From 6c0c0986d7c33ebcc290cad12b02eaacafa796ad Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 22 Feb 2019 09:53:58 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 ++++----- docs/reference/logistic.solution.html | 7 +++--- docs/reference/mccall81_245T.html | 12 ++++----- docs/reference/mkinfit.html | 46 +++++++++++++++++----------------- 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 | 22 ++++++++-------- 9 files changed, 58 insertions(+), 57 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 8e018e96..20949a8f 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.198 0.000 0.198 +#> 0.197 0.000 0.197 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555920cdf0> -#> <environment: 0x5555562c5500> +#> <bytecode: 0x55555920cf58> +#> <environment: 0x5555560a01f8> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a399838> -#> <environment: 0x5555562c5500> +#> <bytecode: 0x55555a322750> +#> <environment: 0x5555560a01f8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Feb 21 16:11:47 2019" +#> [1] "Fri Feb 22 09:49:27 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 1894ed0e..728fbaa9 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -32,7 +32,7 @@ - @@ -126,7 +126,7 @@
-

Function describing exponential decline from a defined starting value, with +

Function describing exponential decline from a defined starting value, with an increasing rate constant, supposedly caused by microbial growth

@@ -211,7 +211,8 @@ #> parent_0 110.9190170 #> kmax 0.1229682 #> k0 65.4803698 -#> r 3.3474197 +#> r 3.3474197
endpoints(m)$distimes
#> DT50 DT90 DT50_k0 DT50_kmax +#> parent 36.86533 62.41511 4297.854 10.83349
#> 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:08 2019 -#> Date of summary: Thu Feb 21 16:12:08 2019 +#> Date of fit: Fri Feb 22 09:49:48 2019 +#> Date of summary: Fri Feb 22 09:49:48 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 3.846 s +#> Fitted with method Port using 574 model solutions performed in 3.837 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:10 2019 -#> Date of summary: Thu Feb 21 16:12:10 2019 +#> Date of fit: Fri Feb 22 09:49:50 2019 +#> Date of summary: Fri Feb 22 09:49:50 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 1.602 s +#> Fitted with method Port using 246 model solutions performed in 1.611 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 5f57189c..addb23e5 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,15 +438,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:13 2019 -#> Date of summary: Thu Feb 21 16:12:13 2019 +#> Date of fit: Fri Feb 22 09:49:53 2019 +#> Date of summary: Fri Feb 22 09:49:53 2019 #> #> 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 0.16 s +#> Fitted with method Port using 64 model solutions performed in 0.159 s #> #> Weighting: none #> @@ -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 -#> 1.035 0.004 1.040
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.015 0.000 1.016
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 -#> 0.819 0.000 0.819
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.821 0.000 0.822
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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:25 2019 -#> Date of summary: Thu Feb 21 16:12:25 2019 +#> Date of fit: Fri Feb 22 09:50:05 2019 +#> Date of summary: Fri Feb 22 09:50:05 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -637,7 +637,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.877 s +#> Fitted with method Port using 186 model solutions performed in 0.853 s #> #> Weighting: none #> @@ -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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:28 2019 -#> Date of summary: Thu Feb 21 16:12:28 2019 +#> Date of fit: Fri Feb 22 09:50:07 2019 +#> Date of summary: Fri Feb 22 09:50:07 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 2.574 s +#> Fitted with method Port using 551 model solutions performed in 2.535 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:29 2019 -#> Date of summary: Thu Feb 21 16:12:29 2019 +#> Date of fit: Fri Feb 22 09:50:08 2019 +#> Date of summary: Fri Feb 22 09:50:08 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 0.756 s +#> Fitted with method Port using 155 model solutions performed in 0.717 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:30 2019 -#> Date of summary: Thu Feb 21 16:12:30 2019 +#> Date of fit: Fri Feb 22 09:50:09 2019 +#> Date of summary: Fri Feb 22 09:50:09 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 0.864 s +#> Fitted with method Port using 174 model solutions performed in 0.796 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:31 2019 -#> Date of summary: Thu Feb 21 16:12:31 2019 +#> Date of fit: Fri Feb 22 09:50:11 2019 +#> Date of summary: Fri Feb 22 09:50:11 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 1.306 s +#> Fitted with method Port using 270 model solutions performed in 1.325 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 16:12:35 2019 -#> Date of summary: Thu Feb 21 16:12:35 2019 +#> Date of fit: Fri Feb 22 09:50:14 2019 +#> Date of summary: Fri Feb 22 09:50:14 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 3.309 s +#> Fitted with method Port using 692 model solutions performed in 3.303 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 79eb89d3..b2f290d1 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 file23f474fcf31d.c 2> file23f474fcf31d.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4d9c2c394c1.c 2> file4d9c2c394c1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 02b809a0..6f789fa4 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -325,17 +325,17 @@ 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 -#> 0.004 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 #> 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 -#> 0.039 0.000 0.039
+#> 0.042 0.000 0.042
# 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 71c347fd..73a25ef2 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 -#> 0.051 0.032 7.366
time_1
#> User System verstrichen -#> 23.290 0.000 23.305
+#> 0.040 0.047 7.314
time_1
#> User System verstrichen +#> 22.751 0.000 22.766
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 3b55635c..1543c328 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 16:13:27 2019 
-#> Date of summary: Thu Feb 21 16:13:27 2019 
+#> Date of fit:     Fri Feb 22 09:51:06 2019 
+#> Date of summary: Fri Feb 22 09:51:06 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index d15b0213..65a6b4ee 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 16:13:35 2019 
-#> Date of summary: Thu Feb 21 16:13:35 2019 
+#> Date of fit:     Fri Feb 22 09:51:14 2019 
+#> Date of summary: Fri Feb 22 09:51:14 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 0.782 s
+#> Fitted with method Port using 153 model solutions performed in 0.775 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 16:13:37 2019 
-#> Date of summary: Thu Feb 21 16:13:37 2019 
+#> Date of fit:     Fri Feb 22 09:51:16 2019 
+#> Date of summary: Fri Feb 22 09:51:16 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 1.579 s
+#> Fitted with method Port using 350 model solutions performed in 1.584 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 16:13:38 2019 
-#> Date of summary: Thu Feb 21 16:13:38 2019 
+#> Date of fit:     Fri Feb 22 09:51:17 2019 
+#> Date of summary: Fri Feb 22 09:51:17 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 0.859 s
+#> Fitted with method Port using 186 model solutions performed in 0.858 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 16:13:39 2019 
-#> Date of summary: Thu Feb 21 16:13:39 2019 
+#> Date of fit:     Fri Feb 22 09:51:18 2019 
+#> Date of summary: Fri Feb 22 09:51:18 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
-- 
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