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Diffstat (limited to 'docs/reference/nlme.html')
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1 files changed, 17 insertions, 15 deletions
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 1b05f882..981845fe 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Estimation of parameter distributions from mmkin row objects — nlme_function • mkin</title> +<title>Helper functions to create nlme models from mmkin row objects — nlme_function • mkin</title> <!-- jquery --> @@ -35,7 +35,7 @@ -<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — nlme_function" /> +<meta property="og:title" content="Helper functions to create nlme models from mmkin row objects — nlme_function" /> <meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of @@ -130,7 +130,7 @@ datasets." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Estimation of parameter distributions from mmkin row objects</h1> + <h1>Helper functions to create nlme models from mmkin row objects</h1> <div class="hidden name"><code>nlme.Rd</code></div> </div> @@ -255,37 +255,39 @@ datasets.</p> <span class='no'>nlme_f_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) <span class='no'>nlme_f_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) <span class='no'>nlme_f_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ]) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo"</span>, <span class='no'>nlme_f_sfo_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo_ff"</span>, <span class='no'>nlme_f_sfo_sfo_ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_fomc_sfo"</span>, <span class='no'>nlme_f_fomc_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) - <span class='co'># Allowing for correlations between random effects leads to non-convergence</span> + <span class='co'># Allowing for correlations between random effects (not shown)</span> + <span class='co'># leads to non-convergence</span> <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_k_parent_sink</span>, <span class='no'>log_k_parent_A1</span>, <span class='no'>log_k_A1_sink</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink): konnte Funktion "nlme_f_sfo_sfo" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>) + <span class='co'># augPred does not see to work on this object, so no plot is shown</span> + <span class='co'># The same model fitted with transformed formation fractions does not converge</span> <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> - <span class='co'># It does converge with this version of reduced random effects</span> - <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, - <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), - <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, - <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, - <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme.formula(value ~ nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1), data = grouped_data_2, fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1, random = pdDiag(parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1), start = mean_dp_sfo_sfo_ff): step halving factor reduced below minimum in PNLS step</span></div><div class='input'> <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_fomc_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_alpha</span>, <span class='no'>log_beta</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_fomc_sfo(name, time, parent_0, log_alpha, log_beta, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_fomc_sfo" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>) + <span class='co'># DFOP-SFO and SFORB-SFO did not converge with full random effects</span> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo): Objekt 'f_nlme_fomc_sfo' nicht gefunden</span></div><div class='input'># } + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_fomc_sfo 1 11 932.5817 967.0755 -455.2909 +#> f_nlme_sfo_sfo 2 9 1089.2492 1117.4714 -535.6246 1 vs 2 160.6675 <.0001</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |