From 9d6a975a0e3850a36889a18b5d9929d27b901ab3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 14:09:45 +0100 Subject: Make some example output more reproducible In order to avoid some unnecessary documentation rebuilds --- docs/reference/transform_odeparms.html | 330 ++++----------------------------- 1 file changed, 41 insertions(+), 289 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 3148f00b..fbc792f1 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -203,157 +203,29 @@ 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: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:09:27 2019 -#> Date of summary: Mon Mar 4 10:09:27 2019 -#> -#> 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 153 model solutions performed in 0.699 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_0 100.750000 -Inf Inf -#> log_k_parent_sink -2.302585 -Inf Inf -#> log_k_parent_m1 -2.301586 -Inf Inf -#> log_k_m1_sink -2.300587 -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 99.600 1.61400 96.330 102.900 -#> log_k_parent_sink -3.038 0.07826 -3.197 -2.879 -#> log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 -#> log_k_m1_sink -5.248 0.13610 -5.523 -4.972 -#> -#> Parameter correlation: -#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> parent_0 1.00000 0.6075 -0.06625 -0.1701 -#> log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 -#> log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 -#> log_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 0.040890 5.616e-02 -#> k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 -#> k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-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
-
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: Mon Mar 4 10:09:29 2019 -#> Date of summary: Mon Mar 4 10:09:29 2019 -#> -#> 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 1.584 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
+fit.s <- summary(fit) +# Transformed and backtransformed parameters +print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 99.60 1.6137 96.33 102.87 +#> log_k_parent_sink -3.04 0.0783 -3.20 -2.88 +#> log_k_parent_m1 -2.98 0.0412 -3.06 -2.90 +#> log_k_m1_sink -5.25 0.1361 -5.52 -4.97
print(fit.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.613712 61.72 2.02e-38 96.32572 1.03e+02 +#> k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04089 5.62e-02 +#> k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04670 5.52e-02 +#> k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03
+
# Compare to the version without transforming rate parameters +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +fit.2.s <- summary(fit.2) +print(fit.2.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 99.59848 1.613710 96.32573 1.03e+02 +#> k_parent_sink 0.04792 0.003750 0.04031 5.55e-02 +#> k_parent_m1 0.05078 0.002094 0.04653 5.50e-02 +#> k_m1_sink 0.00526 0.000716 0.00381 6.71e-03
print(fit.2.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.613710 61.72 2.02e-38 96.32573 1.03e+02 +#> k_parent_sink 0.04792 0.003750 12.78 3.05e-15 0.04031 5.55e-02 +#> k_parent_m1 0.05078 0.002094 24.25 3.41e-24 0.04653 5.50e-02 +#> k_m1_sink 0.00526 0.000716 7.35 5.76e-09 0.00381 6.71e-03
initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value @@ -367,80 +239,16 @@ The transformation of sets of formation fractions is fragile, as it supposes m1 = list(type = "SFO"), 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)
#> mkin version used for fitting: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:09:30 2019 -#> Date of summary: Mon Mar 4 10:09:30 2019 -#> -#> 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 0.86 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) +fit.ff.s <- summary(fit.ff) +print(fit.ff.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 99.598 1.6137 96.3257 102.871 +#> log_k_parent -2.316 0.0419 -2.4006 -2.231 +#> log_k_m1 -5.248 0.1361 -5.5235 -4.972 +#> f_parent_ilr_1 0.041 0.0648 -0.0904 0.172
print(fit.ff.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.613712 61.72 2.02e-38 96.32574 1.03e+02 +#> k_parent 0.09870 0.004132 23.88 5.70e-24 0.09066 1.07e-01 +#> k_m1 0.00526 0.000716 7.35 5.76e-09 0.00399 6.93e-03 +#> f_parent_to_m1 0.51448 0.022880 22.49 4.37e-23 0.46808 5.61e-01
initials <- c("f_parent_to_m1" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 #> 0.5
@@ -451,70 +259,14 @@ The transformation of sets of formation fractions is fragile, as it supposes 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)
#> mkin version used for fitting: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:09:31 2019 -#> Date of summary: Mon Mar 4 10:09:31 2019 -#> -#> 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 0.476 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
+fit.ff.2.s <- summary(fit.ff.2) +print(fit.ff.2.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 84.79 2.9651 78.78 90.80 +#> log_k_parent -2.76 0.0809 -2.92 -2.59 +#> log_k_m1 -4.21 0.1115 -4.44 -3.99
print(fit.ff.2.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 84.7916 2.96505 28.60 3.94e-27 78.7838 90.7994 +#> k_parent 0.0635 0.00514 12.36 5.24e-15 0.0539 0.0748 +#> k_m1 0.0148 0.00165 8.97 4.11e-11 0.0118 0.0185