From 8ec45cd4a89fe8493fd688a0d34e25f279ad95b7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Dec 2016 07:59:20 +0100 Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE) --- docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_L.html | 44 +++++----- docs/articles/FOCUS_Z.R | 93 --------------------- ...6_Z_data_79c4b384b7a683bb55d11555628a14dc.RData | Bin 0 -> 3378 bytes ...006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb | Bin 0 -> 858 bytes ...006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx | Bin 0 -> 172 bytes docs/articles/cache/__packages | 13 +++ docs/articles/compiled_models.html | 30 +++---- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9618 -> 9742 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 10679 -> 10742 bytes docs/articles/mkin.html | 2 +- docs/reference/Extract.mmkin.html | 8 +- docs/reference/mccall81_245T.html | 12 +-- docs/reference/mkinfit.html | 46 +++++----- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 +- docs/reference/mmkin.html | 4 +- docs/reference/plot.mkinfit.html | 4 + docs/reference/plot.mmkin.html | 3 + docs/reference/summary.mkinfit.html | 6 +- docs/reference/synthetic_data_for_UBA.html | 6 +- docs/reference/transform_odeparms.html | 24 +++--- 22 files changed, 116 insertions(+), 189 deletions(-) create mode 100644 docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData create mode 100644 docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb create mode 100644 docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx create mode 100644 docs/articles/cache/__packages diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 782a789d..9640c62f 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -54,7 +54,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2016-11-18

+

2016-12-08

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 68054ec1..6a25282b 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -54,7 +54,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2016-11-18

+

2016-12-08

@@ -76,15 +76,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO) 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:43 2016 
-## Date of summary: Fri Nov 18 22:54:43 2016 
+## Date of fit:     Thu Dec  8 07:59:15 2016 
+## Date of summary: Thu Dec  8 07:59:15 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:44 2016 
-## Date of summary: Fri Nov 18 22:54:44 2016 
+## Date of fit:     Thu Dec  8 07:59:15 2016 
+## Date of summary: Thu Dec  8 07:59:15 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin <-  
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:44 2016 
-## Date of summary: Fri Nov 18 22:54:44 2016 
+## Date of fit:     Thu Dec  8 07:59:16 2016 
+## Date of summary: Thu Dec  8 07:59:16 2016 
 ## 
 ## 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 0.184 s
+## Fitted with method Port using 81 model solutions performed in 0.19 s
 ## 
 ## Weighting: none
 ## 
@@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:45 2016 
-## Date of summary: Fri Nov 18 22:54:46 2016 
+## Date of fit:     Thu Dec  8 07:59:17 2016 
+## Date of summary: Thu Dec  8 07:59:17 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:47 2016 
+## Date of fit:     Thu Dec  8 07:59:18 2016 
+## Date of summary: Thu Dec  8 07:59:18 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:48 2016 
+## Date of fit:     Thu Dec  8 07:59:19 2016 
+## Date of summary: Thu Dec  8 07:59:19 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.108 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
 ## 
 ## Weighting: none
 ## 
@@ -585,15 +585,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:48 2016 
+## Date of fit:     Thu Dec  8 07:59:19 2016 
+## Date of summary: Thu Dec  8 07:59:19 2016 
 ## 
 ## 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 0.145 s
+## Fitted with method Port using 66 model solutions performed in 0.152 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index 5c70b57e..eacefa90 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -20,96 +20,3 @@ FOCUS_2006_Z = data.frame(
 
 FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
 
-## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-------------------
-Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                Z1 = mkinsub("SFO"))
-m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a)
-summary(m.Z.2a, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6-------------------
-Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                   Z1 = mkinsub("SFO"),
-                   use_of_ff = "max")
-
-m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a.ff)
-summary(m.Z.2a.ff, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6-------------------
-Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.3)
-summary(m.Z.3, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7-------------------
-Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-               Z2 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.5)
-
-## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8-------------------
-Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                   Z2 = mkinsub("SFO", "Z3"),
-                   Z3 = mkinsub("SFO"),
-                   use_of_ff = "max")
-m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
-                     parms.ini = m.Z.5$bparms.ode,
-                     quiet = TRUE)
-plot_sep(m.Z.FOCUS)
-summary(m.Z.FOCUS, data = FALSE)$bpar
-endpoints(m.Z.FOCUS)
-
-## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8-------------------
-Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
-m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.1)
-summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
-
-## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8-------------------
-Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO"))
-m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.3)
-
-## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------
-Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFO"))
-m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
-                      parms.ini = m.Z.mkin.3$bparms.ode,
-                      quiet = TRUE)
-plot_sep(m.Z.mkin.4)
-
-## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------
-Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
-m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                      parms.ini = m.Z.mkin.4$bparms.ode[1:4],
-                      quiet = TRUE)
-plot_sep(m.Z.mkin.5)
-
-## ----FOCUS_2006_Z_fits_11a, echo=TRUE-------------------------------
-m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
-                                     k_Z3_bound_free = 0),
-                       fixed_parms = "k_Z3_bound_free",
-                       quiet = TRUE)
-plot_sep(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b, echo=TRUE-------------------------------
-mkinparplot(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE---------------------
-endpoints(m.Z.mkin.5a)
-
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData
new file mode 100644
index 00000000..282678c3
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diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb
new file mode 100644
index 00000000..9c88c526
Binary files /dev/null and b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx
new file mode 100644
index 00000000..5f5be10e
Binary files /dev/null and b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx differ
diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages
new file mode 100644
index 00000000..03ece635
--- /dev/null
+++ b/docs/articles/cache/__packages
@@ -0,0 +1,13 @@
+base
+datasets
+utils
+grDevices
+graphics
+stats
+knitr
+minpack.lm
+rootSolve
+methods
+inline
+parallel
+mkin
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 87913685..d39caf12 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -54,7 +54,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2016-11-18

+            
2016-12-08

           
 
     
@@ -91,21 +91,21 @@ mb.1 <- micr
 print(mb.1)

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6126.4954 6152.1764 6170.8152 6177.8573 6192.9751
-##       Eigenvalue based  864.8441  891.7069  902.0212  918.5697  920.6098
-##      deSolve, compiled  706.9115  711.1015  714.9195  715.2915  718.9235
+##  deSolve, not compiled 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
+##       Eigenvalue based  865.5257  872.4146  892.2705  879.3036  905.6429
+##      deSolve, compiled  716.7534  717.9075  724.6869  719.0617  728.6537
 ##        max neval cld
-##  6208.0929     3   c
-##   922.6498     3  b 
-##   722.5556     3 a

+##  6313.5506     3   c
+##   931.9821     3  b 
+##   738.2457     3 a

 
autoplot(mb.1)

 

-
We see that using the compiled model is by a factor of 8.6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+
We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                         median
-## deSolve, not compiled 8.636839
-## Eigenvalue based      1.284189
+## deSolve, not compiled 8.738789
+## Eigenvalue based      1.222849
 ## deSolve, compiled     1.000000

 
 

@@ -127,18 +127,18 @@ smb.1["median"]/smbprint(mb.2)

 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.163796 13.205491 13.478255 13.247187 13.635484
-##      deSolve, compiled  1.267154  1.268198  1.272722  1.269242  1.275506
+##  deSolve, not compiled 13.487097 13.492149 13.528060 13.497201 13.548541
+##      deSolve, compiled  1.307845  1.318979  1.322967  1.330114  1.330528
 ##        max neval cld
-##  14.023782     3   b
-##   1.281771     3  a

+##  13.599881     3   b
+##   1.330941     3  a

 
smb.2["median"]/smb.2["deSolve, compiled", "median"]

 
##   median
 ## 1     NA
 ## 2     NA

 
autoplot(mb.2)

 

-
Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!

+
Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.44.9000 on

 
## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 55aca8fa..d881a0a2 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 90ac9cbc..b3faa16f 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png differ
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 1292480b..c70f8ddf 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -54,7 +54,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2016-11-18

+            
2016-12-08

           
 
     
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 2bba63eb..4ef3bb00 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -239,7 +239,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>    0.08    0.00    0.08 
+#>   0.064   0.000   0.065 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -428,7 +428,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x4807c50>
+#> <environment: 0x5ce33e0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -450,7 +450,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x4807c50>
+#> <environment: 0x5ce33e0>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -513,7 +513,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Mon Nov 21 16:07:10 2016"
+#> [1] "Thu Dec  8 07:56:34 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 1a8170ff..123af096 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -130,8 +130,8 @@
     fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Optimisation by method Port did not converge.
 #> Convergence code is 1
    summary(fit.1, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:20 2016 
-#> Date of summary: Mon Nov 21 16:07:20 2016 
+#> Date of fit:     Thu Dec  8 07:56:42 2016 
+#> Date of summary: Thu Dec  8 07:56:42 2016 
 #> 
 #> 
 #> Warning: Optimisation by method Port did not converge.
@@ -146,7 +146,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 590 model solutions performed in 3.627 s
+#> Fitted with method Port using 590 model solutions performed in 3.474 s
 #> 
 #> Weighting: none
 #> 
@@ -225,8 +225,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:22 2016 
-#> Date of summary: Mon Nov 21 16:07:22 2016 
+#> Date of fit:     Thu Dec  8 07:56:44 2016 
+#> Date of summary: Thu Dec  8 07:56:44 2016 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -236,7 +236,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.475 s
+#> Fitted with method Port using 246 model solutions performed in 1.44 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index a992db8e..3dd701d3 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -374,15 +374,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:24 2016 
-#> Date of summary: Mon Nov 21 16:07:24 2016 
+#> Date of fit:     Thu Dec  8 07:56:46 2016 
+#> Date of summary: Thu Dec  8 07:56:46 2016 
 #> 
 #> 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 0.162 s
+#> Fitted with method Port using 64 model solutions performed in 0.145 s
 #> 
 #> Weighting: none
 #> 
@@ -451,7 +451,7 @@
   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 elapsed 
-#>   1.368   1.244   1.029 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.172   1.232   0.904 
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 
@@ -528,7 +528,7 @@
 #> Model cost at call  152 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.784   0.032   0.773 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.712   0.044   0.709 
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 
@@ -571,8 +571,8 @@
                       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:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:35 2016 
-#> Date of summary: Mon Nov 21 16:07:35 2016 
+#> Date of fit:     Thu Dec  8 07:56:57 2016 
+#> Date of summary: Thu Dec  8 07:56:57 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -580,7 +580,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.808 s
+#> Fitted with method Port using 185 model solutions performed in 0.77 s
 #> 
 #> Weighting: none
 #> 
@@ -692,8 +692,8 @@
 #>   120       m1    33.31 2.879e+01  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:37 2016 
-#> Date of summary: Mon Nov 21 16:07:37 2016 
+#> Date of fit:     Thu Dec  8 07:56:59 2016 
+#> Date of summary: Thu Dec  8 07:56:59 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -701,7 +701,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 486 model solutions performed in 2.071 s
+#> Fitted with method Port using 486 model solutions performed in 2.019 s
 #> 
 #> Weighting: none then iterative reweighting method obs
 #> 
@@ -813,8 +813,8 @@
 #>   120       m1    33.31 2.881e+01  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:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:38 2016 
-#> Date of summary: Mon Nov 21 16:07:38 2016 
+#> Date of fit:     Thu Dec  8 07:57:00 2016 
+#> Date of summary: Thu Dec  8 07:57:00 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -822,7 +822,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.645 s
+#> Fitted with method Port using 155 model solutions performed in 0.65 s
 #> 
 #> Weighting: mean
 #> 
@@ -935,8 +935,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:39 2016 
-#> Date of summary: Mon Nov 21 16:07:39 2016 
+#> Date of fit:     Thu Dec  8 07:57:01 2016 
+#> Date of summary: Thu Dec  8 07:57:01 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -944,7 +944,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.724 s
+#> Fitted with method Port using 174 model solutions performed in 0.713 s
 #> 
 #> Weighting: manual
 #> 
@@ -1057,8 +1057,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:40 2016 
-#> Date of summary: Mon Nov 21 16:07:40 2016 
+#> Date of fit:     Thu Dec  8 07:57:02 2016 
+#> Date of summary: Thu Dec  8 07:57:02 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1066,7 +1066,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 316 model solutions performed in 1.306 s
+#> Fitted with method Port using 316 model solutions performed in 1.322 s
 #> 
 #> Weighting: manual
 #> 
@@ -1179,8 +1179,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:07:43 2016 
-#> Date of summary: Mon Nov 21 16:07:43 2016 
+#> Date of fit:     Thu Dec  8 07:57:05 2016 
+#> Date of summary: Thu Dec  8 07:57:05 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1188,7 +1188,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 648 model solutions performed in 2.758 s
+#> Fitted with method Port using 648 model solutions performed in 2.818 s
 #> 
 #> Weighting: manual then iterative reweighting method obs
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index dce23299..1044af6b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -188,7 +188,7 @@
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file40bc52407fe7.c 2> file40bc52407fe7.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2> file386742883b12.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index d4d7caff..766b6613 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -290,17 +290,17 @@
                 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 elapsed 
-#>   0.000   0.028   0.004 
  system.time(
+#>   0.012   0.020   0.005 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.016   0.004   0.003 
  system.time(
+#>   0.000   0.020   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", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.052   0.000   0.052 

+#>   0.032   0.000   0.035 

   
   
#>    user  system elapsed 
-#>  16.488   0.116   9.046 
time_1
#>    user  system elapsed 
-#>  22.788   0.004  22.795 

+#>  16.776   0.108   9.353 
time_1
#>    user  system elapsed 
+#>  22.696   0.000  22.701 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340479   0.2659521   0.7505687   0.2494313 
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index f34ef5e5..9969e198 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -99,6 +99,10 @@
     
Solves the differential equations with the optimised and fixed parameters
   from a previous successful call to mkinfit and plots
   the observed data together with the solution of the fitted model.

+
+    
If the current plot device is a tikz device,
+  then latex is being used for the formatting of the chi2 error level, 
+  if show_errmin = TRUE.

     
 
     
# S3 method for mkinfit
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 8fd98372..1d5d0574 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -99,6 +99,9 @@
     
When x is a row selected from an mmkin object ([.mmkin), the same model
   fitted for at least one dataset is shown. When it is a column, the fit of at least one model
   to the same dataset is shown.

+
+    
If the current plot device is a tikz device,
+  then latex is being used for the formatting of the chi2 error level.

     
 
     
# S3 method for mmkin
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 139fd061..b305410d 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -157,15 +157,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:34 2016 
-#> Date of summary: Mon Nov 21 16:08:34 2016 
+#> Date of fit:     Thu Dec  8 07:57:55 2016 
+#> Date of summary: Thu Dec  8 07:57:55 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.082 s
+#> Fitted with method Port using 35 model solutions performed in 0.079 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b050eb25..bc2bb02b 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -155,8 +155,8 @@
 fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE)
 plot_sep(fit)
summary(fit)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:37 2016 
-#> Date of summary: Mon Nov 21 16:08:37 2016 
+#> Date of fit:     Thu Dec  8 07:57:58 2016 
+#> Date of summary: Thu Dec  8 07:57:58 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -165,7 +165,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 351 model solutions performed in 2.261 s
+#> Fitted with method Port using 351 model solutions performed in 2.152 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 2fc74a5a..e1fb0437 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -164,8 +164,8 @@
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:38 2016 
-#> Date of summary: Mon Nov 21 16:08:38 2016 
+#> Date of fit:     Thu Dec  8 07:57:59 2016 
+#> Date of summary: Thu Dec  8 07:57:59 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -173,7 +173,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.637 s
+#> Fitted with method Port using 153 model solutions performed in 0.621 s
 #> 
 #> Weighting: none
 #> 
@@ -241,8 +241,8 @@
 fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:39 2016 
-#> Date of summary: Mon Nov 21 16:08:39 2016 
+#> Date of fit:     Thu Dec  8 07:58:01 2016 
+#> Date of summary: Thu Dec  8 07:58:01 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -250,7 +250,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 327 model solutions performed in 1.357 s
+#> Fitted with method Port using 327 model solutions performed in 1.419 s
 #> 
 #> Weighting: none
 #> 
@@ -331,8 +331,8 @@
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:40 2016 
-#> Date of summary: Mon Nov 21 16:08:40 2016 
+#> Date of fit:     Thu Dec  8 07:58:02 2016 
+#> Date of summary: Thu Dec  8 07:58:02 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -340,7 +340,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.816 s
+#> Fitted with method Port using 185 model solutions performed in 0.814 s
 #> 
 #> Weighting: none
 #> 
@@ -415,8 +415,8 @@
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Mon Nov 21 16:08:41 2016 
-#> Date of summary: Mon Nov 21 16:08:41 2016 
+#> Date of fit:     Thu Dec  8 07:58:03 2016 
+#> Date of summary: Thu Dec  8 07:58:03 2016 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -424,7 +424,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.428 s
+#> Fitted with method Port using 104 model solutions performed in 0.436 s
 #> 
 #> Weighting: none
 #> 
-- 
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