From c4a35c0e141a4bb05ba508914bebdc2884109e76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 11:38:43 +0200 Subject: Exclude more example code from CRAN checks to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE --- docs/reference/transform_odeparms.html | 245 ++++++++++++++++++++++++++++++--- 1 file changed, 224 insertions(+), 21 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index a31b075e..c0ca534c 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes mkin - 0.9.47.3 + 0.9.47.4 @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) -summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting: 0.9.47.3 +summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:25 2018 -#> Date of summary: Fri Sep 14 06:39:25 2018 +#> Date of fit: Fri Sep 14 11:36:07 2018 +#> Date of summary: Fri Sep 14 11:36:07 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 0.642 s +#> Fitted with method Port using 153 model solutions performed in 0.627 s #> #> Weighting: none #> @@ -273,10 +273,82 @@ The transformation of sets of formation fractions is fragile, as it supposes #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70
-
# NOT RUN { -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) -summary(fit.2, data=FALSE) -# }
+
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +summary(fit.2, data=FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:08 2018 +#> Date of summary: Fri Sep 14 11:36:08 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 350 model solutions performed in 1.437 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> 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 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70
initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value @@ -284,29 +356,160 @@ The transformation of sets of formation fractions is fragile, as it supposes transform_odeparms(initials, SFO_SFO)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587
backtransform_odeparms(transformed, SFO_SFO)
#> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002
-
# NOT RUN { -# The case of formation fractions +
# The case of formation fractions SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), - use_of_ff = "max") - + use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) -summary(fit.ff, data = FALSE) -initials <- c("f_parent_to_m1" = 0.5) +summary(fit.ff, data = FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:09 2018 +#> Date of summary: Fri Sep 14 11:36:09 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.773 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> 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 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70
initials <- c("f_parent_to_m1" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) -backtransform_odeparms(transformed, SFO_SFO.ff) - +backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 +#> 0.5
# And without sink SFO_SFO.ff.2 <- mkinmod( parent = list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), - use_of_ff = "max") - + use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) -summary(fit.ff.2, data = FALSE) -# } +summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:36:10 2018 +#> Date of summary: Fri Sep 14 11:36:10 2018 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.424 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11058 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 degrees of freedom +#> +#> 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 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75