFO"), use_of_ff="max")
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-mkinparplot(fit)
    
+mkinparplot(fit)
    
 
+  
+
   
 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index cfd72521..3a55ceae 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,19 +113,23 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Plot the observed data and the fitted model of an mkinfit object
    
+    
+    
     
    
 
+    
    
     
     
    Deprecated function. It now only calls the plot method plot.mkinfit.
    
     
+    
    
 
     
    mkinplot(fit, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
                  
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -160,6 +175,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 4768215b..946e0dfc 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -21,18 +21,24 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -55,8 +61,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -104,23 +115,27 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Produce predictions from a kinetic model using specific parameters
    
+    
+    
     
    
 
+    
    
     
     
    This function produces a time series for all the observed variables in a
   kinetic model as specified by mkinmod, using a specific set of
   kinetic parameters and initial values for the state variables.
    
     
+    
    
 
     
    mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
               use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
         map_output = TRUE, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -305,18 +320,18 @@
     print(mkinpredict(SFO_SFO, c(k_parent_m1=0.05, k_parent_sink=0.1, k_m1_sink=0.01),
                 c(parent=100, m1=0), seq(0, 20, by=0.1),
                 solution_type="eigen")[201,]))
    #>     time   parent       m1
-#> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.003   0.000   0.003 
      system.time(
+#> 201   20 4.978707 27.46227
    #>        User      System verstrichen 
+#>       0.004       0.000       0.004 
      system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
    #>     time   parent       m1
-#> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.002   0.000   0.001 
      system.time(
+#> 201   20 4.978707 27.46227
    #>        User      System verstrichen 
+#>       0.002       0.000       0.002 
      system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
    #>     time   parent       m1
-#> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.033   0.000   0.032 
    
+#> 201   20 4.978707 27.46227
    #>        User      System verstrichen 
+#>       0.035       0.000       0.035 
    
 
+  
+
   
 
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index 5b201616..b53869c7 100644
Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index df83f693..c288bf7c 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -56,8 +62,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -105,18 +116,22 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to plot residuals stored in an mkin object
    
+    
+    
     
    
 
+    
    
     
     
    This function plots the residuals for the specified subset of the 
   observed variables from an mkinfit object. A combined plot of the fitted
   model and the residuals can be obtained using plot.mkinfit
   using the argument show_residuals = TRUE.
    
     
+    
    
 
     
    mkinresplot(object,
     obs_vars = names(object$mkinmod$map),
@@ -124,7 +139,7 @@
     xlab = "Time", ylab = "Residual",
     maxabs = "auto", legend = TRUE, lpos = "topright", ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
                  
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -174,13 +189,13 @@
     
     
    See also
    
 
-    
    mkinplot, for a way to plot the data and the fitted lines of the
- mkinfit object.
    
+    
    mkinplot, for a way to plot the data and the fitted lines of the
+ mkinfit object.
    Examples
    model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
-mkinresplot(fit, "m1")
    
+mkinresplot(fit, "m1")
    
 
+  
+
   
 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index db727427..9f98a077 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,20 +114,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Function to set up a kinetic submodel for one state variable
    
+    
+    
     
    
 
+    
    
     
     
    This is a convenience function to set up the lists used as arguments for
   mkinmod.
    
     
+    
    
 
     
    mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
     
 
     
     
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -191,6 +206,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 6c99f07b..74b6adad 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -21,17 +21,23 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -54,8 +60,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -103,21 +114,25 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Fit one or more kinetic models with one or more state variables to one or more datasets
    
+    
+    
     
    
 
+    
    
     
     
    This function calls mkinfit on all combinations of models and datasets
   specified in its first two arguments.
    
     
+    
    
 
     
    mmkin(models, datasets,
       cores = round(detectCores()/2), cluster = NULL, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -156,7 +171,7 @@
     
     
    See also
    
 
-    
    [.mmkin for subsetting, plot.mmkin for plotting.
    
+    
    [.mmkin for subsetting, plot.mmkin for plotting.
    Examples
    
@@ -225,6 +240,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index 0d54d2fe..f7404448 100644
Binary files a/docs/reference/plot.mkinfit-1.png and b/docs/reference/plot.mkinfit-1.png differ
diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index 377d63b6..93c9efe0 100644
Binary files a/docs/reference/plot.mkinfit-2.png and b/docs/reference/plot.mkinfit-2.png differ
diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index b23ddfe7..7b8a81e2 100644
Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 0dd9f4d6..d44b6f9f 100644
Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 319ba75b..525a8453 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -58,8 +64,12 @@ If the current plot device is a tikz device,
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -107,12 +118,15 @@ If the current plot device is a tikz device,
       
       
 
-      
    
+
    
   
    
     
    
     
    Plot the observed data and the fitted model of an mkinfit object
    
+    
+    
     
    
 
+    
    
     
     
    Solves the differential equations with the optimised and fixed parameters
   from a previous successful call to mkinfit and plots
@@ -121,6 +135,7 @@ If the current plot device is a tikz device,
   then latex is being used for the formatting of the chi2 error level, 
   if show_errmin = TRUE.
    
     
+    
    
 
     
    # S3 method for mkinfit
 plot(x, fit = x,
@@ -137,7 +152,7 @@ plot(x, fit = x,
   show_errmin = FALSE, errmin_digits = 3, …)
 plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
     
 
     
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -244,12 +259,12 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …
 # parent to sink included, use Levenberg-Marquardt for speedSFO_SFO<-mkinmod(parent=mkinsub("SFO", "m1", full="Parent"),
                    m1=mkinsub("SFO", full="Metabolite M1" ))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
-plot(fit)
    plot(fit, show_residuals = TRUE)
    
+plot(fit)
    plot(fit, show_residuals = TRUE)
    
 # Show the observed variables separately
-plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
    
+plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
    
 # Show the observed variables separately, with residuals
 plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
-     show_errmin = TRUE)
    
+     show_errmin = TRUE)
    
 # The same can be obtained with less typing, using the convenience function plot_sep
 plot_sep(fit, lpos = c("topright", "bottomright"))
    
@@ -282,6 +297,8 @@ plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …
       
 
+  
+
   
 
diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png
index c2c25e90..2aa7aad9 100644
Binary files a/docs/reference/plot.mmkin-1.png and b/docs/reference/plot.mmkin-1.png differ
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index b40ae0d5..94b1332a 100644
Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index dfbe014f..ca78fa42 100644
Binary files a/docs/reference/plot.mmkin-3.png and b/docs/reference/plot.mmkin-3.png differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index f1aa789f..a554a489 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -57,8 +63,12 @@ If the current plot device is a tikz device,
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -106,12 +117,15 @@ If the current plot device is a tikz device,
       
       
 
-      
    
+
    
   
    
     
    
     
    Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
    
+    
+    
     
    
 
+    
    
     
     
    When x is a row selected from an mmkin object ([.mmkin), the same model
   fitted for at least one dataset is shown. When it is a column, the fit of at least one model
@@ -119,12 +133,13 @@ If the current plot device is a tikz device,
 
    If the current plot device is a tikz device,
   then latex is being used for the formatting of the chi2 error level.
    
     
+    
    
 
     
    # S3 method for mmkin
 plot(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 3,
               cex = 0.7, rel.height.middle = 0.9, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
           
   
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -171,11 +186,11 @@ If the current plot device is a tikz device,
   fits<-mmkin(c("FOMC", "HS"),
                 list("FOCUS B"=FOCUS_2006_B, "FOCUS C"=FOCUS_2006_C), # named list for titlescores=1, quiet=TRUE, method.modFit="Marq")
-  plot(fits[, "FOCUS C"])
      plot(fits["FOMC", ])
    
+  plot(fits[, "FOCUS C"])
      plot(fits["FOMC", ])
    
   # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot
   # height should be smaller than the plot width (this is not possible for the html pages
   # generated by pkgdown, as far as I know).
-  plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
    
+  plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
    
 
+  
+
   
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 2a469fc2..ade048f0 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,20 +113,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Print mkinds objects
    
+    
+    
     
    
 
+    
    
     
     
    Print mkinds objects.
    
     
+    
    
 
     
    # S3 method for mkinds
 print(x, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
          
                       
   
   
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -151,6 +166,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 30703dfd..64d3a03c 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -21,16 +21,22 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -53,8 +59,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -102,20 +113,24 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Print mkinmod objects
    
+    
+    
     
    
 
+    
    
     
     
    Print mkinmod objects in a way that the user finds his way to get to its components.
    
     
+    
    
 
     
    # S3 method for mkinmod
 print(x, ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -172,6 +187,8 @@
       
 
+  
+
   
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 2c06b1dd..06b3c049 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -21,18 +21,24 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -55,8 +61,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -104,17 +115,21 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Metabolism data set used for checking the software quality of KinGUI
    
+    
+    
     
    
 
+    
    
     
     
    This dataset was used for a comparison of KinGUI and ModelMaker to check the
   software quality of KinGUI in the original publication (Schäfer et al., 2007).
   The results from the fitting are also included.
    
     
+    
    
 
     
    schaefer07_complex_case
    
         
@@ -192,6 +207,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html
index fd714224..bb9fd396 100644
--- a/docs/reference/sigma_rl.html
+++ b/docs/reference/sigma_rl.html
@@ -21,18 +21,24 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -55,8 +61,12 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
@@ -104,21 +115,25 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" />
       
       
 
-      
    
+
    
   
    
     
    
     
    Two component error model of Rocke and Lorenzato
    
+    
+    
     
    
 
+    
    
     
     
    Function describing the standard deviation of the measurement error 
   in dependence of the measured value \(y\):
    
 
    $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$
    
     
+    
    
 
     
    sigma_rl(y, sigma_low, rsd_high)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
 
    
@@ -172,6 +187,8 @@ $$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" />
       
 
+  
+
   
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 37b8fff8..c8919f1c 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -21,12 +21,15 @@
 
 
+
+
+
 
-
-  
-  
+
+
+
 
+
+
+
 
 
@@ -56,8 +62,12 @@
         
-      mkin
+      
+        mkin
+        0.9.47.1
+      
+
     
@@ -105,25 +116,29 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Summary method for class "mkinfit"
    
+    
+    
     
    
 
+    
    
     
     
    Lists model equations, the summary as returned by summary.modFit,
   the chi2 error levels calculated according to FOCUS guidance (2006) as far
   as defined therein, and optionally the data, consisting of observed, predicted
   and residual values.
    
     
+    
    
 
     
    # S3 method for mkinfit
 summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
 # S3 method for summary.mkinfit
 print(x, digits = max(3, getOption("digits") - 3), ...)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
    
 
 
 
 
 
 
 
 
         
       
     
   
 
    
@@ -190,16 +205,16 @@
 
     
    Examples
      summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.4 
-#> Date of fit:     Wed Mar 21 18:14:42 2018 
-#> Date of summary: Wed Mar 21 18:14:42 2018 
+#> R version used for fitting:       3.5.0 
+#> Date of fit:     Wed Jun  6 01:21:46 2018 
+#> Date of summary: Wed Jun  6 01:21:46 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.072 s
+#> Fitted with method Port using 35 model solutions performed in 0.075 s
 #> 
 #> Weighting: none
 #> 
@@ -291,6 +306,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 18da9ff6..6e0ac227 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -65,8 +71,12 @@ Compare also the code in the example section to see the degradation models." />
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
+
     
   
 
@@ -114,12 +125,15 @@ Compare also the code in the example section to see the degradation models." />
       
       
 
-      
    
+
    
   
    
     
    
     
    Synthetic datasets for one parent compound with two metabolites
    
+    
+    
     
    
 
+    
    
     
     
    The 12 datasets were generated using four different models and three different
  variance components. The four models are either the SFO or the DFOP model with either
@@ -135,6 +149,7 @@ Compare also the code in the example section to see the degradation models." />
  with two sequential metabolites (linear pathway), with added variance component 'a'.
    
 
    Compare also the code in the example section to see the degradation models.
    
     
+    
    
 
     
    synthetic_data_for_UBA_2014
    
         
@@ -283,6 +298,8 @@ summary(fit)
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index b1b5e617..090b0c22 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -21,17 +21,23 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -54,8 +60,12 @@
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
 
@@ -103,16 +114,20 @@
       
       
 
-      
    
+
    
   
    
     
    
     
    Three experimental datasets from two water sediment systems and one soil
    
+    
+    
     
    
 
+    
    
     
     
    The datasets were used for the comparative validation of several kinetic evaluation
  software packages (Ranke, 2014).
    
     
+    
    
 
     
    test_data_from_UBA_2014
    
         
@@ -187,6 +202,8 @@
       
    
    
 
+  
+
   
 
 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index fb03cdac..3adb3a10 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -21,12 +21,15 @@
 
 
 
+
+
+
 
 
-
 
-  
-  
+
+
+
 
 
 
 
+
+
+
 
 
 
@@ -61,8 +67,12 @@ The transformation of sets of formation fractions is fragile, as it supposes
         
         
       
-      mkin
+      
+        mkin
+        0.9.47.1
+      
     
    
+
     
   
    
 
@@ -110,12 +121,15 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
 
-      
    
+
    
   
    
     
    
     
    Functions to transform and backtransform kinetic parameters for fitting
    
+    
+    
     
    
 
+    
    
     
     
    The transformations are intended to map parameters that should only take
   on restricted values to the full scale of real numbers. For kinetic rate
@@ -127,13 +141,14 @@ The transformation of sets of formation fractions is fragile, as it supposes
   the same ordering of the components in forward and backward transformation.
   This is no problem for the internal use in mkinfit.
    
     
+    
    
 
     
    transform_odeparms(parms, mkinmod,
                    transform_rates = TRUE, transform_fractions = TRUE)
 backtransform_odeparms(transparms, mkinmod,
                        transform_rates = TRUE, transform_fractions = TRUE)
    
     
-    
     Arguments
    
+    
    Arguments
    
     
    
     
     
    
     
    
@@ -184,9 +199,9 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1=list(type="SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.4 
-#> Date of fit:     Wed Mar 21 18:14:43 2018 
-#> Date of summary: Wed Mar 21 18:14:43 2018 
+#> R version used for fitting:       3.5.0 
+#> Date of fit:     Wed Jun  6 01:21:47 2018 
+#> Date of summary: Wed Jun  6 01:21:47 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -194,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.585 s
+#> Fitted with method Port using 153 model solutions performed in 0.628 s
 #> 
 #> Weighting: none
 #> 
@@ -322,6 +337,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
    
    
 
+  
+
   
 
-- 
cgit v1.2.1