From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- docs/reference/mkinfit.html | 75 +++++++++++++++++++++++---------------------- 1 file changed, 38 insertions(+), 37 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c006ddab..e5bf1203 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -307,7 +307,7 @@ internal rate transformation.

for measurement error in analytical chemistry. Technometrics 37(2), 176-184.

Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. Environments 6(12) 124 -doi: 10.3390/environments6120124 +doi:10.3390/environments6120124 .

@@ -330,16 +330,16 @@ doi: fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) #> mkin version used for fitting: 1.1.0 -#> R version used for fitting: 4.1.2 -#> Date of fit: Mon Mar 7 13:11:56 2022 -#> Date of summary: Mon Mar 7 13:11:56 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:37:57 2022 +#> Date of summary: Wed May 18 20:37:57 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.045 s +#> Fitted using 222 model solutions performed in 0.041 s #> #> Error model: Constant variance #> @@ -374,10 +374,10 @@ doi: #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08 -#> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 +#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -462,7 +462,7 @@ doi: #> $distimes #> DT50 DT90 #> parent 6.89313 22.89848 -#> m1 134.15634 445.65772 +#> m1 134.15634 445.65770 #> # We can show a quick (only one replication) benchmark for this case, as we @@ -471,7 +471,7 @@ doi: # benchmark vignette # \dontrun{ if(require(rbenchmark)) { - benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"), + benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"), deSolve_compiled = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "deSolve", use_compiled = TRUE), eigen = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", @@ -479,10 +479,8 @@ doi: analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", solution_type = "analytical")) } -#> test relative elapsed -#> 3 analytical 1.000 0.573 -#> 1 deSolve_compiled 1.642 0.941 -#> 2 eigen 2.517 1.442 +#> Loading required package: rbenchmark +#> Warning: there is no package called ‘rbenchmark’ # } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO @@ -506,10 +504,13 @@ doi: # Also, the missing standard error for log_beta and the t-tests for alpha # and beta indicate overparameterisation summary(fit.FOMC_SFO.tc, data = FALSE) +#> Warning: NaNs produced +#> Warning: NaNs produced +#> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful #> mkin version used for fitting: 1.1.0 -#> R version used for fitting: 4.1.2 -#> Date of fit: Mon Mar 7 13:12:07 2022 -#> Date of summary: Mon Mar 7 13:12:07 2022 +#> R version used for fitting: 4.2.0 +#> Date of fit: Wed May 18 20:38:07 2022 +#> Date of summary: Wed May 18 20:38:07 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -518,12 +519,12 @@ doi: #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.67 s +#> Fitted using 3924 model solutions performed in 7.107 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood +#> Three-step fitting yielded a higher likelihood than direct fitting #> #> Starting values for parameters to be optimised: #> value type @@ -558,7 +559,7 @@ doi: #> Estimate Std. Error Lower Upper #> parent_0 101.600000 2.6400000 96.240000 107.000000 #> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000 -#> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800 +#> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800 #> log_alpha 5.522000 0.0077320 5.506000 5.538000 #> log_beta 7.806000 NaN NaN NaN #> sigma_low 0.002488 0.0002431 0.001992 0.002984 @@ -566,31 +567,31 @@ doi: #> #> Parameter correlation: #> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta -#> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN -#> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN -#> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN -#> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN +#> parent_0 1.000000 -0.095145 -0.76674 0.70541 NaN +#> log_k_m1 -0.095145 1.000000 0.51428 -0.14381 NaN +#> f_parent_qlogis -0.766743 0.514278 1.00000 -0.61392 NaN +#> log_alpha 0.705413 -0.143809 -0.61392 1.00000 NaN #> log_beta NaN NaN NaN NaN 1 -#> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN -#> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN +#> sigma_low 0.016077 0.001586 0.01548 5.87034 NaN +#> rsd_high 0.006617 -0.011694 -0.05356 0.04848 NaN #> sigma_low rsd_high -#> parent_0 0.016073 0.006626 -#> log_k_m1 0.001586 -0.011700 -#> f_parent_qlogis 0.015476 -0.053566 -#> log_alpha 5.870075 0.048487 +#> parent_0 0.016077 0.006617 +#> log_k_m1 0.001586 -0.011694 +#> f_parent_qlogis 0.015476 -0.053560 +#> log_alpha 5.870339 0.048481 #> log_beta NaN NaN -#> sigma_low 1.000000 -0.652558 -#> rsd_high -0.652558 1.000000 +#> sigma_low 1.000000 -0.652555 +#> rsd_high -0.652555 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02 +#> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02 #> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03 -#> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01 -#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 +#> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.613e-01 5.394e-01 +#> alpha 2.502e+02 0.5624 2.890e-01 2.463e+02 2.542e+02 #> beta 2.455e+03 0.5549 2.915e-01 NA NA #> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 #> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 @@ -630,7 +631,7 @@ doi:
-

Site built with pkgdown 2.0.2.

+

Site built with pkgdown 2.0.3.

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