From af84d618508d5882072ab7b8de481cb5efc60852 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 15:01:03 +0100 Subject: Make example logistic fit quiet --- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/logistic.solution.html | 50 ++-------------------------------- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 42 ++++++++++++++-------------- 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, 54 insertions(+), 100 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index dd088a0f..fe6fc125 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.196 0.000 0.196 +#> 0.199 0.000 0.200 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x555559201470> -#> <environment: 0x555555ce4640> +#> <bytecode: 0x555559227548> +#> <environment: 0x555556ee4048> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a3214d8> -#> <environment: 0x555555ce4640> +#> <bytecode: 0x55555a34ddf0> +#> <environment: 0x555556ee4048> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Feb 21 14:30:10 2019" +#> [1] "Thu Feb 21 14:56:32 2019" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index b0ab72d7..310f1c5a 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -202,54 +202,8 @@ sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07), n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]] - m <- mkinfit("logistic", d_2_1)
#> Model cost at call 1 : 789.6044 -#> Model cost at call 2 : 789.6043 -#> Model cost at call 7 : 716.9934 -#> Model cost at call 12 : 697.1186 -#> Model cost at call 15 : 697.1185 -#> Model cost at call 16 : 697.1184 -#> Model cost at call 17 : 661.1574 -#> Model cost at call 20 : 661.1573 -#> Model cost at call 22 : 620.0542 -#> Model cost at call 25 : 620.0541 -#> Model cost at call 29 : 616.6874 -#> Model cost at call 32 : 616.6874 -#> Model cost at call 33 : 616.6874 -#> Model cost at call 34 : 615.1671 -#> Model cost at call 37 : 615.1671 -#> Model cost at call 39 : 612.0795 -#> Model cost at call 42 : 612.0795 -#> Model cost at call 43 : 612.0795 -#> Model cost at call 44 : 605.9119 -#> Model cost at call 45 : 593.0433 -#> Model cost at call 46 : 548.0815 -#> Model cost at call 47 : 504.9062 -#> Model cost at call 50 : 504.9061 -#> Model cost at call 51 : 504.9061 -#> Model cost at call 53 : 485.929 -#> Model cost at call 55 : 485.929 -#> Model cost at call 56 : 485.929 -#> Model cost at call 58 : 485.241 -#> Model cost at call 60 : 485.241 -#> Model cost at call 61 : 485.2409 -#> Model cost at call 62 : 485.2409 -#> Model cost at call 63 : 484.0717 -#> Model cost at call 69 : 483.9062 -#> Model cost at call 74 : 483.5646 -#> Model cost at call 79 : 483.4908 -#> Model cost at call 84 : 483.4859 -#> Model cost at call 85 : 483.4859 -#> Model cost at call 89 : 483.4848 -#> Model cost at call 90 : 483.4836 -#> Model cost at call 92 : 483.4836 -#> Model cost at call 94 : 483.4836 -#> Model cost at call 97 : 483.4833 -#> Model cost at call 100 : 483.4833 -#> Model cost at call 105 : 483.4832 -#> Model cost at call 108 : 483.4832 -#> Model cost at call 114 : 483.4832 -#> Model cost at call 128 : 483.4832 -#> Optimisation by method Port successfully terminated.
plot_sep(m)
summary(m)$bpar
#> Estimate se_notrans t value Pr(>t) Lower + m <- mkinfit("logistic", d_2_1, quiet = TRUE) + plot_sep(m)
summary(m)$bpar
#> Estimate se_notrans t value Pr(>t) Lower #> parent_0 1.057896e+02 2.3743105248 44.5559374 6.656664e-16 1.006602e+02 #> kmax 6.398190e-02 0.0193490291 3.3067243 2.836921e-03 3.329058e-02 #> k0 1.612775e-04 0.0009640761 0.1672871 4.348592e-01 3.972250e-10 diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index dcfc499f..bed8ed8e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,8 +160,8 @@ 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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:31 2019 -#> Date of summary: Thu Feb 21 14:30:31 2019 +#> Date of fit: Thu Feb 21 14:56:53 2019 +#> Date of summary: Thu Feb 21 14:56:53 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +171,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.822 s +#> Fitted with method Port using 574 model solutions performed in 3.873 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ 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: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:32 2019 -#> Date of summary: Thu Feb 21 14:30:32 2019 +#> Date of fit: Thu Feb 21 14:56:55 2019 +#> Date of summary: Thu Feb 21 14:56:55 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +260,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.601 s +#> Fitted with method Port using 246 model solutions performed in 1.633 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index d09b9232..4f071574 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,8 +438,8 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:35 2019 -#> Date of summary: Thu Feb 21 14:30:35 2019 +#> Date of fit: Thu Feb 21 14:56:58 2019 +#> Date of summary: Thu Feb 21 14:56:58 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -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 -#> 1.017 0.004 1.022
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.036 0.000 1.036
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 -#> 0.845 0.000 0.846
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.830 0.000 0.832
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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:47 2019 -#> Date of summary: Thu Feb 21 14:30:47 2019 +#> Date of fit: Thu Feb 21 14:57:10 2019 +#> Date of summary: Thu Feb 21 14:57:10 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:50 2019 -#> Date of summary: Thu Feb 21 14:30:50 2019 +#> Date of fit: Thu Feb 21 14:57:13 2019 +#> Date of summary: Thu Feb 21 14:57:13 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 2.529 s +#> Fitted with method Port using 551 model solutions performed in 2.543 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:51 2019 -#> Date of summary: Thu Feb 21 14:30:51 2019 +#> Date of fit: Thu Feb 21 14:57:14 2019 +#> Date of summary: Thu Feb 21 14:57:14 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 0.707 s +#> Fitted with method Port using 155 model solutions performed in 0.718 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:52 2019 -#> Date of summary: Thu Feb 21 14:30:52 2019 +#> Date of fit: Thu Feb 21 14:57:15 2019 +#> Date of summary: Thu Feb 21 14:57:15 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 0.792 s +#> Fitted with method Port using 174 model solutions performed in 0.8 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: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:53 2019 -#> Date of summary: Thu Feb 21 14:30:53 2019 +#> Date of fit: Thu Feb 21 14:57:16 2019 +#> Date of summary: Thu Feb 21 14:57:16 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1114,7 +1114,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.243 s +#> Fitted with method Port using 270 model solutions performed in 1.248 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 14:30:57 2019 -#> Date of summary: Thu Feb 21 14:30:57 2019 +#> Date of fit: Thu Feb 21 14:57:19 2019 +#> Date of summary: Thu Feb 21 14:57:19 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 3.27 s +#> Fitted with method Port using 692 model solutions performed in 3.287 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 0710e6de..17d8400d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -231,7 +231,7 @@ 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 file33652d0fd552.c 2> file33652d0fd552.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file522976635fac.c 2> file522976635fac.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 8c5bf22b..414d97a8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -330,12 +330,12 @@ 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 -#> 0.047 0.000 0.047
+#> 0.039 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 75da28c7..7352fb74 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -191,8 +191,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.039 0.040 7.082
time_1
#> User System verstrichen -#> 22.650 0.004 22.666
+#> 0.044 0.036 7.245
time_1
#> User System verstrichen +#> 22.796 0.004 22.814
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 242d9f63..53b94948 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -208,8 +208,8 @@

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:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:48 2019 
-#> Date of summary: Thu Feb 21 14:31:48 2019 
+#> Date of fit:     Thu Feb 21 14:58:11 2019 
+#> Date of summary: Thu Feb 21 14:58:11 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 939fa7b4..3dbacbe8 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ 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:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:57 2019 
-#> Date of summary: Thu Feb 21 14:31:57 2019 
+#> Date of fit:     Thu Feb 21 14:58:19 2019 
+#> Date of summary: Thu Feb 21 14:58:19 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ 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 0.849 s
+#> Fitted with method Port using 153 model solutions performed in 0.765 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ 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:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:59 2019 
-#> Date of summary: Thu Feb 21 14:31:59 2019 
+#> Date of fit:     Thu Feb 21 14:58:21 2019 
+#> Date of summary: Thu Feb 21 14:58:21 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ 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 1.649 s
+#> Fitted with method Port using 350 model solutions performed in 1.58 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ 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:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:32:00 2019 
-#> Date of summary: Thu Feb 21 14:32:00 2019 
+#> Date of fit:     Thu Feb 21 14:58:22 2019 
+#> Date of summary: Thu Feb 21 14:58:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ 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 0.976 s
+#> Fitted with method Port using 186 model solutions performed in 0.872 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ 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:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:32:01 2019 
-#> Date of summary: Thu Feb 21 14:32:01 2019 
+#> Date of fit:     Thu Feb 21 14:58:23 2019 
+#> Date of summary: Thu Feb 21 14:58:23 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ 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 0.512 s
+#> Fitted with method Port using 104 model solutions performed in 0.473 s
 #> 
 #> Weighting: none
 #> 
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