From b51d485d370cab50b08a0ed30669754d96f474be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 12:32:06 +0100 Subject: Include AIC.mmkin to static docs Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 ++++----- docs/reference/index.html | 6 +++++ 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 | 6 ++--- docs/reference/transform_odeparms.html | 24 +++++++++--------- 9 files changed, 61 insertions(+), 55 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index b304c2fb..e3f3ac6d 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.188 0.000 0.188 +#> 0.182 0.000 0.182 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd98970> -#> <environment: 0x55555d417aa8> +#> <bytecode: 0x55555bd94d60> +#> <environment: 0x55555d412b78> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd14308> -#> <environment: 0x55555d417aa8> +#> <bytecode: 0x55555cd0c8b0> +#> <environment: 0x55555d412b78> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 11:40:00 2018" +#> [1] "Mon Nov 26 12:27:35 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/index.html b/docs/reference/index.html index c1d31aff..92f54fc8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -219,6 +219,12 @@

plot(<mmkin>)

Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object

+ + + +

AIC(<mmkin>)

+ +

Calculated the AIC for a column of an mmkin object

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 96082932..ffccd3d5 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ anisole = list(type = "SFO"))
#> 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:20 2018 -#> Date of summary: Mon Nov 26 11:40:20 2018 +#> Date of fit: Mon Nov 26 12:27:54 2018 +#> Date of summary: Mon Nov 26 12:27:54 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.702 s +#> Fitted with method Port using 574 model solutions performed in 3.654 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:22 2018 -#> Date of summary: Mon Nov 26 11:40:22 2018 +#> Date of fit: Mon Nov 26 12:27:56 2018 +#> Date of summary: Mon Nov 26 12:27:56 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.646 s +#> Fitted with method Port using 246 model solutions performed in 1.629 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 77c69f4e..4ed354f0 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -436,15 +436,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:24 2018 -#> Date of summary: Mon Nov 26 11:40:24 2018 +#> Date of fit: Mon Nov 26 12:27:59 2018 +#> Date of summary: Mon Nov 26 12:27:59 2018 #> #> 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 0.156 s +#> Fitted with method Port using 64 model solutions performed in 0.155 s #> #> Weighting: none #> @@ -513,7 +513,7 @@ 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 -#> 0.989 0.000 0.990
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.002 0.000 1.003
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 @@ -588,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.799 0.000 0.800
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.794 0.000 0.793
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 @@ -626,8 +626,8 @@ 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:36 2018 -#> Date of summary: Mon Nov 26 11:40:36 2018 +#> Date of fit: Mon Nov 26 12:28:11 2018 +#> Date of summary: Mon Nov 26 12:28:11 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -635,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.839 s +#> Fitted with method Port using 186 model solutions performed in 0.824 s #> #> Weighting: none #> @@ -743,8 +743,8 @@ #> 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:39 2018 -#> Date of summary: Mon Nov 26 11:40:39 2018 +#> Date of fit: Mon Nov 26 12:28:13 2018 +#> Date of summary: Mon Nov 26 12:28:13 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -752,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.48 s +#> Fitted with method Port using 551 model solutions performed in 2.458 s #> #> Weighting: none #> @@ -865,8 +865,8 @@ #> 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:40 2018 -#> Date of summary: Mon Nov 26 11:40:40 2018 +#> Date of fit: Mon Nov 26 12:28:14 2018 +#> Date of summary: Mon Nov 26 12:28:14 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -874,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.694 s +#> Fitted with method Port using 155 model solutions performed in 0.69 s #> #> Weighting: mean #> @@ -983,8 +983,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:41 2018 -#> Date of summary: Mon Nov 26 11:40:41 2018 +#> Date of fit: Mon Nov 26 12:28:15 2018 +#> Date of summary: Mon Nov 26 12:28:15 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -992,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.778 s +#> Fitted with method Port using 174 model solutions performed in 0.774 s #> #> Weighting: manual #> @@ -1103,8 +1103,8 @@ 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: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:42 2018 -#> Date of summary: Mon Nov 26 11:40:42 2018 +#> Date of fit: Mon Nov 26 12:28:16 2018 +#> Date of summary: Mon Nov 26 12:28:16 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1112,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.225 s +#> Fitted with method Port using 270 model solutions performed in 1.205 s #> #> Weighting: manual #> @@ -1221,8 +1221,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 11:40:45 2018 -#> Date of summary: Mon Nov 26 11:40:45 2018 +#> Date of fit: Mon Nov 26 12:28:19 2018 +#> Date of summary: Mon Nov 26 12:28:19 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1230,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.119 s +#> Fitted with method Port using 692 model solutions performed in 3.1 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 0d644bc4..a9345c8e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ 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 file4252799a8f5a.c 2> file4252799a8f5a.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file5bb92cd04f44.c 2> file5bb92cd04f44.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index bfe71be5..e4bd2ade 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,12 +323,12 @@ 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 0.004
system.time( +#> 0.004 0.000 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")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.002 0.000 0.002
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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 92f12c2a..dc59c63f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -189,8 +189,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.050 0.037 6.958
time_1
#> User System verstrichen -#> 22.101 0.000 22.114
+#> 0.049 0.033 6.949
time_1
#> User System verstrichen +#> 22.053 0.000 22.068
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 554a28e3..b54ceff8 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@

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:       3.5.1 
-#> Date of fit:     Mon Nov 26 11:41:36 2018 
-#> Date of summary: Mon Nov 26 11:41:36 2018 
+#> Date of fit:     Mon Nov 26 12:29:10 2018 
+#> Date of summary: Mon Nov 26 12:29:10 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.083 s
+#> Fitted with method Port using 35 model solutions performed in 0.087 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index e6a42993..7433c5f2 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ 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:       3.5.1 
-#> Date of fit:     Mon Nov 26 11:41:44 2018 
-#> Date of summary: Mon Nov 26 11:41:44 2018 
+#> Date of fit:     Mon Nov 26 12:29:19 2018 
+#> Date of summary: Mon Nov 26 12:29:19 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ 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 0.686 s
+#> Fitted with method Port using 153 model solutions performed in 0.701 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ 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:       3.5.1 
-#> Date of fit:     Mon Nov 26 11:41:45 2018 
-#> Date of summary: Mon Nov 26 11:41:45 2018 
+#> Date of fit:     Mon Nov 26 12:29:20 2018 
+#> Date of summary: Mon Nov 26 12:29:20 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ 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 1.558 s
+#> Fitted with method Port using 350 model solutions performed in 1.597 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ 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:       3.5.1 
-#> Date of fit:     Mon Nov 26 11:41:46 2018 
-#> Date of summary: Mon Nov 26 11:41:46 2018 
+#> Date of fit:     Mon Nov 26 12:29:22 2018 
+#> Date of summary: Mon Nov 26 12:29:22 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ 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 0.828 s
+#> Fitted with method Port using 186 model solutions performed in 0.857 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ 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:       3.5.1 
-#> Date of fit:     Mon Nov 26 11:41:47 2018 
-#> Date of summary: Mon Nov 26 11:41:47 2018 
+#> Date of fit:     Mon Nov 26 12:29:22 2018 
+#> Date of summary: Mon Nov 26 12:29:22 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ 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 0.464 s
+#> Fitted with method Port using 104 model solutions performed in 0.474 s
 #> 
 #> Weighting: none
 #> 
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