From 4596667b19f032232ceb8f3f762aaad5d69c15be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 Jul 2019 15:57:24 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/AIC.mmkin.html | 2 +- docs/reference/CAKE_export.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 2 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/NAFTA_SOP_2015.html | 2 +- docs/reference/NAFTA_SOP_Attachment.html | 2 +- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/endpoints.html | 2 +- docs/reference/experimental_data_for_UBA.html | 2 +- docs/reference/geometric_mean.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/logistic.solution.html | 2 +- docs/reference/max_twa_parent.html | 2 +- docs/reference/mccall81_245T.html | 2 +- docs/reference/mkin_long_to_wide.html | 2 +- docs/reference/mkin_wide_to_long.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinerrplot.html | 2 +- docs/reference/mkinfit.html | 51 +++++++++++++++----------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 8 ++-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 +-- docs/reference/nafta.html | 2 +- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/plot.nafta.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/print.nafta.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 12 +++--- docs/reference/synthetic_data_for_UBA.html | 2 +- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 2 +- 52 files changed, 91 insertions(+), 84 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a5626847..4e686c98 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 5db220ee..b9684490 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index edfa70d3..4a0432e0 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 37c0b361..6026529c 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 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 b1165f1d..6da112f3 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.5 + 0.9.49.6 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 03a15a5a..729e23b2 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.5 + 0.9.49.6 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 6046ec88..a0bdd522 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.5 + 0.9.49.6 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 278425f6..d92d7d6a 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 0d29deb2..86721dd2 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 69c0a9ef..072ec4c3 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -67,7 +67,7 @@ The form given here differs slightly from the original reference by Gustafson mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index e14f80ec..a3dee0f4 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index ca0db0bb..99467f51 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 5b4ac227..cc760dd7 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 1af62530..6bb19a4b 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 483869c4..c0d849e6 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index b49700f8..91b153a7 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -67,7 +67,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 4ce43f9f..cf873540 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -65,7 +65,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index c180dce2..4c4c6f45 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -66,7 +66,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index bb94fd11..512cb6e4 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -91,7 +91,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 286b40d4..2626e08b 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 3eac2872..d6bd247f 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/index.html b/docs/reference/index.html index b645ea5a..1f0a7327 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index a6cf4867..6c914dd4 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -69,7 +69,7 @@ The total number of estimated parameters returned with the value mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index cee169d2..eb4b0de0 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index ad19853d..596e51ec 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -67,7 +67,7 @@ guidance." /> mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1af77f6b..aa888f0f 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -65,7 +65,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 6f0d5376..479bc5dd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -65,7 +65,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 869c4586..c95fe952 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -64,7 +64,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 89f40abf..2a34173c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -63,7 +63,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 8fd09215..359ce5f5 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -64,7 +64,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index a0201963..80f0abf5 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -68,7 +68,7 @@ mkin - 0.9.49.5 + 0.9.49.6 diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 0983007e..e9ad9343 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ Per default, parameters in the kinetic models are internally transformed in mkin - 0.9.49.5 + 0.9.49.6 @@ -327,7 +327,8 @@ Per default, parameters in the kinetic models are internally transformed in error_model_algorithm

If the error model is "const", the error model algorithm is ignored, because no special algorithm is needed and unweighted (also known as - ordinary) least squares fitting can be applied.

+ ordinary) least squares fitting (listed as "OLS" in the summary) can be + applied.

The default algorithm "d_3" will directly minimize the negative log-likelihood and - independently - also use the three step algorithm described below. The fit with the higher likelihood is returned.

@@ -397,21 +398,21 @@ Per default, parameters in the kinetic models are internally transformed in

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.5 
+summary(fit)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:21 2019 
-#> Date of summary: Thu Jul  4 08:02:21 2019 
+#> Date of fit:     Fri Jul  5 15:50:49 2019 
+#> Date of summary: Fri Jul  5 15:50:49 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.464 s
+#> Fitted using 222 model solutions performed in 0.455 s
 #> 
 #> Error model: Constant variance 
 #> 
-#> Error model algorithm: d_3 
+#> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
 #>              value   type
@@ -481,7 +482,10 @@ Per default, parameters in the kinetic models are internally transformed in
   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)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.507       0.004       1.511 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.502       0.000       1.503 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>         99.598483         -3.038220         -2.980300         -5.247500 
+#>             sigma 
+#>          3.125504 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -553,7 +557,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.078       0.000       1.078 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.089       0.000       1.089 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>         99.598483         -3.038220         -2.980300         -5.247500 
+#>             sigma 
+#>          3.125504 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -583,10 +590,10 @@ Per default, parameters in the kinetic models are internally transformed in
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data

 
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.5 
+                      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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:37 2019 
-#> Date of summary: Thu Jul  4 08:02:37 2019 
+#> Date of fit:     Fri Jul  5 15:51:05 2019 
+#> Date of summary: Fri Jul  5 15:51:05 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -594,11 +601,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.096 s
+#> Fitted using 421 model solutions performed in 1.08 s
 #> 
 #> Error model: Constant variance 
 #> 
-#> Error model algorithm: d_3 
+#> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
 #>                     value   type
@@ -702,10 +709,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   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
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.5 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:40 2019 
-#> Date of summary: Thu Jul  4 08:02:40 2019 
+#> Date of fit:     Fri Jul  5 15:51:08 2019 
+#> Date of summary: Fri Jul  5 15:51:08 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -713,7 +720,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.574 s
+#> Fitted using 979 model solutions performed in 2.623 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -834,10 +841,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.5 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:49 2019 
-#> Date of summary: Thu Jul  4 08:02:49 2019 
+#> Date of fit:     Fri Jul  5 15:51:17 2019 
+#> Date of summary: Fri Jul  5 15:51:17 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -845,7 +852,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.379 s
+#> Fitted using 2289 model solutions performed in 9.215 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 39fe631b..12832ef5 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -68,7 +68,7 @@ For the definition of model types and their parameters, the equations given
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
@@ -234,7 +234,7 @@ 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 file6e9c38dae9ed.c 2> file6e9c38dae9ed.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file2cf21d96d281.c 2> file2cf21d96d281.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 71fd6245..05a597a1 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 5ac632c8..f32e0758 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index ef847245..53739b55 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
@@ -328,17 +328,17 @@
                 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
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.002       0.000       0.002 
  system.time(
+#>       0.002       0.000       0.001 
  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 verstrichen 
-#>       0.022       0.000       0.021 

+#>       0.022       0.000       0.022 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
 #> Sum of squared residuals at call 3: 552.5739
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 45722db4..1c485c93 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 4d81f639..e3035247 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 38c46b6e..abd42f92 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
@@ -194,8 +194,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.055       0.032       5.069 
time_1
#>        User      System verstrichen 
-#>      19.260       0.000      19.271 

+#>       0.044       0.040       4.908 
time_1
#>        User      System verstrichen 
+#>      19.106       0.000      19.171 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index e0c3c0e2..1153f553 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 5cab42fd..7c6f2aac 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -68,7 +68,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 0b626d1b..ef734bc8 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -67,7 +67,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index fdc6e0ac..55fea47c 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -67,7 +67,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 7c401533..5eb42e68 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 4ca7631b..96279b89 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index 10afb77d..af0d9f65 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 50e07d37..a9c64362 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index b73b81f4..cbf253f9 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -68,7 +68,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index c4d2653d..2fa2dbe7 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
@@ -209,21 +209,21 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:04:08 2019 
-#> Date of summary: Thu Jul  4 08:04:08 2019 
+#> Date of fit:     Fri Jul  5 15:52:35 2019 
+#> Date of summary: Fri Jul  5 15:52:35 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.268 s
+#> Fitted using 131 model solutions performed in 0.266 s
 #> 
 #> Error model: Constant variance 
 #> 
-#> Error model algorithm: d_3 
+#> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
 #>                    value   type
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 4a7ca728..1f8bc914 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -78,7 +78,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index e40d320f..8899ed11 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index bf134334..72b4c2a7 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -71,7 +71,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.49.5
+        0.9.49.6
       
     
 
-- 
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