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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-22 13:14:31 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-22 13:17:40 +0200
commit0af6a61b84cc29cdbfad16a6fc7ee0e6f88c7d0f (patch)
tree7cb2715570688cac8c94b58e4ef78ba8afa29cc3 /docs/dev/reference
parentcb3adccaa4cdebc36c506fcb76c0d7c1d7e4e455 (diff)
Really fix check for nlme::varConstProp
And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent().
Diffstat (limited to 'docs/dev/reference')
-rw-r--r--docs/dev/reference/nlme.mmkin.html51
1 files changed, 48 insertions, 3 deletions
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index d186d785..6e83b700 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -448,7 +448,7 @@ with additional elements</p>
#&gt; parent 11.07091 104.6320 31.49738 4.462384 46.20825
#&gt; A1 162.30536 539.1667 NA NA NA
#&gt; </div><div class='input'>
- <span class='kw'>if</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='co'># tc error model for nlme available</span>
+ <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'>&gt;</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</span>
<span class='co'>#f_2_tc &lt;- mmkin(list("SFO-SFO" = m_sfo_sfo,</span>
<span class='co'># "SFO-SFO-ff" = m_sfo_sfo_ff,</span>
@@ -469,11 +469,56 @@ with additional elements</p>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span>
<span class='op'>}</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in if (findFunction("varConstProp")) { f_tc &lt;- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc") f_nlme_sfo_tc &lt;- nlme(f_tc["SFO", ]) f_nlme_dfop_tc &lt;- nlme(f_tc["DFOP", ]) AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) print(f_nlme_dfop_tc)}: argument is not interpretable as logical</span></div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'>&lt;-</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>,
+</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr)
+#&gt; Data: "Not shown"
+#&gt; Log-likelihood: -238.4298
+#&gt; Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+#&gt; parent_0 log_k1 log_k2 g_ilr
+#&gt; 94.04774463 -1.82339924 -4.16715509 0.04020161
+#&gt;
+#&gt; Random effects:
+#&gt; Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+#&gt; Level: ds
+#&gt; Structure: Diagonal
+#&gt; parent_0 log_k1 log_k2 g_ilr Residual
+#&gt; StdDev: 2.473883 0.8499901 1.337187 0.3294411 1
+#&gt;
+#&gt; Variance function:
+#&gt; Structure: Constant plus proportion of variance covariate
+#&gt; Formula: ~fitted(.)
+#&gt; Parameter estimates:
+#&gt; const prop
+#&gt; 2.23222625 0.01262414
+#&gt; Number of Observations: 90
+#&gt; Number of Groups: 5 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'>&lt;-</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>
<span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'>&lt;-</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_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
- <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
+ <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink)
+#&gt; Data: "Not shown"
+#&gt; Log-likelihood: -472.976
+#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
+#&gt; parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink
+#&gt; 87.975536 -3.669816 -4.164127 -4.645073
+#&gt;
+#&gt; Random effects:
+#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
+#&gt; Level: ds
+#&gt; Structure: Diagonal
+#&gt; parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual
+#&gt; StdDev: 3.992214 1.77702 1.054733 0.4821383 6.482585
+#&gt;
+#&gt; Variance function:
+#&gt; Structure: Different standard deviations per stratum
+#&gt; Formula: ~1 | name
+#&gt; Parameter estimates:
+#&gt; parent A1
+#&gt; 1.0000000 0.2050003
+#&gt; Number of Observations: 170
+#&gt; Number of Groups: 5 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span>
<span class='co'># parent and A1 are too similar in this case, so that the model is</span>
<span class='co'># overparameterised</span>
<span class='co'>#f_nlme_dfop_sfo_obs &lt;- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span>

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