diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 17:24:53 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 17:24:53 +0100 |
| commit | aa74f5a30853fb0a15c99c283e072f08ee819149 (patch) | |
| tree | 988ec89e22b48fff4544653a4c3443356bab3071 /docs/dev/reference/nlme.mmkin.html | |
| parent | a1631098acfc3352e19c331e568bd6f5766b3c3d (diff) | |
saemix.mmkin and nlme.mmkin inherit from mixed.mmkin
With a plot method. The class mixed.mmkin is currently only a virtual
class created to unify the plotting method.
Diffstat (limited to 'docs/dev/reference/nlme.mmkin.html')
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 61 |
1 files changed, 31 insertions, 30 deletions
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index c3cc53ff..defef75d 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'>nlme</span><span class='op'>(</span> +<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span> <span class='va'>model</span>, data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>fixed</span>, @@ -253,8 +253,8 @@ parameters taken from the mmkin object are used</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Upon success, a fitted nlme.mmkin object, which is an nlme object -with additional elements</p> + <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object +with additional elements. It also inherits from 'mixed.mmkin'.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of @@ -262,7 +262,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code></p></div> + <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a>, +parms.nlme.mmkin</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>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>, @@ -288,21 +289,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.5635 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.17015133 -1.80015306 -4.14738870 0.02290935 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.17015185 -1.80015278 -4.14738834 0.03239833 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.488249 0.8447275 1.32965 0.4651789 2.321364 #> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><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> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 +#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 #> </div><div class='input'> <span class='co'># \dontrun{</span> <span class='va'>f_nlme_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> @@ -353,35 +354,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -404.9582, nlminb iterations: 1 +#> LME step: Loglik: -404.9583, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 +#> -0.4114356 0.9798646 1.3524300 0.7293315 0.3354323 1.3647313 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3644 -#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 +#> PNLS step: RSS = 630.3633 +#> fixed effects: 93.82269 -5.455993 -0.9601037 -1.862196 -4.199671 0.07824609 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7885368 0.5822683 +#> 0.7897284 0.5822782 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 +#> ds1 ds2 ds3 ds4 ds5 ds6 +#> -0.37122411 0.00305562 1.44336560 0.72467122 0.30160310 1.40762692 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3633 -#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 +#> PNLS step: RSS = 630.3637 +#> fixed effects: 93.82269 -5.455992 -0.9601036 -1.862196 -4.199671 0.0782462 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 4.789774e-07 2.200661e-05 </div><div class='input'> +#> 1.375673e-06 9.758294e-06 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>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> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> <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> </div><div class='output co'>#> $ff @@ -400,7 +401,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30536 539.1667 NA NA NA +#> A1 162.30523 539.1663 NA NA NA #> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>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 class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> @@ -425,23 +426,23 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.4298 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.04774463 -1.82339924 -4.16715509 0.04020161 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.04774566 -1.82339808 -4.16715311 0.05685186 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.473883 0.8499901 1.337187 0.3294411 1 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.473881 0.8499884 1.337185 0.4659005 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23222625 0.01262414 </div><div class='input'> +#> 2.23224114 0.01262341 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> |