From 282f88f9e28e683f524d5e05d65d8b18ab856a8d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:49:58 +0100 Subject: Further improvement of the logLik.mkinfit help Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 +++++----- docs/reference/logLik.mkinfit.html | 8 +++++-- docs/reference/mccall81_245T.html | 12 +++++----- docs/reference/mkinfit.html | 44 +++++++++++++++++----------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 ++-- docs/reference/mmkin.html | 4 ++-- docs/reference/summary.mkinfit.html | 4 ++-- docs/reference/transform_odeparms.html | 24 +++++++++---------- 9 files changed, 59 insertions(+), 55 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 33d90e5b..51da42fc 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.182 0.000 0.183 +#> 0.183 0.000 0.183 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be42410> -#> <environment: 0x55555bc697f8> +#> <bytecode: 0x55555be28e50> +#> <environment: 0x55555bc4d2b0> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd2ca88> -#> <environment: 0x55555bc697f8> +#> <bytecode: 0x55555cd2fbb8> +#> <environment: 0x55555bc4d2b0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 09:27:40 2018" +#> [1] "Mon Nov 26 09:45:35 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 5fd6c6d7..b1901703 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -41,7 +41,9 @@ 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. + observation as standard deviation in calculating its likelihood + and the total number of estimated parameters is equal to the + number of fitted degradation model parameters. 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 @@ -147,7 +149,9 @@ In the case of iterative reweighting, the variances obtained by this 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.

+ observation as standard deviation in calculating its likelihood + and the total number of estimated parameters is equal to the + number of fitted degradation model parameters.

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 diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 2cd933e9..981c633a 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 09:27:59 2018 -#> Date of summary: Mon Nov 26 09:27:59 2018 +#> Date of fit: Mon Nov 26 09:45:54 2018 +#> Date of summary: Mon Nov 26 09:45:54 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 3.635 s +#> Fitted with method Port using 574 model solutions performed in 3.641 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 09:28:01 2018 -#> Date of summary: Mon Nov 26 09:28:01 2018 +#> Date of fit: Mon Nov 26 09:45:56 2018 +#> Date of summary: Mon Nov 26 09:45:56 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 1.623 s +#> Fitted with method Port using 246 model solutions performed in 1.627 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index addd9c30..883dda22 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 09:28:04 2018 -#> Date of summary: Mon Nov 26 09:28:04 2018 +#> Date of fit: Mon Nov 26 09:45:59 2018 +#> Date of summary: Mon Nov 26 09:45:59 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 -#> 1.009 0.000 1.009
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.974 0.000 0.975
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 -#> 0.909 0.000 0.910
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.79 0.00 0.79
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 09:28:16 2018 -#> Date of summary: Mon Nov 26 09:28:16 2018 +#> Date of fit: Mon Nov 26 09:46:10 2018 +#> Date of summary: Mon Nov 26 09:46:10 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 0.927 s +#> Fitted with method Port using 186 model solutions performed in 0.889 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 09:28:18 2018 -#> Date of summary: Mon Nov 26 09:28:18 2018 +#> Date of fit: Mon Nov 26 09:46:13 2018 +#> Date of summary: Mon Nov 26 09:46:13 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 2.509 s +#> Fitted with method Port using 551 model solutions performed in 2.441 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 09:28:19 2018 -#> Date of summary: Mon Nov 26 09:28:19 2018 +#> Date of fit: Mon Nov 26 09:46:14 2018 +#> Date of summary: Mon Nov 26 09:46:14 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 0.68 s +#> Fitted with method Port using 155 model solutions performed in 0.679 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 09:28:20 2018 -#> Date of summary: Mon Nov 26 09:28:20 2018 +#> Date of fit: Mon Nov 26 09:46:15 2018 +#> Date of summary: Mon Nov 26 09:46:15 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 0.775 s +#> Fitted with method Port using 174 model solutions performed in 0.771 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 09:28:22 2018 -#> Date of summary: Mon Nov 26 09:28:22 2018 +#> Date of fit: Mon Nov 26 09:46:16 2018 +#> Date of summary: Mon Nov 26 09:46:16 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 1.203 s +#> Fitted with method Port using 270 model solutions performed in 1.2 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 09:28:25 2018 -#> Date of summary: Mon Nov 26 09:28:25 2018 +#> Date of fit: Mon Nov 26 09:46:19 2018 +#> Date of summary: Mon Nov 26 09:46:19 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 3.078 s +#> Fitted with method Port using 692 model solutions performed in 3.079 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 448c0e8e..d947aff5 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 file775a236112e7.c 2> file775a236112e7.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 84e6591b..88858539 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 -#> 0.004 0.000 0.004
system.time( +#> 0.005 0.000 0.005
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 0.002
system.time( +#> 0.002 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 a27cf5db..49117199 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 -#> 0.038 0.036 6.851
time_1
#> User System verstrichen -#> 21.780 0.000 21.791
+#> 0.037 0.036 7.001
time_1
#> User System verstrichen +#> 21.838 0.000 21.852
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 7f510c67..e63ab87e 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 09:29:14 2018 
-#> Date of summary: Mon Nov 26 09:29:14 2018 
+#> Date of fit:     Mon Nov 26 09:47:09 2018 
+#> Date of summary: Mon Nov 26 09:47:09 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 24b50890..c0ff16fd 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 09:29:22 2018 
-#> Date of summary: Mon Nov 26 09:29:22 2018 
+#> Date of fit:     Mon Nov 26 09:47:17 2018 
+#> Date of summary: Mon Nov 26 09:47:17 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 0.683 s
+#> Fitted with method Port using 153 model solutions performed in 0.673 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 09:29:24 2018 
-#> Date of summary: Mon Nov 26 09:29:24 2018 
+#> Date of fit:     Mon Nov 26 09:47:18 2018 
+#> Date of summary: Mon Nov 26 09:47:18 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 1.594 s
+#> Fitted with method Port using 350 model solutions performed in 1.529 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 09:29:25 2018 
-#> Date of summary: Mon Nov 26 09:29:25 2018 
+#> Date of fit:     Mon Nov 26 09:47:20 2018 
+#> Date of summary: Mon Nov 26 09:47:20 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 0.819 s
+#> Fitted with method Port using 186 model solutions performed in 0.847 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 09:29:26 2018 
-#> Date of summary: Mon Nov 26 09:29:26 2018 
+#> Date of fit:     Mon Nov 26 09:47:20 2018 
+#> Date of summary: Mon Nov 26 09:47:20 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 0.486 s
+#> Fitted with method Port using 104 model solutions performed in 0.457 s
 #> 
 #> Weighting: none
 #> 
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