From be809ea23b256f627216958fcd90489ee0844ab8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Feb 2019 14:50:13 +0100 Subject: Add plotting tests, add nafta to pkgdown --- DESCRIPTION | 5 +- _pkgdown.yml | 1 + docs/articles/FOCUS_D.html | 8 +- docs/articles/FOCUS_L.html | 44 +- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/articles/web_only/FOCUS_Z.html | 2 +- docs/articles/web_only/compiled_models.html | 12 +- docs/reference/Extract.mmkin.html | 12 +- docs/reference/index.html | 6 + docs/reference/mccall81_245T.html | 12 +- docs/reference/mkinfit.html | 46 +- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/transform_odeparms.html | 24 +- test.log | 20 +- tests/figs/deps.txt | 3 + tests/figs/plotting/mmkin-plot-for-focus-c.svg | 569 +++++++++++++++++++++ .../plotting/mmkin-plot-for-sfo-focus-c-and-d.svg | 300 +++++++++++ tests/testthat/test_plots_twa.R | 61 +++ tests/testthat/test_twa.R | 49 -- 23 files changed, 1044 insertions(+), 150 deletions(-) create mode 100644 tests/figs/deps.txt create mode 100644 tests/figs/plotting/mmkin-plot-for-focus-c.svg create mode 100644 tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg create mode 100644 tests/testthat/test_plots_twa.R delete mode 100644 tests/testthat/test_twa.R diff --git a/DESCRIPTION b/DESCRIPTION index 138440fc..87823866 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.48.1 -Date: 2019-02-21 +Date: 2019-02-22 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -19,7 +19,8 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, purpose. Imports: stats, graphics, methods, FME, deSolve, R6, minpack.lm, rootSolve, inline, parallel, plyr -Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr +Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr +Remotes: r-lib/vdiffr License: GPL LazyLoad: yes LazyData: yes diff --git a/_pkgdown.yml b/_pkgdown.yml index 20854d5b..03305d9a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -10,6 +10,7 @@ reference: - mkinmod - mkinfit - mmkin + - nafta - title: Show results desc: Functions working with mkinfit objects contents: diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index ad8413dc..a470cdb6 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -85,7 +85,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-02-22

+

2019-02-25

@@ -163,8 +163,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:30 2019 
-## Date of summary: Fri Feb 22 20:48:31 2019 
+## Date of fit:     Mon Feb 25 14:54:38 2019 
+## Date of summary: Mon Feb 25 14:54:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.731 s
+## Fitted with method Port using 153 model solutions performed in 0.712 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 17c7bf59..e8a81075 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
@@ -111,15 +111,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:32 2019 
-## Date of summary: Fri Feb 22 20:48:32 2019 
+## Date of fit:     Mon Feb 25 14:54:40 2019 
+## Date of summary: Mon Feb 25 14:54:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.105 s
+## Fitted with method Port using 37 model solutions performed in 0.096 s
 ## 
 ## Weighting: none
 ## 
@@ -202,15 +202,15 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:34 2019 
-## Date of summary: Fri Feb 22 20:48:34 2019 
+## Date of fit:     Mon Feb 25 14:54:42 2019 
+## Date of summary: Mon Feb 25 14:54:42 2019 
 ## 
 ## 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 1.604 s
+## Fitted with method Port using 611 model solutions performed in 1.529 s
 ## 
 ## Weighting: none
 ## 
@@ -297,15 +297,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:35 2019 
-## Date of summary: Fri Feb 22 20:48:35 2019 
+## Date of fit:     Mon Feb 25 14:54:42 2019 
+## Date of summary: Mon Feb 25 14:54:42 2019 
 ## 
 ## 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 0.216 s
+## Fitted with method Port using 81 model solutions performed in 0.199 s
 ## 
 ## Weighting: none
 ## 
@@ -368,8 +368,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:36 2019 
-## Date of summary: Fri Feb 22 20:48:36 2019 
+## Date of fit:     Mon Feb 25 14:54:44 2019 
+## Date of summary: Mon Feb 25 14:54:44 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.864 s
+## Fitted with method Port using 336 model solutions performed in 0.853 s
 ## 
 ## Weighting: none
 ## 
@@ -460,8 +460,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:37 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.362 s
+## Fitted with method Port using 137 model solutions performed in 0.348 s
 ## 
 ## Weighting: none
 ## 
@@ -561,15 +561,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:38 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.123 s
+## Fitted with method Port using 46 model solutions performed in 0.112 s
 ## 
 ## Weighting: none
 ## 
@@ -621,15 +621,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 20:48:38 2019 
-## Date of summary: Fri Feb 22 20:48:38 2019 
+## Date of fit:     Mon Feb 25 14:54:45 2019 
+## Date of summary: Mon Feb 25 14:54:45 2019 
 ## 
 ## 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 0.184 s
+## Fitted with method Port using 66 model solutions performed in 0.165 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 9baa44e4..bffd19dd 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -85,7 +85,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 8c340557..83b05989 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -85,7 +85,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index b1e2811c..c3ee7415 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -85,7 +85,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index fbf2de33..4209d2bc 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -85,7 +85,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-02-22

+            
2019-02-25

       
       
       
@@ -126,9 +126,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.484    1.000     2.483        0
-## 1 deSolve, not compiled            3  17.963    7.231    17.951        0
-## 2      Eigenvalue based            3   3.146    1.267     3.144        0
+## 3     deSolve, compiled            3   2.394    1.000     2.388    0.004
+## 1 deSolve, not compiled            3  17.923    7.487    17.910    0.000
+## 2      Eigenvalue based            3   3.021    1.262     3.018    0.000
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,8 +157,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.232    1.000     4.226    0.004
-## 1 deSolve, not compiled            3  37.946    8.966    37.924    0.000
+## 2     deSolve, compiled            3   4.162    1.000     4.158        0
+## 1 deSolve, not compiled            3  37.536    9.019    37.517        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index e3285ed3..95b1558e 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.201       0.000       0.200 
+#>       0.196       0.000       0.196 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559103bf0>
-#> <environment: 0x55555a51ba10>
+#> <bytecode: 0x555559255c78>
+#> <environment: 0x55555add1128>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a537b00>
-#> <environment: 0x55555a51ba10>
+#> <bytecode: 0x55555a1e9540>
+#> <environment: 0x55555add1128>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,7 +560,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Feb 22 20:46:31 2019"
+#> [1] "Mon Feb 25 14:52:43 2019"
 #> 
 #> $version
 #> [1] "0.9.48.1"
diff --git a/docs/reference/index.html b/docs/reference/index.html
index f31a72fe..24f3df0c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -151,6 +151,12 @@
           
mmkin() 

         
         
Fit one or more kinetic models with one or more state variables to one or more datasets

+      
+        
+        
+          
nafta() 

+        
+        
Evaluate parent kinetics using the NAFTA guidance

       
     
       
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 7b3418de..bcc871d8 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
     summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:54 2019 
-#> Date of summary: Fri Feb 22 20:46:54 2019 
+#> Date of fit:     Mon Feb 25 14:53:05 2019 
+#> Date of summary: Mon Feb 25 14:53:05 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 4.461 s
+#> Fitted with method Port using 574 model solutions performed in 3.873 s
 #> 
 #> Weighting: none
 #> 
@@ -249,8 +249,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:56 2019 
-#> Date of summary: Fri Feb 22 20:46:56 2019 
+#> Date of fit:     Mon Feb 25 14:53:07 2019 
+#> Date of summary: Mon Feb 25 14:53:07 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.709 s
+#> Fitted with method Port using 246 model solutions performed in 1.623 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index dfdddb25..80278890 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:46:59 2019 
-#> Date of summary: Fri Feb 22 20:46:59 2019 
+#> Date of fit:     Mon Feb 25 14:53:09 2019 
+#> Date of summary: Mon Feb 25 14:53:09 2019 
 #> 
 #> 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 0.185 s
+#> Fitted with method Port using 64 model solutions performed in 0.168 s
 #> 
 #> Weighting: none
 #> 
@@ -515,7 +515,7 @@
   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 verstrichen 
-#>       1.071       0.000       1.072 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.038       0.000       1.039 
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 
@@ -590,7 +590,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.852       0.000       0.852 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.827       0.000       0.827 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -628,8 +628,8 @@
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:11 2019 
-#> Date of summary: Fri Feb 22 20:47:11 2019 
+#> Date of fit:     Mon Feb 25 14:53:22 2019 
+#> Date of summary: Mon Feb 25 14:53:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.864 s
+#> Fitted with method Port using 186 model solutions performed in 0.898 s
 #> 
 #> Weighting: none
 #> 
@@ -745,8 +745,8 @@
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:14 2019 
-#> Date of summary: Fri Feb 22 20:47:14 2019 
+#> Date of fit:     Mon Feb 25 14:53:24 2019 
+#> Date of summary: Mon Feb 25 14:53:24 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.584 s
+#> Fitted with method Port using 551 model solutions performed in 2.572 s
 #> 
 #> Weighting: none
 #> 
@@ -867,8 +867,8 @@
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:15 2019 
-#> Date of summary: Fri Feb 22 20:47:15 2019 
+#> Date of fit:     Mon Feb 25 14:53:25 2019 
+#> Date of summary: Mon Feb 25 14:53:25 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.716 s
+#> Fitted with method Port using 155 model solutions performed in 0.709 s
 #> 
 #> Weighting: mean
 #> 
@@ -985,8 +985,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:16 2019 
-#> Date of summary: Fri Feb 22 20:47:16 2019 
+#> Date of fit:     Mon Feb 25 14:53:26 2019 
+#> Date of summary: Mon Feb 25 14:53:26 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.83 s
+#> Fitted with method Port using 174 model solutions performed in 0.81 s
 #> 
 #> Weighting: manual
 #> 
@@ -1105,8 +1105,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:17 2019 
-#> Date of summary: Fri Feb 22 20:47:17 2019 
+#> Date of fit:     Mon Feb 25 14:53:28 2019 
+#> Date of summary: Mon Feb 25 14:53:28 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.286 s
+#> Fitted with method Port using 270 model solutions performed in 1.25 s
 #> 
 #> Weighting: manual
 #> 
@@ -1223,8 +1223,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:47:21 2019 
-#> Date of summary: Fri Feb 22 20:47:21 2019 
+#> Date of fit:     Mon Feb 25 14:53:31 2019 
+#> Date of summary: Mon Feb 25 14:53:31 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.38 s
+#> Fitted with method Port using 692 model solutions performed in 3.302 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 64fba5e5..ba26c686 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file622753352edd.c 2> file622753352edd.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file481263217c00.c 2> file481263217c00.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 2b4c33aa..738eeb9d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,7 +325,7 @@
                 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 verstrichen 
-#>       0.004       0.000       0.003 
  system.time(
+#>       0.003       0.000       0.003 
  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
@@ -335,7 +335,7 @@
                 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 verstrichen 
-#>       0.039       0.000       0.040 

+#>       0.047       0.000       0.047 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call  1 :  552.5739 
 #> Model cost at call  3 :  552.5739 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 71ec89e8..1a60e3ea 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.052       0.044       7.383 
time_1
#>        User      System verstrichen 
-#>      23.652       0.004      23.672 

+#>       0.036       0.039       7.196 
time_1
#>        User      System verstrichen 
+#>      22.818       0.000      22.834 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 39ef962c..f0d4a060 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:16 2019 
-#> Date of summary: Fri Feb 22 20:48:16 2019 
+#> Date of fit:     Mon Feb 25 14:54:24 2019 
+#> Date of summary: Mon Feb 25 14:54:24 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.088 s
+#> Fitted with method Port using 35 model solutions performed in 0.085 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 9d18fbb2..1071a932 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:24 2019 
-#> Date of summary: Fri Feb 22 20:48:24 2019 
+#> Date of fit:     Mon Feb 25 14:54:32 2019 
+#> Date of summary: Mon Feb 25 14:54:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ 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 0.717 s
+#> Fitted with method Port using 153 model solutions performed in 0.704 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:26 2019 
-#> Date of summary: Fri Feb 22 20:48:26 2019 
+#> Date of fit:     Mon Feb 25 14:54:34 2019 
+#> Date of summary: Mon Feb 25 14:54:34 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.661 s
+#> Fitted with method Port using 350 model solutions performed in 1.62 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:27 2019 
-#> Date of summary: Fri Feb 22 20:48:27 2019 
+#> Date of fit:     Mon Feb 25 14:54:35 2019 
+#> Date of summary: Mon Feb 25 14:54:35 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.871 s
+#> Fitted with method Port using 186 model solutions performed in 0.856 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Fri Feb 22 20:48:28 2019 
-#> Date of summary: Fri Feb 22 20:48:28 2019 
+#> Date of fit:     Mon Feb 25 14:54:36 2019 
+#> Date of summary: Mon Feb 25 14:54:36 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.484 s
+#> Fitted with method Port using 104 model solutions performed in 0.482 s
 #> 
 #> Weighting: none
 #> 
diff --git a/test.log b/test.log
index 5a71534f..345746e2 100644
--- a/test.log
+++ b/test.log
@@ -1,28 +1,30 @@
 Loading mkin
 Testing mkin
 ✔ | OK F W S | Context
-
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.5 s]
-
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.2 s]
-
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  1     1 | Iteratively reweighted least squares (IRLS) fitting
✔ |  1     1 | Iteratively reweighted least squares (IRLS) fitting [9.0 s]
+
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.4 s]
+
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ |  7       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  8       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.1 s]
+
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  1     1 | Iteratively reweighted least squares (IRLS) fitting
✔ |  1     1 | Iteratively reweighted least squares (IRLS) fitting [8.8 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_irls.R:44: skip: Reweighting method 'tc' works
 Too much trouble with datasets that are randomly generated
 ────────────────────────────────────────────────────────────────────────────────
 
⠏ |  0       | Fitting the logistic model
⠋ |  1       | Fitting the logistic model
⠙ |  1     1 | Fitting the logistic model
✔ |  1     1 | Fitting the logistic model [0.5 s]
 ────────────────────────────────────────────────────────────────────────────────
-test_logistic.R:42: skip: The logistic fit can be done via differential equation
+test_logistic.R:41: skip: The logistic fit can be done via differential equation
 Skip slow fit of logistic model using deSolve without compilation
 ────────────────────────────────────────────────────────────────────────────────
 
⠏ |  0       | Model predictions with mkinpredict
⠋ |  1       | Model predictions with mkinpredict
⠙ |  2       | Model predictions with mkinpredict
⠹ |  3       | Model predictions with mkinpredict
✔ |  3       | Model predictions with mkinpredict [0.3 s]
-
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [23.9 s]
-
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [6.0 s]
+
⠏ |  0       | Evaluations according to the NAFTA guidance from 2015
⠋ |  1       | Evaluations according to the NAFTA guidance from 2015
⠙ |  1   1   | Evaluations according to the NAFTA guidance from 2015
⠙ |  2       | Evaluations according to the NAFTA guidance from 2015
⠹ |  3       | Evaluations according to the NAFTA guidance from 2015
⠸ |  4       | Evaluations according to the NAFTA guidance from 2015
⠼ |  5       | Evaluations according to the NAFTA guidance from 2015
⠴ |  6       | Evaluations according to the NAFTA guidance from 2015
⠦ |  7       | Evaluations according to the NAFTA guidance from 2015
✔ |  7       | Evaluations according to the NAFTA guidance from 2015 [0.7 s]
+
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [23.8 s]
+
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
⠸ |  4       | Calculation of maximum time weighted average concentrations (TWAs)
⠼ |  5       | Calculation of maximum time weighted average concentrations (TWAs)
⠴ |  6       | Calculation of maximum time weighted average concentrations (TWAs)
⠦ |  7       | Calculation of maximum time weighted average concentrations (TWAs)
⠧ |  8       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  8       | Calculation of maximum time weighted average concentrations (TWAs) [7.2 s]
+
⠏ |  0       | Plotting
⠋ |  1       | Plotting
⠙ |  2       | Plotting
✔ |  2       | Plotting [0.4 s]
+
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s]
 
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.5 s]
-
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
⠸ |  4       | Calculation of maximum time weighted average concentrations (TWAs)
⠼ |  5       | Calculation of maximum time weighted average concentrations (TWAs)
⠴ |  6       | Calculation of maximum time weighted average concentrations (TWAs)
⠦ |  7       | Calculation of maximum time weighted average concentrations (TWAs)
⠧ |  8       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  8       | Calculation of maximum time weighted average concentrations (TWAs) [8.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 65.5 s
+Duration: 65.9 s
 
-OK:       50
+OK:       59
 Failed:   0
 Warnings: 0
 Skipped:  2
diff --git a/tests/figs/deps.txt b/tests/figs/deps.txt
new file mode 100644
index 00000000..0f6c3754
--- /dev/null
+++ b/tests/figs/deps.txt
@@ -0,0 +1,3 @@
+- vdiffr-svg-engine: 1.0
+- vdiffr: 0.3.0.9000
+- freetypeharfbuzz: 0.2.5
diff --git a/tests/figs/plotting/mmkin-plot-for-focus-c.svg b/tests/figs/plotting/mmkin-plot-for-focus-c.svg
new file mode 100644
index 00000000..1c697328
--- /dev/null
+++ b/tests/figs/plotting/mmkin-plot-for-focus-c.svg
@@ -0,0 +1,569 @@
+
+
+
+  
+
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+parent
+
+  
+    
+  
+
+FOCUS_C
+SFO
+ 
+χ
+2
+ 
+error level
+=
+15.8%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+-10
+-5
+0
+5
+10
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+SFO residuals
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOCUS_C
+FOMC
+ 
+χ
+2
+ 
+error level
+=
+6.66%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+
+
+-3
+-1
+1
+2
+3
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOMC residuals
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOCUS_C
+DFOP
+ 
+χ
+2
+ 
+error level
+=
+2.66%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+
+
+-1.5
+-0.5
+0.5
+1.5
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+DFOP residuals
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOCUS_C
+HS
+ 
+χ
+2
+ 
+error level
+=
+4.7%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+-2
+-1
+0
+1
+2
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+HS residuals
+
+  
+    
+  
+
+
diff --git a/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg b/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg
new file mode 100644
index 00000000..72496e86
--- /dev/null
+++ b/tests/figs/plotting/mmkin-plot-for-sfo-focus-c-and-d.svg
@@ -0,0 +1,300 @@
+
+
+
+  
+
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+parent
+
+  
+    
+  
+
+SFO
+FOCUS_C
+ 
+χ
+2
+ 
+error level
+=
+15.8%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+120
+
+
+
+
+
+
+-10
+-5
+0
+5
+10
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOCUS_C residuals
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+0
+20
+40
+60
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+100
+
+
+  
+    
+  
+
+Time
+Observed
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+SFO
+FOCUS_D
+ 
+χ
+2
+ 
+error level
+=
+6.45%
+
+  
+    
+  
+
+
+  
+    
+  
+
+
+
+
+
+
+
+0
+20
+40
+60
+80
+
+
+
+
+
+
+-10
+-5
+0
+5
+10
+
+
+  
+    
+  
+
+Time
+Residual
+
+  
+    
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+
+FOCUS_D residuals
+
+  
+    
+  
+
+
diff --git a/tests/testthat/test_plots_twa.R b/tests/testthat/test_plots_twa.R
new file mode 100644
index 00000000..fe0ba325
--- /dev/null
+++ b/tests/testthat/test_plots_twa.R
@@ -0,0 +1,61 @@
+# Copyright (C) 2016-2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see 
+
+models <- c("SFO", "FOMC", "DFOP", "HS")
+fits <- mmkin(models,
+  list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+  quiet = TRUE, cores = if (Sys.getenv("TRAVIS") == "") 15 else 1)
+
+context("Calculation of maximum time weighted average concentrations (TWAs)")
+
+test_that("Time weighted average concentrations are correct", {
+  skip_on_cran()
+
+  outtimes_10 <- seq(0, 10, length.out = 10000)
+
+  for (ds in c("FOCUS_C", "FOCUS_D")) {
+    for (model in models) {
+      fit <- fits[[model, ds]]
+      bpar <- summary(fit)$bpar[, "Estimate"]
+      pred_10 <- mkinpredict(fit$mkinmod,
+                  odeparms = bpar[2:length(bpar)],
+                  odeini = c(parent = bpar[[1]]),
+                  outtimes = outtimes_10)
+      twa_num <- mean(pred_10$parent)
+      names(twa_num) <- 10
+      twa_ana <- max_twa_parent(fit, 10)
+
+      # Test for absolute difference (scale = 1)
+      # The tolerance can be reduced if the length of outtimes is increased,
+      # but this needs more computing time so we stay with lenght.out = 10k
+      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
+    }
+  }
+})
+
+context("Plotting")
+
+test_that("Plotting mmkin objects is reproducible", {
+  skip_on_cran()
+  mmkin_FOCUS_C <- function() plot(fits[, "FOCUS_C"])
+  mmkin_SFO <- function() plot(fits["SFO",])
+
+  vdiffr::expect_doppelganger("mmkin plot for FOCUS C", mmkin_FOCUS_C)
+  vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
+})
+
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
deleted file mode 100644
index 42b74a7f..00000000
--- a/tests/testthat/test_twa.R
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright (C) 2016,2017,2018 Johannes Ranke
-# Contact: jranke@uni-bremen.de
-
-# This file is part of the R package mkin
-
-# mkin is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see 
-
-context("Calculation of maximum time weighted average concentrations (TWAs)")
-
-
-test_that("Time weighted average concentrations are correct", {
-  skip_on_cran()
-  twa_models <- c("SFO", "FOMC", "DFOP", "HS")
-  fits <- mmkin(twa_models,
-                list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
-                quiet = TRUE, cores = if (Sys.getenv("TRAVIS") == "") 15 else 1)
-
-  outtimes_10 <- seq(0, 10, length.out = 10000)
-
-  for (ds in c("FOCUS_C", "FOCUS_D")) {
-    for (model in twa_models) {
-      fit <- fits[[model, ds]]
-      bpar <- summary(fit)$bpar[, "Estimate"]
-      pred_10 <- mkinpredict(fit$mkinmod,
-                  odeparms = bpar[2:length(bpar)],
-                  odeini = c(parent = bpar[[1]]),
-                  outtimes = outtimes_10)
-      twa_num <- mean(pred_10$parent)
-      names(twa_num) <- 10
-      twa_ana <- max_twa_parent(fit, 10)
-
-      # Test for absolute difference (scale = 1)
-      # The tolerance can be reduced if the length of outtimes is increased,
-      # but this needs more computing time so we stay with lenght.out = 10k
-      expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
-    }
-  }
-})
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