diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-03 17:40:55 +0200 |
| commit | 8c19fc5261dc53dc7880b3f54f8f2adf413de996 (patch) | |
| tree | 193aad4a3b2920ad6bff1d54cd18e992ac179bdd /docs/reference/confint.mkinfit.html | |
| parent | 312255078d2529f485a81df2a53d5928622ae81f (diff) | |
| parent | 47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 (diff) | |
Merge branch 'master' into mxkin
Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log
Diffstat (limited to 'docs/reference/confint.mkinfit.html')
| -rw-r--r-- | docs/reference/confint.mkinfit.html | 107 |
1 files changed, 47 insertions, 60 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index ea69c3bb..1dd6288b 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -76,7 +76,7 @@ method of Venzon and Moolgavkar (1988)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -151,10 +151,19 @@ method of Venzon and Moolgavkar (1988).</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - - <span class='no'>level</span>, <span class='no'>cutoff</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>), - <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>( + <span class='no'>object</span>, + <span class='no'>parm</span>, + <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, + <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - <span class='no'>level</span>, + <span class='no'>cutoff</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"quadratic"</span>, <span class='st'>"profile"</span>), + <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='no'>...</span> +)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -253,52 +262,30 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> User System verstrichen -#> 51.058 0.000 51.088 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> +<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='error'>Error in mkinpredict.mkinmod(mkinmod, parms, odeini, outtimes, solution_type = solution_type, use_compiled = use_compiled, method.ode = method.ode, atol = atol, rtol = rtol, ...): Differential equations were not integrated for all output times because</span> +#> <span class='error'>NaN values occurred in output from ode()</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 11.39 0 11.4</span></div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> <span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> <span class='co'># minor interest), we get a nice performance improvement from about 50</span> <span class='co'># seconds to about 12 seconds if we use at least four cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> User System verstrichen -#> 0.005 0.004 11.349 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003650 1.027703e+02 -#> k_parent_sink 0.040762501 5.549764e-02 -#> k_parent_m1 0.046786482 5.500879e-02 -#> k_m1_sink 0.003892605 6.702778e-03 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) +#> 20.058 0.122 11.784 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) <span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841649 1.027931e+02 +#> parent_0 96.403841641 1.027931e+02 #> k_parent_sink 0.041033378 5.596269e-02 #> k_parent_m1 0.046777902 5.511931e-02 #> k_m1_sink 0.004012217 6.897547e-03 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841653 102.79312450 +#> parent_0 96.403841648 102.79312450 #> k_parent_sink 0.040485331 0.05535491 -#> k_parent_m1 0.046611581 0.05494364 +#> k_parent_m1 0.046611582 0.05494364 #> k_m1_sink 0.003835483 0.00668582 #> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> <span class='co'># intervals based on the internal parameter transformation are less</span> <span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> <span class='co'># interval based on the untransformed fit for k_m1_sink</span> -<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) -<span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent_sink TRUE FALSE -#> k_parent_m1 TRUE FALSE -#> k_m1_sink FALSE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006650 0.008380 -#> k_parent_m1 0.000183 0.002010 -#> k_m1_sink 0.030700 0.029100 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006800 0.002570 -#> k_parent_m1 0.003740 0.001180 -#> k_m1_sink 0.014700 0.002530 -#> sigma 0.055000 0.032700</div><div class='input'> +<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_untransformed' nicht gefunden</span></div><div class='input'> <span class='co'># Investigate a case with formation fractions</span> <span class='no'>f_d_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -309,16 +296,16 @@ On Windows machines, cores > 1 is currently not supported.</p></td> #> f_parent_to_m1 0.471328495 5.611550e-01 #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) <span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403840123 1.027931e+02 -#> k_parent 0.090823791 1.072543e-01 +#> parent_0 96.403839992 1.027931e+02 +#> k_parent 0.090823790 1.072543e-01 #> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118710 5.595960e-01 +#> f_parent_to_m1 0.469118711 5.595960e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403840057 1.027931e+02 -#> k_parent 0.090491932 1.069035e-01 +#> parent_0 96.403839944 1.027931e+02 +#> k_parent 0.090491931 1.069035e-01 #> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113361 5.598386e-01 +#> f_parent_to_m1 0.469113362 5.598386e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='co'># While the confidence interval for the parent rate constant is closer to</span> @@ -330,16 +317,16 @@ On Windows machines, cores > 1 is currently not supported.</p></td> #> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE -#> sigma FALSE TRUE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408012 0.0002217857 -#> k_parent 0.0009596303 0.0009003981 -#> k_m1 0.0307277425 0.0290579163 -#> f_parent_to_m1 0.0046884178 0.0027782643 +#> sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.0005408026 0.0002217846 +#> k_parent 0.0009596414 0.0009003877 +#> k_m1 0.0307277403 0.0290579212 +#> f_parent_to_m1 0.0046884168 0.0027782604 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408019 0.0002217863 -#> k_parent 0.0046099989 0.0023730118 -#> k_m1 0.0146746451 0.0025300990 -#> f_parent_to_m1 0.0046997668 0.0023460293 +#> parent_0 0.0005408031 0.0002217851 +#> k_parent 0.0046100089 0.0023730230 +#> k_m1 0.0146746442 0.0025300972 +#> f_parent_to_m1 0.0046997642 0.0023460268 #> sigma 0.0550252516 0.0327066836</div><div class='input'> <span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> <span class='co'># therefore we use the quadratic approximation</span> @@ -351,17 +338,17 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>f_tc_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596183241 106.19937044 -#> k_M1 0.037605436 0.04490758 -#> k_M2 0.008568746 0.01087675 -#> f_parent_to_M1 0.021464277 0.62023879 -#> f_parent_to_M2 0.015166876 0.37975352 -#> k1 0.273897622 0.33388081 -#> k2 0.018614564 0.02250380 -#> g 0.671943572 0.73583247 -#> sigma_low 0.251284138 0.83992136 -#> rsd_high 0.040410998 0.07661999</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59618 106.1994</div><div class='input'># } +#> parent_0 94.596218141 106.19934683 +#> k_M1 0.037605440 0.04490756 +#> k_M2 0.008568747 0.01087674 +#> f_parent_to_M1 0.021466788 0.62023878 +#> f_parent_to_M2 0.015168650 0.37975352 +#> k1 0.273897581 0.33388066 +#> k2 0.018614556 0.02250379 +#> g 0.671943831 0.73583255 +#> sigma_low 0.251283700 0.83992071 +#> rsd_high 0.040411017 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.59622 106.1993</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |