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authorJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:35:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:40:09 +0100
commitde040ca33f6b13ef89be89718510f30631b67903 (patch)
tree049ba22116371b4f578c0b315da15371c093ce51 /docs/reference/transform_odeparms.html
parent47030f0342b66b1520b8a20844a0569d492d188e (diff)
Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference/transform_odeparms.html')
-rw-r--r--docs/reference/transform_odeparms.html353
1 files changed, 28 insertions, 325 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 7433c5f2..b9d96b1e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -1,6 +1,6 @@
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@@ -9,17 +9,17 @@
<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title>
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@@ -46,7 +46,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
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@@ -62,14 +63,15 @@ The transformation of sets of formation fractions is fragile, as it supposes
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
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@@ -195,321 +197,25 @@ The transformation of sets of formation fractions is fragile, as it supposes
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
- <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
-#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Mon Nov 26 12:29:19 2018
-#&gt; Date of summary: Mon Nov 26 12:29:19 2018
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.701 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent_sink 0.1000 deparm
-#&gt; k_parent_m1 0.1001 deparm
-#&gt; k_m1_sink 0.1002 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent_sink -2.302585 -Inf Inf
-#&gt; log_k_parent_m1 -2.301586 -Inf Inf
-#&gt; log_k_m1_sink -2.300587 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.600 1.61400 96.330 102.900
-#&gt; log_k_parent_sink -3.038 0.07826 -3.197 -2.879
-#&gt; log_k_parent_m1 -2.980 0.04124 -3.064 -2.897
-#&gt; log_k_m1_sink -5.248 0.13610 -5.523 -4.972
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
-#&gt; log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
-#&gt; log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
-#&gt; log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02
-#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02
-#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.827 3 6
-#&gt; m1 4.490 1 9
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_sink 0.4855
-#&gt; parent_m1 0.5145
-#&gt; m1_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'>
-</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
-#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Mon Nov 26 12:29:20 2018
-#&gt; Date of summary: Mon Nov 26 12:29:20 2018
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 350 model solutions performed in 1.597 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent_sink 0.1000 deparm
-#&gt; k_parent_m1 0.1001 deparm
-#&gt; k_m1_sink 0.1002 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.7500 -Inf Inf
-#&gt; k_parent_sink 0.1000 0 Inf
-#&gt; k_parent_m1 0.1001 0 Inf
-#&gt; k_m1_sink 0.1002 0 Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.600000 1.6140000 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02
-#&gt; k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02
-#&gt; k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
-#&gt; k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
-#&gt; k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
-#&gt; k_m1_sink -0.17006 -0.6253 0.47164 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02
-#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02
-#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.827 3 6
-#&gt; m1 4.490 1 9
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_sink 0.4855
-#&gt; parent_m1 0.5145
-#&gt; m1_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'>
-<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
-<span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>)
-<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
-<span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)
-<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(fit, data = FALSE): Objekt 'fit' nicht gefunden</span></div><div class='input'>
+</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden</span></div><div class='input'>
+<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)</div><div class='output co'>#&gt; <span class='error'>Error in rownames(fit$start): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)</div><div class='output co'>#&gt; <span class='error'>Error in rownames(fit$start_transformed): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; <span class='error'>Error in transform_odeparms(initials, SFO_SFO): konnte Funktion "transform_odeparms" nicht finden</span></div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; <span class='error'>Error in backtransform_odeparms(transformed, SFO_SFO): konnte Funktion "backtransform_odeparms" nicht finden</span></div><div class='input'>
</div><div class='input'><span class='co'># The case of formation fractions</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
- <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
-#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Mon Nov 26 12:29:22 2018
-#&gt; Date of summary: Mon Nov 26 12:29:22 2018
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.857 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt; f_parent_to_m1 0.5000 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
-#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
-#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
-#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
-#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
-#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
-#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
-#&gt;
-#&gt; Residual standard error: 3.211 on 36 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
-#&gt; k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01
-#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
-#&gt; f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.459 2 7
-#&gt; m1 4.690 2 8
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_m1 0.5145
-#&gt; parent_sink 0.4855
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
-<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)
-<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; f_parent_to_m1
-#&gt; 0.5 </div><div class='input'>
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
+<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.ff, data = FALSE): Objekt 'fit.ff' nicht gefunden</span></div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; <span class='error'>Error in transform_odeparms(initials, SFO_SFO.ff): konnte Funktion "transform_odeparms" nicht finden</span></div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; <span class='error'>Error in backtransform_odeparms(transformed, SFO_SFO.ff): konnte Funktion "backtransform_odeparms" nicht finden</span></div><div class='input'>
<span class='co'># And without sink</span>
<span class='no'>SFO_SFO.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
- <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-
-<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
-#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Mon Nov 26 12:29:22 2018
-#&gt; Date of summary: Mon Nov 26 12:29:22 2018
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.474 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 84.790 2.96500 78.78 90.800
-#&gt; log_k_parent -2.756 0.08088 -2.92 -2.593
-#&gt; log_k_m1 -4.214 0.11150 -4.44 -3.988
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1
-#&gt; parent_0 1.0000 0.11058 0.46156
-#&gt; log_k_parent 0.1106 1.00000 0.06274
-#&gt; log_k_m1 0.4616 0.06274 1.00000
-#&gt;
-#&gt; Residual standard error: 8.333 on 37 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000
-#&gt; k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483
-#&gt; k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 19.66 3 16
-#&gt; parent 17.56 2 7
-#&gt; m1 18.71 1 9
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 10.91 36.25
-#&gt; m1 46.89 155.75</div></pre>
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'>
+
+<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.ff.2, data = FALSE): Objekt 'fit.ff.2' nicht gefunden</span></div></pre>
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<h2>Contents</h2>
@@ -522,9 +228,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
</ul>
<h2>Author</h2>
-
- Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -534,9 +238,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
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- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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