From 396e40d2c45d81a8e74c41a2f632665021e980a1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 26 Feb 2019 20:28:15 +0100 Subject: NAFTA SOP Attachment vignette Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0 --- docs/reference/AIC.mmkin.html | 4 +- docs/reference/Extract.mmkin.html | 12 +- docs/reference/NAFTA_SOP_2015.html | 13 +- docs/reference/NAFTA_SOP_Attachment-1.png | Bin 0 -> 42277 bytes docs/reference/NAFTA_SOP_Attachment.html | 217 ++++++++++++++++++++++++++++++ docs/reference/index.html | 4 +- docs/reference/mccall81_245T.html | 12 +- docs/reference/mkinfit.html | 44 +++--- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/nafta.html | 19 ++- docs/reference/plot.nafta.html | 12 +- docs/reference/print.nafta.html | 8 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/transform_odeparms.html | 24 ++-- 16 files changed, 310 insertions(+), 75 deletions(-) create mode 100644 docs/reference/NAFTA_SOP_Attachment-1.png create mode 100644 docs/reference/NAFTA_SOP_Attachment.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 69552d5f..2a4a6de4 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -160,8 +160,8 @@

Examples

  f <- mmkin(c("SFO", "FOMC", "DFOP"),
     list("FOCUS A" = FOCUS_2006_A,
-         "FOCUS C" = FOCUS_2006_C))
-  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.32452

+         "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE)
#> Warning: Optimisation by method Port did not converge:
+#> false convergence (8)
  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.32452

   # For FOCUS A, the models fit almost equally well, so the higher the number
   # of parameters, the higher (worse) the AIC
   AIC(f[, "FOCUS A"])
#>      df      AIC
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 873d75bd..f10805a0 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.195       0.000       0.195 
+#>       0.071       0.000       0.071 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555925ca08>
-#> <environment: 0x55555b668200>
+#> <bytecode: 0x55555bb55ad0>
+#> <environment: 0x55555c4dcf70>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a590818>
-#> <environment: 0x55555b668200>
+#> <bytecode: 0x55555c537298>
+#> <environment: 0x55555c4dcf70>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,7 +560,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Tue Feb 26 09:27:10 2019"
+#> [1] "Tue Feb 26 20:23:09 2019"
 #> 
 #> $version
 #> [1] "0.9.48.1"
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index 4a2c71a9..f4d89222 100644
--- a/docs/reference/NAFTA_SOP_2015.html
+++ b/docs/reference/NAFTA_SOP_2015.html
@@ -152,7 +152,8 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Calculation of the Jacobian failed for the cost function of the untransformed model.
+#> No t-test results will be available
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
 #> 
@@ -168,8 +169,8 @@
 #> $IORE
 #>                         Estimate Pr(>t)        Lower        Upper
 #> parent_0            9.685291e+01     NA 8.752855e+01 1.061773e+02
-#> k__iore_parent_sink 8.403374e-14     NA 1.092054e-19 6.466412e-08
-#> N_parent            6.684458e+00     NA 3.538511e+00 9.830405e+00
+#> k__iore_parent_sink 8.403401e-14     NA 1.092058e-19 6.466429e-08
+#> N_parent            6.684457e+00     NA 3.538510e+00 9.830404e+00
 #> 
 #> $DFOP
 #>              Estimate       Pr(>t)        Lower        Upper
@@ -181,9 +182,9 @@
 #> 
 #> DTx values:
 #>      DT50    DT90 DT50_rep
-#> SFO   407    1352      407
-#> IORE  541 5192066  1562968
-#> DFOP  429    2383      841
+#> SFO   407    1350      407
+#> IORE  541 5190000  1560000
+#> DFOP  429    2380      841
 #> 
 #> Representative half-life:
 #> [1] 841.4096
  plot(nafta_evaluation)

diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png
new file mode 100644
index 00000000..d781cdb0
Binary files /dev/null and b/docs/reference/NAFTA_SOP_Attachment-1.png differ
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
new file mode 100644
index 00000000..63b47855
--- /dev/null
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -0,0 +1,217 @@
+
+
+
+  
+  
+
+
+
+Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkin
+
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+
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+  
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+    

+      

+      
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+      
+      

+
+

+  

+    

+    
Example datasets from Attachment 1 to the NAFTA SOP published 2015

+    
+    
+    

+
+    

+    
+    
Data taken from from Attachment 1 of the SOP.

+    
+    

+
+    
NAFTA_SOP_Attachment

+        
+    
Format

+
+    
Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable
+  for the evaluation with nafta

+    
+    
Source

+
+    
NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
+  in environmental media. NAFTA Technical Working Group on Pesticides
+  https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation
+  accessed 2019-02-22

+
US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
+  Calculate Representative Half-life Values and Characterizing Pesticide
+  Degradation
+  https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

+    
+
+    
Examples

+    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
+#>       SFO      IORE      DFOP 
+#> 465.21753  56.27506  32.06401 
+#> 
+#> Critical sum of squares for checking the SFO model:
+#> [1] 64.4304
+#> 
+#> Parameters:
+#> $SFO
+#>                  Estimate       Pr(>t)        Lower       Upper
+#> parent_0      95.84012168 1.095639e-21 92.120517864 99.55972549
+#> k_parent_sink  0.01024015 1.710227e-12  0.008996874  0.01165524
+#> 
+#> $IORE
+#>                         Estimate       Pr(>t)        Lower        Upper
+#> parent_0            1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02
+#> k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05
+#> N_parent            2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00
+#> 
+#> $DFOP
+#>              Estimate       Pr(>t) Lower Upper
+#> parent_0 9.994630e+01 4.330861e-27    NA    NA
+#> k1       2.674255e-02 3.171390e-05    NA    NA
+#> k2       2.161318e-12 5.000000e-01    NA    NA
+#> g        6.465276e-01 2.129114e-05    NA    NA
+#> 
+#> 
+#> DTx values:
+#>      DT50     DT90 DT50_rep
+#> SFO  67.7 2.25e+02 6.77e+01
+#> IORE 58.2 1.07e+03 3.22e+02
+#> DFOP 55.5 5.84e+11 3.21e+11
+#> 
+#> Representative half-life:
+#> [1] 321.5119
  plot(nafta_att_p5a)

+  

+  
+

+
+      

+      

+  
Developed by Johannes Ranke.

+

+
+

+  
Site built with pkgdown 1.3.0.9000.

+

+      

+   

+
+  
+
+  
+
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a251dc33..4e57fd3d 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -338,7 +338,9 @@
         
           
plot(<nafta>) 

         
-        
Plot the results of the three models used in the NAFTA scheme

+        
Plot the results of the three models used in the NAFTA scheme. The plots
+  are ordered with increasing complexity of the model in this function 
+  (SFO, then IORE, then DFOP).

       
     
       
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 1845a31c..2e5f0ac2 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:     Tue Feb 26 09:27:31 2019 
-#> Date of summary: Tue Feb 26 09:27:31 2019 
+#> Date of fit:     Tue Feb 26 20:23:32 2019 
+#> Date of summary: Tue Feb 26 20:23:32 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 3.812 s
+#> Fitted with method Port using 574 model solutions performed in 3.765 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:     Tue Feb 26 09:27:33 2019 
-#> Date of summary: Tue Feb 26 09:27:33 2019 
+#> Date of fit:     Tue Feb 26 20:23:34 2019 
+#> Date of summary: Tue Feb 26 20:23:34 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 1.597 s
+#> Fitted with method Port using 246 model solutions performed in 1.601 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 53f46988..84c0fc49 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:     Tue Feb 26 09:27:36 2019 
-#> Date of summary: Tue Feb 26 09:27:36 2019 
+#> Date of fit:     Tue Feb 26 20:23:36 2019 
+#> Date of summary: Tue Feb 26 20:23:36 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 0.163 s
+#> Fitted with method Port using 64 model solutions performed in 0.161 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 
-#>       1.008       0.000       1.008 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.081       0.000       1.081 
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 
-#>       0.812       0.000       0.813 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.812       0.000       0.812 
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:     Tue Feb 26 09:27:48 2019 
-#> Date of summary: Tue Feb 26 09:27:48 2019 
+#> Date of fit:     Tue Feb 26 20:23:48 2019 
+#> Date of summary: Tue Feb 26 20:23:48 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 0.845 s
+#> Fitted with method Port using 186 model solutions performed in 0.852 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:     Tue Feb 26 09:27:50 2019 
-#> Date of summary: Tue Feb 26 09:27:50 2019 
+#> Date of fit:     Tue Feb 26 20:23:51 2019 
+#> Date of summary: Tue Feb 26 20:23:51 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 2.523 s
+#> Fitted with method Port using 551 model solutions performed in 2.6 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:     Tue Feb 26 09:27:51 2019 
-#> Date of summary: Tue Feb 26 09:27:51 2019 
+#> Date of fit:     Tue Feb 26 20:23:52 2019 
+#> Date of summary: Tue Feb 26 20:23:52 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 0.705 s
+#> Fitted with method Port using 155 model solutions performed in 0.704 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:     Tue Feb 26 09:27:52 2019 
-#> Date of summary: Tue Feb 26 09:27:52 2019 
+#> Date of fit:     Tue Feb 26 20:23:53 2019 
+#> Date of summary: Tue Feb 26 20:23:53 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 0.8 s
+#> Fitted with method Port using 174 model solutions performed in 0.796 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:     Tue Feb 26 09:27:54 2019 
-#> Date of summary: Tue Feb 26 09:27:54 2019 
+#> Date of fit:     Tue Feb 26 20:23:54 2019 
+#> Date of summary: Tue Feb 26 20:23:54 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -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:     Tue Feb 26 09:27:57 2019 
-#> Date of summary: Tue Feb 26 09:27:57 2019 
+#> Date of fit:     Tue Feb 26 20:23:58 2019 
+#> Date of summary: Tue Feb 26 20:23:58 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 3.246 s
+#> Fitted with method Port using 692 model solutions performed in 3.182 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index bcf39e7f..a6dd68c5 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 file4a116f6acbf1.c 2> file4a116f6acbf1.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file240f6aec3e43.c 2> file240f6aec3e43.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index a38de769..bab6deb8 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       0.004 
  system.time(
+#>       0.003       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
@@ -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 
-#>       0.040       0.000       0.039 

+#>       0.039       0.000       0.040 

   
    # 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 6613f35c..0078baed 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       0.024       7.037 
time_1
#>        User      System verstrichen 
-#>      22.463       0.000      22.476 

+#>       0.059       0.021       6.916 
time_1
#>        User      System verstrichen 
+#>      22.506       0.000      22.518 

 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/nafta.html b/docs/reference/nafta.html
index b1d45272..9b879786 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -133,7 +133,7 @@
     
     

 
-    
nafta(ds, title = NA, quiet = FALSE)

+    
nafta(ds, title = NA, quiet = FALSE, …)

     
     
Arguments

     
@@ -153,6 +153,10 @@
       
+    
+      
+      
+    
quiet
       
Should the evaluation text be shown?

     
…
Further arguments passed to mmkin.

     

     
     
Value

@@ -175,7 +179,8 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Calculation of the Jacobian failed for the cost function of the untransformed model.
+#> No t-test results will be available
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
 #> 
@@ -191,8 +196,8 @@
 #> $IORE
 #>                         Estimate Pr(>t)        Lower        Upper
 #> parent_0            9.685291e+01     NA 8.752855e+01 1.061773e+02
-#> k__iore_parent_sink 8.403374e-14     NA 1.092054e-19 6.466412e-08
-#> N_parent            6.684458e+00     NA 3.538511e+00 9.830405e+00
+#> k__iore_parent_sink 8.403401e-14     NA 1.092058e-19 6.466429e-08
+#> N_parent            6.684457e+00     NA 3.538510e+00 9.830404e+00
 #> 
 #> $DFOP
 #>              Estimate       Pr(>t)        Lower        Upper
@@ -204,9 +209,9 @@
 #> 
 #> DTx values:
 #>      DT50    DT90 DT50_rep
-#> SFO   407    1352      407
-#> IORE  541 5192066  1562968
-#> DFOP  429    2383      841
+#> SFO   407    1350      407
+#> IORE  541 5190000  1560000
+#> DFOP  429    2380      841
 #> 
 #> Representative half-life:
 #> [1] 841.4096
  plot(nafta_evaluation)

diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index 76da1ffa..7949d36c 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -6,7 +6,9 @@
 
 
 
-Plot the results of the three models used in the NAFTA scheme — plot.nafta • mkin
+Plot the results of the three models used in the NAFTA scheme. The plots
+  are ordered with increasing complexity of the model in this function 
+  (SFO, then IORE, then DFOP). — plot.nafta • mkin
 
 
 
@@ -30,7 +32,9 @@
 
 
 
-
+
 
 
 
@@ -118,7 +122,9 @@
 

   

     

-    
Plot the results of the three models used in the NAFTA scheme

+    
Plot the results of the three models used in the NAFTA scheme. The plots
+  are ordered with increasing complexity of the model in this function 
+  (SFO, then IORE, then DFOP).

     
     
     

diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index ac276857..44f1f6e5 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -32,7 +32,9 @@
 
 
 
-
+
 
 
 
@@ -125,7 +127,9 @@
 
     

     
-    
Print nafta objects.

+    
Print nafta objects. The results for the three models
+  are printed in the order of increasing model complexity,
+  i.e. SFO, then IORE, and finally DFOP.

     
     

 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index ca0b1c4c..6ec72f80 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:     Tue Feb 26 09:28:49 2019 
-#> Date of summary: Tue Feb 26 09:28:49 2019 
+#> Date of fit:     Tue Feb 26 20:24:50 2019 
+#> Date of summary: Tue Feb 26 20:24:50 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 0.085 s
+#> Fitted with method Port using 35 model solutions performed in 0.084 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index bcfbe975..6e65f609 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:     Tue Feb 26 09:28:57 2019 
-#> Date of summary: Tue Feb 26 09:28:57 2019 
+#> Date of fit:     Tue Feb 26 20:24:58 2019 
+#> Date of summary: Tue Feb 26 20:24:58 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 0.7 s
+#> Fitted with method Port using 153 model solutions performed in 0.707 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:     Tue Feb 26 09:28:59 2019 
-#> Date of summary: Tue Feb 26 09:28:59 2019 
+#> Date of fit:     Tue Feb 26 20:25:00 2019 
+#> Date of summary: Tue Feb 26 20:25:00 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 1.59 s
+#> Fitted with method Port using 350 model solutions performed in 1.584 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:     Tue Feb 26 09:29:00 2019 
-#> Date of summary: Tue Feb 26 09:29:00 2019 
+#> Date of fit:     Tue Feb 26 20:25:01 2019 
+#> Date of summary: Tue Feb 26 20:25:01 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 0.844 s
+#> Fitted with method Port using 186 model solutions performed in 0.867 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:     Tue Feb 26 09:29:01 2019 
-#> Date of summary: Tue Feb 26 09:29:01 2019 
+#> Date of fit:     Tue Feb 26 20:25:02 2019 
+#> Date of summary: Tue Feb 26 20:25:02 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 0.467 s
+#> Fitted with method Port using 104 model solutions performed in 0.472 s
 #> 
 #> Weighting: none
 #> 
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