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/nlme.mmkin.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/nlme.mmkin.html')
| -rw-r--r-- | docs/reference/nlme.mmkin.html | 33 |
1 files changed, 15 insertions, 18 deletions
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index d446a2a2..d41f9abd 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja </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> @@ -256,7 +256,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -287,7 +287,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193937 43.85442</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="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> @@ -321,9 +321,9 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-plt img"><img src="nlme.mmkin-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.404 -533.5910 1 vs 2 249.3274 <.0001</span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> @@ -338,12 +338,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462384 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30507 539.1658 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30550 539.1672 NA NA NA</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="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span> @@ -371,7 +371,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04773 -1.82340 -4.16716 0.05686 </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05685 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> @@ -385,7 +385,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223593 0.01262367 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.23222933 0.01262399 </span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">f_2_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> @@ -418,7 +418,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049994 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2050005 </span> <span class="r-in"><span> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span> <span class="r-in"><span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span></span></span> @@ -428,12 +428,9 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span> -<span class="r-out co"><span class="r-pr">#></span> p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 </span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.435 -394.7669 1 vs 2 28.32084 <.0001</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> |