From 3621588c04cbaa393ba62c97137f6aec746d114f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 26 Nov 2018 09:09:43 +0100 Subject: Support logLik and AIC for manual weights Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 10 ++++---- docs/reference/logLik.mkinfit.html | 9 ++++--- 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 | 6 ++--- docs/reference/transform_odeparms.html | 24 +++++++++---------- 9 files changed, 59 insertions(+), 56 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index a595dd0d..ec2c7eb7 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be3c890> -#> <environment: 0x55555bc2f5a0> +#> <bytecode: 0x55555be327a0> +#> <environment: 0x55555bc27c20> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd74468> -#> <environment: 0x55555bc2f5a0> +#> <bytecode: 0x55555cd76230> +#> <environment: 0x55555bc27c20> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 23 20:45:37 2018" +#> [1] "Mon Nov 26 09:05:19 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 1dda313f..250bc1d8 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -158,13 +158,16 @@ m1 = mkinsub("SFO") )
#> Successfully compiled differential equation model from auto-generated C code.
d_t <- FOCUS_2006_D d_t[23:24, "value"] <- c(NA, NA) # can't cope with zero values at the moment - f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) + f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity) f_obs <- mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE) f_tc <- mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE) - AIC(f_nw, f_obs, f_tc)
#> df AIC + d_t$err <- d_t$value # Manual weighting assuming sigma ~ y + f_man <- mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE) + AIC(f_nw, f_obs, f_tc, f_man)
#> df AIC #> f_nw 5 204.4619 #> f_obs 6 205.8727 -#> f_tc 6 143.8773
+#> f_tc 6 143.8773 +#> f_man 4 291.8000
#> 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: Fri Nov 23 20:45:55 2018 -#> Date of summary: Fri Nov 23 20:45:55 2018 +#> Date of fit: Mon Nov 26 09:05:38 2018 +#> Date of summary: Mon Nov 26 09:05:38 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 3.63 s +#> Fitted with method Port using 574 model solutions performed in 3.64 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: Fri Nov 23 20:45:57 2018 -#> Date of summary: Fri Nov 23 20:45:57 2018 +#> Date of fit: Mon Nov 26 09:05:40 2018 +#> Date of summary: Mon Nov 26 09:05:40 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 1.547 s +#> Fitted with method Port using 246 model solutions performed in 1.626 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b2e7363d..2017a35c 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: Fri Nov 23 20:46:00 2018 -#> Date of summary: Fri Nov 23 20:46:00 2018 +#> Date of fit: Mon Nov 26 09:05:43 2018 +#> Date of summary: Mon Nov 26 09:05:43 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 -#> 0.978 0.000 0.978
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 -#> 0.794 0.000 0.795
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.796 0.000 0.796
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: Fri Nov 23 20:46:12 2018 -#> Date of summary: Fri Nov 23 20:46:12 2018 +#> Date of fit: Mon Nov 26 09:05:54 2018 +#> Date of summary: Mon Nov 26 09:05:54 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 0.816 s +#> Fitted with method Port using 186 model solutions performed in 0.885 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: Fri Nov 23 20:46:14 2018 -#> Date of summary: Fri Nov 23 20:46:14 2018 +#> Date of fit: Mon Nov 26 09:05:57 2018 +#> Date of summary: Mon Nov 26 09:05:57 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 2.451 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: Fri Nov 23 20:46:15 2018 -#> Date of summary: Fri Nov 23 20:46:15 2018 +#> Date of fit: Mon Nov 26 09:05:58 2018 +#> Date of summary: Mon Nov 26 09:05:58 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 0.687 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: Fri Nov 23 20:46:16 2018 -#> Date of summary: Fri Nov 23 20:46:16 2018 +#> Date of fit: Mon Nov 26 09:05:59 2018 +#> Date of summary: Mon Nov 26 09:05:59 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 0.789 s +#> Fitted with method Port using 174 model solutions performed in 0.772 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: Fri Nov 23 20:46:17 2018 -#> Date of summary: Fri Nov 23 20:46:17 2018 +#> Date of fit: Mon Nov 26 09:06:00 2018 +#> Date of summary: Mon Nov 26 09:06:00 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 1.212 s +#> Fitted with method Port using 270 model solutions performed in 1.201 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: Fri Nov 23 20:46:21 2018 -#> Date of summary: Fri Nov 23 20:46:21 2018 +#> Date of fit: Mon Nov 26 09:06:03 2018 +#> Date of summary: Mon Nov 26 09:06:03 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 3.081 s +#> Fitted with method Port using 692 model solutions performed in 3.087 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index e16a4147..a7f26322 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 file32ab4b1aa093.c 2> file32ab4b1aa093.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file672328842b40.c 2> file672328842b40.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 9b8be306..f26422a4 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,7 +323,7 @@ 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 0.003
system.time( +#> 0.003 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 @@ -333,7 +333,7 @@ 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 -#> 0.047 0.000 0.047
+#> 0.041 0.000 0.040
# 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 fda9ba60..eb2e5bcf 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 -#> 0.033 0.040 6.952
time_1
#> User System verstrichen -#> 21.739 0.000 21.752
+#> 0.043 0.032 6.850
time_1
#> User System verstrichen +#> 21.779 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 a0ef5efe..9cb43d42 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:     Fri Nov 23 20:47:10 2018 
-#> Date of summary: Fri Nov 23 20:47:10 2018 
+#> Date of fit:     Mon Nov 26 09:06:53 2018 
+#> Date of summary: Mon Nov 26 09:06:53 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 0.081 s
+#> Fitted with method Port using 35 model solutions performed in 0.083 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index f98580cb..6178527b 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:     Fri Nov 23 20:47:18 2018 
-#> Date of summary: Fri Nov 23 20:47:18 2018 
+#> Date of fit:     Mon Nov 26 09:07:01 2018 
+#> Date of summary: Mon Nov 26 09:07:01 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 0.666 s
+#> Fitted with method Port using 153 model solutions performed in 0.687 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:     Fri Nov 23 20:47:20 2018 
-#> Date of summary: Fri Nov 23 20:47:20 2018 
+#> Date of fit:     Mon Nov 26 09:07:03 2018 
+#> Date of summary: Mon Nov 26 09:07:03 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 1.539 s
+#> Fitted with method Port using 350 model solutions performed in 1.537 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:     Fri Nov 23 20:47:21 2018 
-#> Date of summary: Fri Nov 23 20:47:21 2018 
+#> Date of fit:     Mon Nov 26 09:07:04 2018 
+#> Date of summary: Mon Nov 26 09:07:04 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 0.824 s
+#> Fitted with method Port using 186 model solutions performed in 0.827 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:     Fri Nov 23 20:47:22 2018 
-#> Date of summary: Fri Nov 23 20:47:22 2018 
+#> Date of fit:     Mon Nov 26 09:07:04 2018 
+#> Date of summary: Mon Nov 26 09:07:04 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 0.458 s
+#> Fitted with method Port using 104 model solutions performed in 0.454 s
 #> 
 #> Weighting: none
 #> 
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