From 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 16:55:20 +0100 Subject: Restore NAMESPACE which was accidentally overwritten by pkgdown -> roxygen --- docs/reference/transform_odeparms.html | 316 +++++++++++++++++++++++++++++++-- 1 file changed, 306 insertions(+), 10 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index b9d96b1e..d3c20ed8 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -198,24 +198,320 @@ The transformation of sets of formation fractions is fragile, as it supposes

Examples

SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
#> Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE),     m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> Error in summary(fit, data = FALSE): Objekt 'fit' nicht gefunden

-
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Error in mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(fit.2, data=FALSE)
#> Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden

-initials <- fit$start$value
#> Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden
names(initials) <- rownames(fit$start)
#> Error in rownames(fit$start): Objekt 'fit' nicht gefunden
transformed <- fit$start_transformed$value
#> Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden
names(transformed) <- rownames(fit$start_transformed)
#> Error in rownames(fit$start_transformed): Objekt 'fit' nicht gefunden
transform_odeparms(initials, SFO_SFO)
#> Error in transform_odeparms(initials, SFO_SFO): konnte Funktion "transform_odeparms" nicht finden
backtransform_odeparms(transformed, SFO_SFO)
#> Error in backtransform_odeparms(transformed, SFO_SFO): konnte Funktion "backtransform_odeparms" nicht finden

+  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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:52:31 2019 
+#> Date of summary: Thu Jan 31 16:52:31 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 0.703 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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:52:33 2019 
+#> Date of summary: Thu Jan 31 16:52:33 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 1.597 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$value
+names(transformed) <- rownames(fit$start_transformed)
+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 

 
# 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")
#> Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE),     m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden

-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(fit.ff, data = FALSE)
#> Error in summary(fit.ff, data = FALSE): Objekt 'fit.ff' nicht gefunden
initials <- c("f_parent_to_m1" = 0.5)
-transformed <- transform_odeparms(initials, SFO_SFO.ff)
#> Error in transform_odeparms(initials, SFO_SFO.ff): konnte Funktion "transform_odeparms" nicht finden
backtransform_odeparms(transformed, SFO_SFO.ff)
#> Error in backtransform_odeparms(transformed, SFO_SFO.ff): konnte Funktion "backtransform_odeparms" nicht finden

+  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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:52:34 2019 
+#> Date of summary: Thu Jan 31 16:52:34 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 0.898 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)
#> 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")
#> Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = FALSE),     m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden

-
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(fit.ff.2, data = FALSE)
#> Error in summary(fit.ff.2, data = FALSE): Objekt 'fit.ff.2' nicht gefunden
+ 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: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:35 2019 +#> Date of summary: Thu Jan 31 16:52:35 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 0.482 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