From 396e40d2c45d81a8e74c41a2f632665021e980a1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 26 Feb 2019 20:28:15 +0100 Subject: NAFTA SOP Attachment vignette Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0 --- docs/reference/mkinfit.html | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 53f46988..84c0fc49 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:36 2019 -#> Date of summary: Tue Feb 26 09:27:36 2019 +#> Date of fit: Tue Feb 26 20:23:36 2019 +#> Date of summary: Tue Feb 26 20:23:36 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 0.163 s +#> Fitted with method Port using 64 model solutions performed in 0.161 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 -#> 1.008 0.000 1.008
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.081 0.000 1.081
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 @@ -590,7 +590,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.812 0.000 0.813
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.812 0.000 0.812
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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:48 2019 -#> Date of summary: Tue Feb 26 09:27:48 2019 +#> Date of fit: Tue Feb 26 20:23:48 2019 +#> Date of summary: Tue Feb 26 20:23:48 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 0.845 s +#> Fitted with method Port using 186 model solutions performed in 0.852 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:50 2019 -#> Date of summary: Tue Feb 26 09:27:50 2019 +#> Date of fit: Tue Feb 26 20:23:51 2019 +#> Date of summary: Tue Feb 26 20:23:51 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 2.523 s +#> Fitted with method Port using 551 model solutions performed in 2.6 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:51 2019 -#> Date of summary: Tue Feb 26 09:27:51 2019 +#> Date of fit: Tue Feb 26 20:23:52 2019 +#> Date of summary: Tue Feb 26 20:23:52 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 0.705 s +#> Fitted with method Port using 155 model solutions performed in 0.704 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:52 2019 -#> Date of summary: Tue Feb 26 09:27:52 2019 +#> Date of fit: Tue Feb 26 20:23:53 2019 +#> Date of summary: Tue Feb 26 20:23:53 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 0.8 s +#> Fitted with method Port using 174 model solutions performed in 0.796 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:54 2019 -#> Date of summary: Tue Feb 26 09:27:54 2019 +#> Date of fit: Tue Feb 26 20:23:54 2019 +#> Date of summary: Tue Feb 26 20:23:54 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:57 2019 -#> Date of summary: Tue Feb 26 09:27:57 2019 +#> Date of fit: Tue Feb 26 20:23:58 2019 +#> Date of summary: Tue Feb 26 20:23:58 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 3.246 s +#> Fitted with method Port using 692 model solutions performed in 3.182 s #> #> Weighting: manual #> -- cgit v1.2.1