From d89e3d22eb9dc383897b09e9c5aa1b57f65cdbf0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 14:34:45 +0100 Subject: Add the logistic model --- docs/articles/FOCUS_D.html | 10 +- docs/articles/FOCUS_L.html | 58 +++--- 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 | 14 +- docs/news/index.html | 7 +- docs/reference/Extract.mmkin.html | 12 +- docs/reference/index.html | 6 + docs/reference/logistic.solution-1.png | Bin 0 -> 63411 bytes docs/reference/logistic.solution-2.png | Bin 0 -> 29229 bytes docs/reference/logistic.solution.html | 295 ++++++++++++++++++++++++++++ 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 | 4 +- docs/reference/transform_odeparms.html | 24 +-- 19 files changed, 403 insertions(+), 101 deletions(-) create mode 100644 docs/reference/logistic.solution-1.png create mode 100644 docs/reference/logistic.solution-2.png create mode 100644 docs/reference/logistic.solution.html (limited to 'docs') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 9acab53a..6a8500a0 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

-

2019-01-31

+

2019-02-21

@@ -161,10 +161,10 @@

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

summary(fit)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:37 2019 
-## Date of summary: Thu Jan 31 16:52:38 2019 
+## Date of fit:     Thu Feb 21 14:32:03 2019 
+## Date of summary: Thu Feb 21 14:32:04 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 0.695 s
+## Fitted with method Port using 153 model solutions performed in 0.735 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e3ca9aff..265dd96c 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

-

2019-01-31

+

2019-02-21

@@ -109,17 +109,17 @@

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:39 2019 
-## Date of summary: Thu Jan 31 16:52:39 2019 
+## Date of fit:     Thu Feb 21 14:32:06 2019 
+## Date of summary: Thu Feb 21 14:32:06 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 0.094 s
+## Fitted with method Port using 37 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -200,17 +200,17 @@
 plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

summary(m.L1.FOMC, data = FALSE)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:41 2019 
-## Date of summary: Thu Jan 31 16:52:41 2019 
+## Date of fit:     Thu Feb 21 14:32:08 2019 
+## Date of summary: Thu Feb 21 14:32:08 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 1.49 s
+## Fitted with method Port using 611 model solutions performed in 1.547 s
 ## 
 ## Weighting: none
 ## 
@@ -295,17 +295,17 @@
      main = "FOCUS L2 - FOMC")

summary(m.L2.FOMC, data = FALSE)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:42 2019 
-## Date of summary: Thu Jan 31 16:52:42 2019 
+## Date of fit:     Thu Feb 21 14:32:08 2019 
+## Date of summary: Thu Feb 21 14:32:08 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 0.198 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
 ## 
 ## Weighting: none
 ## 
@@ -366,10 +366,10 @@
      main = "FOCUS L2 - DFOP")

summary(m.L2.DFOP, data = FALSE)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:43 2019 
-## Date of summary: Thu Jan 31 16:52:43 2019 
+## Date of fit:     Thu Feb 21 14:32:09 2019 
+## Date of summary: Thu Feb 21 14:32:09 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 0.839 s
+## Fitted with method Port using 336 model solutions performed in 0.86 s
 ## 
 ## Weighting: none
 ## 
@@ -458,10 +458,10 @@
 

The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

summary(mm.L3[["DFOP", 1]])
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:44 2019 
-## Date of summary: Thu Jan 31 16:52:44 2019 
+## Date of fit:     Thu Feb 21 14:32:10 2019 
+## Date of summary: Thu Feb 21 14:32:11 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 0.341 s
+## Fitted with method Port using 137 model solutions performed in 0.351 s
 ## 
 ## Weighting: none
 ## 
@@ -559,17 +559,17 @@
 

The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

summary(mm.L4[["SFO", 1]], data = FALSE)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:44 2019 
-## Date of summary: Thu Jan 31 16:52:45 2019 
+## Date of fit:     Thu Feb 21 14:32:11 2019 
+## Date of summary: Thu Feb 21 14:32:11 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 0.11 s
+## Fitted with method Port using 46 model solutions performed in 0.113 s
 ## 
 ## Weighting: none
 ## 
@@ -619,17 +619,17 @@
 ##        DT50 DT90
 ## parent  106  352
summary(mm.L4[["FOMC", 1]], data = FALSE)
-
## mkin version used for fitting:    0.9.47.5 
+
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 16:52:45 2019 
-## Date of summary: Thu Jan 31 16:52:45 2019 
+## Date of fit:     Thu Feb 21 14:32:11 2019 
+## Date of summary: Thu Feb 21 14:32:11 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 0.162 s
+## Fitted with method Port using 66 model solutions performed in 0.168 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 488ca302..c5b0d9c1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -85,7 +85,7 @@
       

Introduction to mkin

Johannes Ranke

-

2019-01-31

+

2019-02-21

diff --git a/docs/articles/twa.html b/docs/articles/twa.html index d50b23ba..8a1f82a8 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

-

2019-01-31

+

2019-02-21

diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 84bd971f..c55abdbc 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

-

2019-01-31

+

2019-02-21

diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 08bb9b44..3a37d114 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

-

2019-01-31

+

2019-02-21

@@ -126,9 +126,9 @@ }
## Lade nötiges Paket: rbenchmark
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.353    1.000     2.352        0
-## 1 deSolve, not compiled            3  17.619    7.488    17.609        0
-## 2      Eigenvalue based            3   2.899    1.232     2.898        0
+## 3     deSolve, compiled            3   2.429    1.000     2.427        0
+## 1 deSolve, not compiled            3  17.826    7.339    17.815        0
+## 2      Eigenvalue based            3   2.968    1.222     2.967        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,13 +157,13 @@
 }
## Successfully compiled differential equation model from auto-generated C code.
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.180    1.000     4.177        0
-## 1 deSolve, not compiled            3  37.331    8.931    37.312        0
+## 2     deSolve, compiled            3   4.234    1.000     4.232        0
+## 1 deSolve, not compiled            3  37.807    8.929    37.785        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

-

This vignette was built with mkin 0.9.47.5 on

+

This vignette was built with mkin 0.9.47.6 on

## R version 3.5.2 (2018-12-20)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)
diff --git a/docs/news/index.html b/docs/news/index.html index 7736a28d..4a4d71fe 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -119,9 +119,9 @@ -
+

-mkin 0.9.47.6 (2019-01-31) Unreleased +mkin 0.9.48.1 (2019-02-21) Unreleased

  • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects

  • @@ -132,6 +132,7 @@
  • ‘mkinfit’: Improve the correctness of the fitted two component error model by fitting the mean absolute deviance at each observation against the observed values, weighting with the current two-component error model

  • ‘tests/testthat/test_irls.R’: Test if the components of the error model used to generate the data can be reproduced with moderate accuracy

  • Add the function ‘CAKE_export’ to facilitate cross-checking of results

  • +
  • Implement the logistic model (only tested for parent fits)

@@ -675,7 +676,7 @@

Contents

#> 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:05 2019 -#> Date of summary: Thu Jan 31 16:51:05 2019 +#> Date of fit: Thu Feb 21 14:30:31 2019 +#> Date of summary: Thu Feb 21 14:30:31 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 3.87 s +#> Fitted with method Port using 574 model solutions performed in 3.822 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:07 2019 -#> Date of summary: Thu Jan 31 16:51:07 2019 +#> Date of fit: Thu Feb 21 14:30:32 2019 +#> Date of summary: Thu Feb 21 14:30:32 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 1.618 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 42845d68..d09b9232 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:10 2019 -#> Date of summary: Thu Jan 31 16:51:10 2019 +#> Date of fit: Thu Feb 21 14:30:35 2019 +#> Date of summary: Thu Feb 21 14:30:35 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 0.162 s +#> Fitted with method Port using 64 model solutions performed in 0.16 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 -#> 1.022 0.000 1.025
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.017 0.004 1.022
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
#> $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 -#> 0.823 0.000 0.823
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.845 0.000 0.846
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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:22 2019 -#> Date of summary: Thu Jan 31 16:51:22 2019 +#> Date of fit: Thu Feb 21 14:30:47 2019 +#> Date of summary: Thu Feb 21 14:30:47 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 0.872 s +#> Fitted with method Port using 186 model solutions performed in 0.86 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:24 2019 -#> Date of summary: Thu Jan 31 16:51:24 2019 +#> Date of fit: Thu Feb 21 14:30:50 2019 +#> Date of summary: Thu Feb 21 14:30:50 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 2.558 s +#> Fitted with method Port using 551 model solutions performed in 2.529 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:25 2019 -#> Date of summary: Thu Jan 31 16:51:25 2019 +#> Date of fit: Thu Feb 21 14:30:51 2019 +#> Date of summary: Thu Feb 21 14:30:51 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 0.711 s +#> Fitted with method Port using 155 model solutions performed in 0.707 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:26 2019 -#> Date of summary: Thu Jan 31 16:51:26 2019 +#> Date of fit: Thu Feb 21 14:30:52 2019 +#> Date of summary: Thu Feb 21 14:30:52 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 0.807 s +#> Fitted with method Port using 174 model solutions performed in 0.792 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:28 2019 -#> Date of summary: Thu Jan 31 16:51:28 2019 +#> Date of fit: Thu Feb 21 14:30:53 2019 +#> Date of summary: Thu Feb 21 14:30:53 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 1.257 s +#> Fitted with method Port using 270 model solutions performed in 1.243 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:51:31 2019 -#> Date of summary: Thu Jan 31 16:51:31 2019 +#> Date of fit: Thu Feb 21 14:30:57 2019 +#> Date of summary: Thu Feb 21 14:30:57 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 3.3 s +#> Fitted with method Port using 692 model solutions performed in 3.27 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 84b335f7..0710e6de 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 file165a4bc987b7.c 2> file165a4bc987b7.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file33652d0fd552.c 2> file33652d0fd552.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index c34da511..8c5bf22b 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 -#> 0.003 0.000 0.003
system.time( +#> 0.004 0.000 0.004
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 @@ -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 -#> 0.042 0.000 0.042
+#> 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 3fa5c9a5..75da28c7 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 -#> 0.045 0.036 7.264
time_1
#> User System verstrichen -#> 22.905 0.000 22.919
+#> 0.039 0.040 7.082
time_1
#> User System verstrichen +#> 22.650 0.004 22.666
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 2815eccb..242d9f63 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -208,8 +208,8 @@

Examples

summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:52:23 2019 -#> Date of summary: Thu Jan 31 16:52:23 2019 +#> Date of fit: Thu Feb 21 14:31:48 2019 +#> Date of summary: Thu Feb 21 14:31:48 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index d3c20ed8..939fa7b4 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:52:31 2019 -#> Date of summary: Thu Jan 31 16:52:31 2019 +#> Date of fit: Thu Feb 21 14:31:57 2019 +#> Date of summary: Thu Feb 21 14:31:57 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 0.703 s +#> Fitted with method Port using 153 model solutions performed in 0.849 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:52:33 2019 -#> Date of summary: Thu Jan 31 16:52:33 2019 +#> Date of fit: Thu Feb 21 14:31:59 2019 +#> Date of summary: Thu Feb 21 14:31:59 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 1.597 s +#> Fitted with method Port using 350 model solutions performed in 1.649 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:52:34 2019 -#> Date of summary: Thu Jan 31 16:52:34 2019 +#> Date of fit: Thu Feb 21 14:32:00 2019 +#> Date of summary: Thu Feb 21 14:32:00 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 0.898 s +#> Fitted with method Port using 186 model solutions performed in 0.976 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Jan 31 16:52:35 2019 -#> Date of summary: Thu Jan 31 16:52:35 2019 +#> Date of fit: Thu Feb 21 14:32:01 2019 +#> Date of summary: Thu Feb 21 14:32:01 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 0.482 s +#> Fitted with method Port using 104 model solutions performed in 0.512 s #> #> Weighting: none #> -- cgit v1.2.1