From 1c7b39f3c542de75a1ba685fec3c154bef8a3301 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 18:30:21 +0200 Subject: Static documentation rebuilt by pkgdown to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly --- docs/articles/FOCUS_D.html | 6 ++--- docs/articles/FOCUS_L.html | 42 ++++++++++++++--------------- docs/articles/twa.html | 2 +- docs/articles/web_only/benchmarks.html | 20 +++++++------- docs/articles/web_only/compiled_models.html | 10 +++---- docs/reference/mkinfit.html | 28 +++++++++---------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 ++--- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++--- 10 files changed, 63 insertions(+), 63 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index c22eb2c3..53164ffd 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -170,8 +170,8 @@
summary(fit)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:05 2019 
-## Date of summary: Wed Sep 18 17:55:06 2019 
+## Date of fit:     Wed Sep 18 18:24:07 2019 
+## Date of summary: Wed Sep 18 18:24:08 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +179,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.003 s
+## Fitted using 389 model solutions performed in 1.014 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 428ca84f..50c83db6 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -116,15 +116,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:08 2019 
-## Date of summary: Wed Sep 18 17:55:08 2019 
+## Date of fit:     Wed Sep 18 18:24:09 2019 
+## Date of summary: Wed Sep 18 18:24:09 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.293 s
+## Fitted using 133 model solutions performed in 0.287 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -218,8 +218,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:10 2019 
-## Date of summary: Wed Sep 18 17:55:10 2019 
+## Date of fit:     Wed Sep 18 18:24:12 2019 
+## Date of summary: Wed Sep 18 18:24:12 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.914 s
+## Fitted using 899 model solutions performed in 1.954 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -323,15 +323,15 @@
 
summary(m.L2.FOMC, data = FALSE)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:11 2019 
-## Date of summary: Wed Sep 18 17:55:11 2019 
+## Date of fit:     Wed Sep 18 18:24:13 2019 
+## Date of summary: Wed Sep 18 18:24:13 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.511 s
+## Fitted using 239 model solutions performed in 0.497 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -399,8 +399,8 @@
 
summary(m.L2.DFOP, data = FALSE)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:12 2019 
-## Date of summary: Wed Sep 18 17:55:12 2019 
+## Date of fit:     Wed Sep 18 18:24:14 2019 
+## Date of summary: Wed Sep 18 18:24:14 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,7 +409,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.217 s
+## Fitted using 572 model solutions performed in 1.215 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -499,8 +499,8 @@
 
summary(mm.L3[["DFOP", 1]])
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:14 2019 
-## Date of summary: Wed Sep 18 17:55:14 2019 
+## Date of fit:     Wed Sep 18 18:24:16 2019 
+## Date of summary: Wed Sep 18 18:24:16 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,7 +509,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.803 s
+## Fitted using 373 model solutions performed in 0.778 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -605,15 +605,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:15 2019 
-## Date of summary: Wed Sep 18 17:55:15 2019 
+## Date of fit:     Wed Sep 18 18:24:17 2019 
+## Date of summary: Wed Sep 18 18:24:17 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.301 s
+## Fitted using 142 model solutions performed in 0.293 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -670,15 +670,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Wed Sep 18 17:55:15 2019 
-## Date of summary: Wed Sep 18 17:55:15 2019 
+## Date of fit:     Wed Sep 18 18:24:17 2019 
+## Date of summary: Wed Sep 18 18:24:17 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.458 s
+## Fitted using 224 model solutions performed in 0.46 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 799349d9..2d44a89d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -130,7 +130,7 @@
 

\[f_\textrm{twa} = \frac{1}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]

-

Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the ‘max_twa_parent’ function. If the same is needed for metabolites, the function ‘max_twa’ from the ‘pfm’ package can be used.

+

Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the max_twa_parent() function. If the same is needed for metabolites, the function pfm::max_twa() from the ‘pfm’ package can be used.

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 144c4c29..d46e738a 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -204,70 +204,70 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.940 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.970 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.631 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.524 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.507 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.607 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.282 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.617 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.727 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.543 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.634 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.579 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.295 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.341 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.13 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.101 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.064 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.211 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.034 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.041 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 6594c3e6..1876e2b3 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -165,9 +165,9 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.143    1.000     3.141        0
-## 1 deSolve, not compiled            3  28.853    9.180    28.839        0
-## 2      Eigenvalue based            3   4.427    1.409     4.425        0
+## 3     deSolve, compiled            3   3.129    1.000     3.127        0
+## 1 deSolve, not compiled            3  28.841    9.217    28.827        0
+## 2      Eigenvalue based            3   4.433    1.417     4.430        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -216,8 +216,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.956    1.000     4.952        0
-## 1 deSolve, not compiled            3  53.338   10.762    53.312        0
+## 2     deSolve, compiled            3   4.860    1.000     4.857        0
+## 1 deSolve, not compiled            3  53.877   11.086    53.850        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 954086b5..dc052f2a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -408,15 +408,15 @@ Per default, parameters in the kinetic models are internally transformed in fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 17:53:04 2019 -#> Date of summary: Wed Sep 18 17:53:04 2019 +#> Date of fit: Wed Sep 18 18:22:06 2019 +#> Date of summary: Wed Sep 18 18:22:06 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 0.467 s +#> Fitted using 222 model solutions performed in 0.459 s #> #> Error model: Constant variance #> @@ -490,7 +490,7 @@ 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 -#> 1.524 0.000 1.527
coef(fit)
#> NULL
#> $ff +#> 1.494 0.000 1.496
coef(fit)
#> NULL
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -563,7 +563,7 @@ 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 -#> 1.115 0.000 1.116
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.056 0.000 1.057
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -599,8 +599,8 @@ Per default, parameters in the kinetic models are internally transformed in 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 17:53:19 2019 -#> Date of summary: Wed Sep 18 17:53:19 2019 +#> Date of fit: Wed Sep 18 18:22:22 2019 +#> Date of summary: Wed Sep 18 18:22:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.167 s +#> Fitted using 421 model solutions performed in 1.15 s #> #> Error model: Constant variance #> @@ -718,8 +718,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 17:53:22 2019 -#> Date of summary: Wed Sep 18 17:53:22 2019 +#> Date of fit: Wed Sep 18 18:22:24 2019 +#> Date of summary: Wed Sep 18 18:22:24 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.583 s +#> Fitted using 979 model solutions performed in 2.553 s #> #> Error model: Variance unique to each observed variable #> @@ -850,8 +850,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 17:53:31 2019 -#> Date of summary: Wed Sep 18 17:53:31 2019 +#> Date of fit: Wed Sep 18 18:22:34 2019 +#> Date of summary: Wed Sep 18 18:22:34 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.35 s +#> Fitted using 2289 model solutions performed in 9.369 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 4c73a0db..a5cdd04d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -239,7 +239,7 @@ 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 file195c26c6bf0a.c 2> file195c26c6bf0a.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file310b6c1fede0.c 2> file310b6c1fede0.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f2c6f87f..97d3ca3a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -332,17 +332,17 @@ 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 -#> 0.003 0.000 0.003
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 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.001 0.000 0.001
system.time( +#> 0.001 0.000 0.002
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 0.022
+#> 0.021 0.000 0.022
# \dontrun{ # 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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index eac99579..81ebde7c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -199,8 +199,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.013 0.027 5.014
time_1
#> User System verstrichen -#> 19.047 0.000 19.057
+#> 0.013 0.039 5.128
time_1
#> User System verstrichen +#> 18.942 0.000 18.951
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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index cc2ac55a..c5d58911 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -215,15 +215,15 @@

Examples

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: 3.6.1 -#> Date of fit: Wed Sep 18 17:54:50 2019 -#> Date of summary: Wed Sep 18 17:54:50 2019 +#> Date of fit: Wed Sep 18 18:23:52 2019 +#> Date of summary: Wed Sep 18 18:23:52 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.27 s +#> Fitted using 131 model solutions performed in 0.268 s #> #> Error model: Constant variance #> -- cgit v1.2.1