diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:08:43 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-05-19 17:10:16 +0200 |
| commit | cf54ccca37d27480dbf8d59eb027300518f7ad75 (patch) | |
| tree | 81a9d5955f716a74822ecb65dc83daeeb7efbba6 /docs/reference/mkinfit.html | |
| parent | c931057ce8f05d3a0dfefea72b73903efb82e900 (diff) | |
Prepare release of v1.2.4v1.2.4
- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 66 |
1 files changed, 33 insertions, 33 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index cb5039d1..88848768 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ </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">1.2.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> </span> </div> @@ -401,10 +401,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:45 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:45 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:57 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:57 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -446,10 +446,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.013e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.637e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.681e-08 1.013e-07 8.637e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -534,7 +534,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 6.89313 22.89848</span> -<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65772</span> +<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65771</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span></span> @@ -552,9 +552,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.264</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.197 0.316</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.227 0.588</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.226</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.845 0.417</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.354 0.532</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -581,10 +581,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:32:49 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:32:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:16:01 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:16:01 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -593,7 +593,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 0.694 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.718 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -633,7 +633,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 101.600000 2.6400000 96.240000 107.000000</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 5.522000 0.0077320 5.506000 5.538000</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 7.806000 NaN NaN NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 0.002488 0.0002431 0.001992 0.002984</span> @@ -641,30 +641,30 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095161 -0.76675 0.70542 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095161 1.000000 0.51429 -0.14382 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766750 0.514286 1.00000 -0.61393 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705417 -0.143821 -0.61393 1.00000 NaN</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN NaN NaN 1</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016086 0.001583 0.01547 5.87036 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006618 -0.011695 -0.05356 0.04848 NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low rsd_high</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016073 0.006626</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011700</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053566</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870075 0.048487</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016086 0.006618</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001583 -0.011695</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015466 -0.053560</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870361 0.048483</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652558</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652558 1.000000</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652545</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652545 1.000000</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> <span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> <span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> <span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.310e-26 9.624e+01 1.070e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.316e-20 4.613e-01 5.394e-01</span> <span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02</span> <span class="r-out co"><span class="r-pr">#></span> beta 2.455e+03 0.5549 2.915e-01 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03</span> |