From deca771bee44019b96e5562215ea45f5f902a339 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 21 Nov 2016 16:26:01 +0100 Subject: Rebuild some more topics with fix for dots argument --- docs/reference/Extract.mmkin.html | 8 ++--- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 48 +++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 8 ++--- docs/reference/mkinresplot.html | 2 +- docs/reference/mmkin.html | 6 ++-- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/summary.mkinfit.html | 8 ++--- docs/reference/synthetic_data_for_UBA.html | 6 ++-- docs/reference/transform_odeparms.html | 24 +++++++-------- 14 files changed, 66 insertions(+), 66 deletions(-) diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index bcf11173..2bba63eb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -239,7 +239,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.065 +#> 0.08 0.00 0.08 #> #> $mkinmod #> <mkinmod> model generated with @@ -428,7 +428,7 @@ #> } #> return(mC) #> } -#> <environment: 0x58e8e58> +#> <environment: 0x4807c50> #> #> $cost_notrans #> function (P) @@ -450,7 +450,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x58e8e58> +#> <environment: 0x4807c50> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -513,7 +513,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 18 22:52:07 2016" +#> [1] "Mon Nov 21 16:07:10 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 8eac2a55..1a8170ff 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: Fri Nov 18 22:52:15 2016 -#> Date of summary: Fri Nov 18 22:52:15 2016 +#> Date of fit: Mon Nov 21 16:07:20 2016 +#> Date of summary: Mon Nov 21 16:07:20 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 3.397 s +#> Fitted with method Port using 590 model solutions performed in 3.627 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: Fri Nov 18 22:52:16 2016 -#> Date of summary: Fri Nov 18 22:52:16 2016 +#> Date of fit: Mon Nov 21 16:07:22 2016 +#> Date of summary: Mon Nov 21 16:07:22 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 1.471 s +#> Fitted with method Port using 246 model solutions performed in 1.475 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 2f32348e..a992db8e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -336,7 +336,7 @@
Should a trace of the parameter values be listed?
-
&#8230;
+
…
Further arguments that will be passed to modFit.
@@ -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: Fri Nov 18 22:52:19 2016 -#> Date of summary: Fri Nov 18 22:52:19 2016 +#> Date of fit: Mon Nov 21 16:07:24 2016 +#> Date of summary: Mon Nov 21 16:07:24 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 0.145 s +#> Fitted with method Port using 64 model solutions performed in 0.162 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 -#> 1.244 1.176 0.911
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.368 1.244 1.029
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 -#> 0.724 0.040 0.713
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.784 0.032 0.773
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: Fri Nov 18 22:52:29 2016 -#> Date of summary: Fri Nov 18 22:52:29 2016 +#> Date of fit: Mon Nov 21 16:07:35 2016 +#> Date of summary: Mon Nov 21 16:07:35 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 0.757 s +#> Fitted with method Port using 185 model solutions performed in 0.808 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: Fri Nov 18 22:52:31 2016 -#> Date of summary: Fri Nov 18 22:52:31 2016 +#> Date of fit: Mon Nov 21 16:07:37 2016 +#> Date of summary: Mon Nov 21 16:07:37 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 2.046 s +#> Fitted with method Port using 486 model solutions performed in 2.071 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: Fri Nov 18 22:52:32 2016 -#> Date of summary: Fri Nov 18 22:52:32 2016 +#> Date of fit: Mon Nov 21 16:07:38 2016 +#> Date of summary: Mon Nov 21 16:07:38 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 0.64 s +#> Fitted with method Port using 155 model solutions performed in 0.645 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: Fri Nov 18 22:52:33 2016 -#> Date of summary: Fri Nov 18 22:52:33 2016 +#> Date of fit: Mon Nov 21 16:07:39 2016 +#> Date of summary: Mon Nov 21 16:07:39 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 0.752 s +#> Fitted with method Port using 174 model solutions performed in 0.724 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: Fri Nov 18 22:52:34 2016 -#> Date of summary: Fri Nov 18 22:52:34 2016 +#> Date of fit: Mon Nov 21 16:07:40 2016 +#> Date of summary: Mon Nov 21 16:07:40 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 1.28 s +#> Fitted with method Port using 316 model solutions performed in 1.306 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: Fri Nov 18 22:52:37 2016 -#> Date of summary: Fri Nov 18 22:52:37 2016 +#> Date of fit: Mon Nov 21 16:07:43 2016 +#> Date of summary: Mon Nov 21 16:07:43 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 2.631 s +#> Fitted with method Port using 648 model solutions performed in 2.758 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 0ec62a2b..dce23299 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 file2d971c8bce81.c 2> file2d971c8bce81.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file40bc52407fe7.c 2> file40bc52407fe7.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index cfd4b396..1b8a9828 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -107,7 +107,7 @@
an object of class mkinfit.
-
&#8230;
+
…
further arguments passed to plot.mkinfit.
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index a36e485b..d4d7caff 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -161,7 +161,7 @@ Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to FALSE). -
&#8230;
+
…
Further arguments passed to the ode solver in case such a solver is used.
@@ -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 -#> 0.008 0.020 0.005
system.time( +#> 0.000 0.028 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 elapsed -#> 0.012 0.004 0.002
system.time( +#> 0.016 0.004 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 -#> 0.036 0.000 0.034
+#> 0.052 0.000 0.052
#> user system elapsed -#> 16.184 0.108 9.158
time_1
#> user system elapsed -#> 21.764 0.000 21.764
+#> 16.488 0.116 9.046
time_1
#> user system elapsed +#> 22.788 0.004 22.795
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 a19ee195..f34ef5e5 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -206,7 +206,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
The number of significant digits for rounding the FOCUS chi2 error percentage.
-
&#8230;
+
…
Further arguments passed to plot.
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 71b1cac5..8fd98372 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -135,7 +135,7 @@
The relative height of the middle plot, if more than two rows of plots are shown.
-
&#8230;
+
…
Further arguments passed to plot.mkinfit and mkinresplot.
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 7796b0dd..a102410a 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -108,7 +108,7 @@
An mkinds object.
-
&#8230;
+
…
Not used.
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 9c22b621..139fd061 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -133,7 +133,7 @@
Number of digits to use for printing
-
&#8230;
+
…
optional arguments passed to methods like print.
@@ -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:     Fri Nov 18 22:53:26 2016 
-#> Date of summary: Fri Nov 18 22:53:26 2016 
+#> Date of fit:     Mon Nov 21 16:08:34 2016 
+#> Date of summary: Mon Nov 21 16:08:34 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 0.078 s
+#> Fitted with method Port using 35 model solutions performed in 0.082 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 7eb4b193..b050eb25 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:     Fri Nov 18 22:53:29 2016 
-#> Date of summary: Fri Nov 18 22:53:29 2016 
+#> Date of fit:     Mon Nov 21 16:08:37 2016 
+#> Date of summary: Mon Nov 21 16:08:37 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 2.1 s
+#> Fitted with method Port using 351 model solutions performed in 2.261 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 84d3d0e1..2fc74a5a 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:     Fri Nov 18 22:53:30 2016 
-#> Date of summary: Fri Nov 18 22:53:30 2016 
+#> Date of fit:     Mon Nov 21 16:08:38 2016 
+#> Date of summary: Mon Nov 21 16:08:38 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 0.618 s
+#> Fitted with method Port using 153 model solutions performed in 0.637 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:     Fri Nov 18 22:53:31 2016 
-#> Date of summary: Fri Nov 18 22:53:31 2016 
+#> Date of fit:     Mon Nov 21 16:08:39 2016 
+#> Date of summary: Mon Nov 21 16:08:39 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 1.335 s
+#> Fitted with method Port using 327 model solutions performed in 1.357 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:     Fri Nov 18 22:53:32 2016 
-#> Date of summary: Fri Nov 18 22:53:32 2016 
+#> Date of fit:     Mon Nov 21 16:08:40 2016 
+#> Date of summary: Mon Nov 21 16:08:40 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 0.749 s
+#> Fitted with method Port using 185 model solutions performed in 0.816 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:     Fri Nov 18 22:53:33 2016 
-#> Date of summary: Fri Nov 18 22:53:33 2016 
+#> Date of fit:     Mon Nov 21 16:08:41 2016 
+#> Date of summary: Mon Nov 21 16:08:41 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 0.426 s
+#> Fitted with method Port using 104 model solutions performed in 0.428 s
 #> 
 #> Weighting: none
 #> 
-- 
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