diff options
Diffstat (limited to 'docs/reference/loftest.html')
| -rw-r--r-- | docs/reference/loftest.html | 93 |
1 files changed, 56 insertions, 37 deletions
diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index bc9ec146..614b8eea 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -75,7 +75,7 @@ lrtest.default from the lmtest package." /> </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">0.9.50.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span> </span> </div> @@ -112,6 +112,9 @@ lrtest.default from the lmtest package." /> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> </ul> </li> <li> @@ -120,8 +123,8 @@ lrtest.default from the lmtest package." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -139,7 +142,7 @@ lrtest.default from the lmtest package." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Lack-of-fit test for models fitted to data with replicates</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small> <div class="hidden name"><code>loftest.Rd</code></div> </div> @@ -150,10 +153,10 @@ compares the likelihoods using the likelihood ratio test <code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> from the lmtest package.</p> </div> - <pre class="usage"><span class='fu'>loftest</span>(<span class='no'>object</span>, <span class='no'>...</span>) + <pre class="usage"><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> <span class='co'># S3 method for mkinfit</span> -<span class='fu'>loftest</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> +<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -180,9 +183,11 @@ of replicate samples.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='no'>test_data</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>) -<span class='no'>sfo_fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_fit</span>) <span class='co'># We see a clear pattern in the residuals</span></div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_fit</span>) <span class='co'># We have a clear lack of fit</span></div><div class='output co'>#> Likelihood ratio test +<span class='va'>test_data</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span> +<span class='va'>sfo_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We see a clear pattern in the residuals</span> +</div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We have a clear lack of fit</span> +</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: SFO with error model const @@ -192,9 +197,11 @@ of replicate samples.</p> #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> <span class='co'># We try a different model (the one that was used to generate the data)</span> -<span class='no'>dfop_fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>dfop_fit</span>) <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span></div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span> -<span class='fu'>loftest</span>(<span class='no'>dfop_fit</span>) <span class='co'># no lack of fit</span></div><div class='output co'>#> Likelihood ratio test +<span class='va'>dfop_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span> +</div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span> +<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># no lack of fit</span> +</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: DFOP with error model const @@ -202,10 +209,11 @@ of replicate samples.</p> #> 1 10 -40.710 #> 2 5 -42.453 -5 3.485 0.6257</div><div class='input'><span class='co'>#</span> <span class='co'># This is the anova model used internally for the comparison</span> -<span class='no'>test_data_anova</span> <span class='kw'><-</span> <span class='no'>test_data</span> -<span class='no'>test_data_anova</span>$<span class='no'>time</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova</span>$<span class='no'>time</span>) -<span class='no'>anova_fit</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span>(<span class='no'>value</span> ~ <span class='no'>time</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>test_data_anova</span>) -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>anova_fit</span>)</div><div class='output co'>#> +<span class='va'>test_data_anova</span> <span class='op'><-</span> <span class='va'>test_data</span> +<span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> +<span class='va'>anova_fit</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='va'>time</span>, data <span class='op'>=</span> <span class='va'>test_data_anova</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> +</div><div class='output co'>#> #> Call: #> lm(formula = value ~ time, data = test_data_anova) #> @@ -230,12 +238,16 @@ of replicate samples.</p> #> Residual standard error: 3.285 on 9 degrees of freedom #> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 #> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09 -#> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span>(<span class='no'>anova_fit</span>) <span class='co'># We get the same likelihood and degrees of freedom</span></div><div class='output co'>#> 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span> -<span class='no'>test_data_2</span> <span class='kw'><-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span> -<span class='no'>m_synth_SFO_lin</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>sfo_lin_fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_lin_fit</span>) <span class='co'># not a good model, we try parallel formation</span></div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_lin_fit</span>)</div><div class='output co'>#> Likelihood ratio test +#> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> <span class='co'># We get the same likelihood and degrees of freedom</span> +</div><div class='output co'>#> 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span> +<span class='va'>test_data_2</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> +<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, + M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, + M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_lin_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> <span class='co'># not a good model, we try parallel formation</span> +</div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> +</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0 @@ -244,10 +256,13 @@ of replicate samples.</p> #> 2 7 -171.927 -21 156.64 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='no'>m_synth_SFO_par</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>sfo_par_fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_par</span>, <span class='no'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>sfo_par_fit</span>) <span class='co'># much better for metabolites</span></div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>sfo_par_fit</span>)</div><div class='output co'>#> Likelihood ratio test +<span class='va'>m_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <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='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, + M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, + M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> <span class='co'># much better for metabolites</span> +</div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> +</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0 @@ -256,10 +271,13 @@ of replicate samples.</p> #> 2 7 -156.331 -21 125.45 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='no'>m_synth_DFOP_par</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='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>dfop_par_fit</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'>test_data_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span>(<span class='no'>dfop_par_fit</span>) <span class='co'># No visual lack of fit</span></div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span>(<span class='no'>dfop_par_fit</span>) <span class='co'># no lack of fit found by the test</span></div><div class='output co'>#> Likelihood ratio test +<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <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='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, + M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, + M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>dfop_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># No visual lack of fit</span> +</div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># no lack of fit found by the test</span> +</div><div class='output co'>#> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0 @@ -267,11 +285,12 @@ of replicate samples.</p> #> 1 28 -93.606 #> 2 9 -102.763 -19 18.313 0.5016</div><div class='input'><span class='co'>#</span> <span class='co'># The anova model used for comparison in the case of transformation products</span> -<span class='no'>test_data_anova_2</span> <span class='kw'><-</span> <span class='no'>dfop_par_fit</span>$<span class='no'>data</span> -<span class='no'>test_data_anova_2</span>$<span class='no'>variable</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova_2</span>$<span class='no'>variable</span>) -<span class='no'>test_data_anova_2</span>$<span class='no'>time</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span>(<span class='no'>test_data_anova_2</span>$<span class='no'>time</span>) -<span class='no'>anova_fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span>(<span class='no'>observed</span> ~ <span class='no'>time</span>:<span class='no'>variable</span> - <span class='fl'>1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>test_data_anova_2</span>) -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>anova_fit_2</span>)</div><div class='output co'>#> +<span class='va'>test_data_anova_2</span> <span class='op'><-</span> <span class='va'>dfop_par_fit</span><span class='op'>$</span><span class='va'>data</span> +<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span><span class='op'>)</span> +<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> +<span class='va'>anova_fit_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>observed</span> <span class='op'>~</span> <span class='va'>time</span><span class='op'>:</span><span class='va'>variable</span> <span class='op'>-</span> <span class='fl'>1</span>, data <span class='op'>=</span> <span class='va'>test_data_anova_2</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit_2</span><span class='op'>)</span> +</div><div class='output co'>#> #> Call: #> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2) #> @@ -314,7 +333,7 @@ of replicate samples.</p> #> Residual standard error: 2.225 on 25 degrees of freedom #> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 #> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16 -#> </div><div class='input'># } +#> </div><div class='input'><span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -331,7 +350,7 @@ of replicate samples.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> |