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Diffstat (limited to 'docs/dev/reference/nlme.html')
| -rw-r--r-- | docs/dev/reference/nlme.html | 41 |
1 files changed, 10 insertions, 31 deletions
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index 78d132e9..55a94443 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.4.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span> </span> </div> @@ -155,8 +155,6 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m <pre class="usage"><span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span> -<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span>, test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>, conf.level <span class='op'>=</span> <span class='fl'>0.6</span><span class='op'>)</span> - <span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> @@ -166,30 +164,11 @@ datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.m <th>object</th> <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td> </tr> - <tr> - <th>random</th> - <td><p>Should a list with fixed and random effects be returned?</p></td> - </tr> - <tr> - <th>test_log_parms</th> - <td><p>If TRUE, log parameters are only considered in -the mean calculations if their untransformed counterparts (most likely -rate constants) pass the t-test for significant difference from zero.</p></td> - </tr> - <tr> - <th>conf.level</th> - <td><p>Possibility to adjust the required confidence level -for parameter that are tested if requested by 'test_log_parms'.</p></td> - </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A function that can be used with nlme</p> -<p>If random is FALSE (default), a named vector containing mean values -of the fitted degradation model parameters. If random is TRUE, a list with -fixed and random effects, in the format required by the start argument of -nlme for the case of a single grouping variable ds.</p> <p>A <code><a href='https://rdrr.io/pkg/nlme/man/groupedData.html'>groupedData</a></code> object</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> @@ -217,7 +196,7 @@ nlme for the case of a single grouping variable ds.</p> <span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>d1 <span class='op'>=</span> <span class='va'>d1</span>, d2 <span class='op'>=</span> <span class='va'>d2</span>, d3 <span class='op'>=</span> <span class='va'>d3</span><span class='op'>)</span> <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>mean_dp</span> <span class='op'><-</span> <span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +<span class='va'>mean_dp</span> <span class='op'><-</span> <span class='fu'><a href='mean_degparms.html'>mean_degparms</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> <span class='va'>grouped_data</span> <span class='op'><-</span> <span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> <span class='va'>nlme_f</span> <span class='op'><-</span> <span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> <span class='co'># These assignments are necessary for these objects to be</span> @@ -237,28 +216,28 @@ nlme for the case of a single grouping variable ds.</p> #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik -#> 298.2781 307.7372 -144.1391 +#> 300.6824 310.2426 -145.3412 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent_sink Residual -#> StdDev: 0.937473 0.7098105 3.83543 +#> StdDev: 1.697361 0.6801209 3.666073 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 #> Value Std.Error DF t-value p-value -#> parent_0 101.76838 1.1445443 45 88.91607 0 -#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0 +#> parent_0 100.99378 1.3890416 46 72.70753 0 +#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.034 +#> log_k_parent_sink 0.027 #> #> Standardized Within-Group Residuals: -#> Min Q1 Med Q3 Max -#> -2.61693595 -0.21853231 0.05740682 0.57209372 3.04598764 +#> Min Q1 Med Q3 Max +#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 #> -#> Number of Observations: 49 +#> Number of Observations: 50 #> Number of Groups: 3 </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='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> </div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span> <span class='co'># variable</span> |