From 62e66eb483aef4edcfd839e475354ef1ddb9e49f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:32:07 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 +++++----- docs/reference/logLik.mkinfit.html | 32 +++++++++++++++++++++++-- docs/reference/mccall81_245T.html | 12 +++++----- docs/reference/mkinfit.html | 44 +++++++++++++++++----------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 ++--- docs/reference/mmkin.html | 4 ++-- docs/reference/summary.mkinfit.html | 4 ++-- docs/reference/transform_odeparms.html | 24 +++++++++---------- 9 files changed, 84 insertions(+), 56 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index ec2c7eb7..33d90e5b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.184 0.000 0.184 +#> 0.182 0.000 0.183 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be327a0> -#> <environment: 0x55555bc27c20> +#> <bytecode: 0x55555be42410> +#> <environment: 0x55555bc697f8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd76230> -#> <environment: 0x55555bc27c20> +#> <bytecode: 0x55555cd2ca88> +#> <environment: 0x55555bc697f8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 09:05:19 2018" +#> [1] "Mon Nov 26 09:27:40 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 250bc1d8..5fd6c6d7 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -33,7 +33,21 @@ + calculated using dnorm, i.e. assuming normal distribution. +The total number of estimated parameters returned with the value + of the likelihood is calculated as the sum of fitted degradation + model parameters and the fitted error model parameters. +For the case of unweighted least squares fitting, we calculate one + constant standard deviation from the residuals using sd + and add one to the number of fitted degradation model parameters. +For the case of manual weighting, we use the weight given for each + observation as standard deviation in calculating its likelihood. +In the case of iterative reweighting, the variances obtained by this + procedure are used in the likelihood calculations, and the number of + estimated parameters is obtained by the number of degradation model + parameters plus the number of variance model parameters, i.e. the number of + observed variables if the reweighting method is "obs", and two if the + reweighting method is "tc"." /> @@ -125,7 +139,21 @@

This function simply calculates the product of the likelihood densities - calc

+ calculated using dnorm, i.e. assuming normal distribution.

+

The total number of estimated parameters returned with the value + of the likelihood is calculated as the sum of fitted degradation + model parameters and the fitted error model parameters.

+

For the case of unweighted least squares fitting, we calculate one + constant standard deviation from the residuals using sd + and add one to the number of fitted degradation model parameters.

+

For the case of manual weighting, we use the weight given for each + observation as standard deviation in calculating its likelihood.

+

In the case of iterative reweighting, the variances obtained by this + procedure are used in the likelihood calculations, and the number of + estimated parameters is obtained by the number of degradation model + parameters plus the number of variance model parameters, i.e. the number of + observed variables if the reweighting method is "obs", and two if the + reweighting method is "tc".

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 505da201..2cd933e9 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 09:05:38 2018 -#> Date of summary: Mon Nov 26 09:05:38 2018 +#> Date of fit: Mon Nov 26 09:27:59 2018 +#> Date of summary: Mon Nov 26 09:27:59 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 3.64 s +#> Fitted with method Port using 574 model solutions performed in 3.635 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 09:05:40 2018 -#> Date of summary: Mon Nov 26 09:05:40 2018 +#> Date of fit: Mon Nov 26 09:28:01 2018 +#> Date of summary: Mon Nov 26 09:28:01 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 1.626 s +#> Fitted with method Port using 246 model solutions performed in 1.623 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 2017a35c..addd9c30 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -436,8 +436,8 @@ 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 09:05:43 2018 -#> Date of summary: Mon Nov 26 09:05:43 2018 +#> Date of fit: Mon Nov 26 09:28:04 2018 +#> Date of summary: Mon Nov 26 09:28:04 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -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 -#> 0.974 0.000 0.975
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.009 0.000 1.009
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 -#> 0.796 0.000 0.796
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.909 0.000 0.910
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 09:05:54 2018 -#> Date of summary: Mon Nov 26 09:05:54 2018 +#> Date of fit: Mon Nov 26 09:28:16 2018 +#> Date of summary: Mon Nov 26 09:28:16 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 0.885 s +#> Fitted with method Port using 186 model solutions performed in 0.927 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 09:05:57 2018 -#> Date of summary: Mon Nov 26 09:05:57 2018 +#> Date of fit: Mon Nov 26 09:28:18 2018 +#> Date of summary: Mon Nov 26 09:28:18 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 2.451 s +#> Fitted with method Port using 551 model solutions performed in 2.509 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 09:05:58 2018 -#> Date of summary: Mon Nov 26 09:05:58 2018 +#> Date of fit: Mon Nov 26 09:28:19 2018 +#> Date of summary: Mon Nov 26 09:28:19 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 0.69 s +#> Fitted with method Port using 155 model solutions performed in 0.68 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 09:05:59 2018 -#> Date of summary: Mon Nov 26 09:05:59 2018 +#> Date of fit: Mon Nov 26 09:28:20 2018 +#> Date of summary: Mon Nov 26 09:28:20 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 0.772 s +#> Fitted with method Port using 174 model solutions performed in 0.775 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 09:06:00 2018 -#> Date of summary: Mon Nov 26 09:06:00 2018 +#> Date of fit: Mon Nov 26 09:28:22 2018 +#> Date of summary: Mon Nov 26 09:28:22 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 1.201 s +#> Fitted with method Port using 270 model solutions performed in 1.203 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 09:06:03 2018 -#> Date of summary: Mon Nov 26 09:06:03 2018 +#> Date of fit: Mon Nov 26 09:28:25 2018 +#> Date of summary: Mon Nov 26 09:28:25 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 3.087 s +#> Fitted with method Port using 692 model solutions performed in 3.078 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index a7f26322..448c0e8e 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 file672328842b40.c 2> file672328842b40.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file775a236112e7.c 2> file775a236112e7.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f26422a4..84e6591b 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,17 +323,17 @@ 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( +#> 0.004 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 #> 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 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.041 0.000 0.040
+#> 0.039 0.000 0.039
# 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 eb2e5bcf..a27cf5db 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 -#> 0.043 0.032 6.850
time_1
#> User System verstrichen -#> 21.779 0.000 21.791
+#> 0.038 0.036 6.851
time_1
#> User System verstrichen +#> 21.780 0.000 21.791
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 9cb43d42..7f510c67 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,8 +206,8 @@

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:       3.5.1 
-#> Date of fit:     Mon Nov 26 09:06:53 2018 
-#> Date of summary: Mon Nov 26 09:06:53 2018 
+#> Date of fit:     Mon Nov 26 09:29:14 2018 
+#> Date of summary: Mon Nov 26 09:29:14 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6178527b..24b50890 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 09:07:01 2018 
-#> Date of summary: Mon Nov 26 09:07:01 2018 
+#> Date of fit:     Mon Nov 26 09:29:22 2018 
+#> Date of summary: Mon Nov 26 09:29:22 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 0.687 s
+#> Fitted with method Port using 153 model solutions performed in 0.683 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 09:07:03 2018 
-#> Date of summary: Mon Nov 26 09:07:03 2018 
+#> Date of fit:     Mon Nov 26 09:29:24 2018 
+#> Date of summary: Mon Nov 26 09:29:24 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 1.537 s
+#> Fitted with method Port using 350 model solutions performed in 1.594 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 09:07:04 2018 
-#> Date of summary: Mon Nov 26 09:07:04 2018 
+#> Date of fit:     Mon Nov 26 09:29:25 2018 
+#> Date of summary: Mon Nov 26 09:29:25 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 0.827 s
+#> Fitted with method Port using 186 model solutions performed in 0.819 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 09:07:04 2018 
-#> Date of summary: Mon Nov 26 09:07:04 2018 
+#> Date of fit:     Mon Nov 26 09:29:26 2018 
+#> Date of summary: Mon Nov 26 09:29:26 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 0.454 s
+#> Fitted with method Port using 104 model solutions performed in 0.486 s
 #> 
 #> Weighting: none
 #> 
-- 
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