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Fixed parameter table headers.
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@mhahsler
mhahsler committed May 14, 2024
1 parent 9b86f5c commit 2af3577
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113 changes: 64 additions & 49 deletions docs/seriation_criteria.html
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Original file line number Diff line number Diff line change
Expand Up @@ -198,26 +198,26 @@ <h3 class="anchored" data-anchor-id="arc">ARc</h3>
<h3 class="anchored" data-anchor-id="bar">BAR</h3>
<p>Banded Anti-Robinson form criterion: Measure for closeness to the anti-Robinson form in a band of size b (Earle and Hurley, 2015).</p>
<ul>
<li><p>merit: FALSE</p></li>
<li><p>optimized by: <a href="seriation_methods.html#qap_bar">QAP_BAR</a>, <a href="seriation_methods.html#dendser_bar">DendSer_BAR</a></p></li>
<li><p>additional parameters:</p>
<li>merit: FALSE</li>
<li>optimized by: <a href="seriation_methods.html#qap_bar">QAP_BAR</a>, <a href="seriation_methods.html#dendser_bar">DendSer_BAR</a></li>
<li>additional parameters:</li>
</ul>
<table class="table">
<thead>
<tr class="header">
<th style="text-align: right;">de</th>
<th>fault values he</th>
<th style="text-align: left;">lp</th>
<th style="text-align: left;"></th>
<th style="text-align: left;">default</th>
<th style="text-align: left;">help</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right;">b</td>
<td>NULL</td>
<td style="text-align: left;">b</td>
<td style="text-align: left;">NULL</td>
<td style="text-align: left;">band size defaults to a band of 20% of n</td>
</tr>
</tbody>
</table></li>
</ul>
</table>
</section>
<section id="gradient_raw" class="level3">
<h3 class="anchored" data-anchor-id="gradient_raw">Gradient_raw</h3>
Expand Down Expand Up @@ -277,26 +277,31 @@ <h3 class="anchored" data-anchor-id="ls">LS</h3>
<h3 class="anchored" data-anchor-id="mds_stress">MDS_stress</h3>
<p>Normalized stress of a configuration given by a seriation order</p>
<ul>
<li><p>merit: FALSE</p></li>
<li><p>optimized by: <a href="seriation_methods.html#mds">MDS</a>, <a href="seriation_methods.html#isomds">isoMDS</a>, <a href="seriation_methods.html#sammon_mapping">Sammon_mapping</a>, <a href="seriation_methods.html#monomds">monoMDS</a>, <a href="seriation_methods.html#metamds">metaMDS</a></p></li>
<li><p>additional parameters:</p>
<li>merit: FALSE</li>
<li>optimized by: <a href="seriation_methods.html#mds">MDS</a>, <a href="seriation_methods.html#isomds">isoMDS</a>, <a href="seriation_methods.html#sammon_mapping">Sammon_mapping</a>, <a href="seriation_methods.html#monomds">monoMDS</a>, <a href="seriation_methods.html#metamds">metaMDS</a></li>
<li>additional parameters:</li>
</ul>
<table class="table">
<colgroup>
<col style="width: 4%">
<col style="width: 7%">
<col style="width: 88%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: right;">de</th>
<th>fault values he</th>
<th style="text-align: left;">lp</th>
<th style="text-align: left;"></th>
<th style="text-align: left;">default</th>
<th style="text-align: left;">help</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right;">warn</td>
<td>FALSE</td>
<td style="text-align: left;">warn</td>
<td style="text-align: left;">FALSE</td>
<td style="text-align: left;">produce a warning if the 1D MDS fit does not preserve the given order (see ? seriation::uniscale).</td>
</tr>
</tbody>
</table></li>
</ul>
</table>
</section>
<section id="me" class="level3">
<h3 class="anchored" data-anchor-id="me">ME</h3>
Expand Down Expand Up @@ -338,36 +343,41 @@ <h3 class="anchored" data-anchor-id="path_length">Path_length</h3>
<h3 class="anchored" data-anchor-id="rgar">RGAR</h3>
<p>Relative generalized anti-Robinson events: Counts Anti-Robinson events in a variable band of size w around the main diagonal and normalizes by the maximum of possible events (Tien et al, 2008).</p>
<ul>
<li><p>merit: FALSE</p></li>
<li><p>optimized by: N/A</p></li>
<li><p>additional parameters:</p>
<li>merit: FALSE</li>
<li>optimized by: N/A</li>
<li>additional parameters:</li>
</ul>
<table class="table">
<colgroup>
<col style="width: 9%">
<col style="width: 8%">
<col style="width: 83%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: right;">de</th>
<th>fault values he</th>
<th style="text-align: left;">lp</th>
<th style="text-align: left;"></th>
<th style="text-align: left;">default</th>
<th style="text-align: left;">help</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right;">w</td>
<td>NULL</td>
<td style="text-align: left;">w</td>
<td style="text-align: left;">NULL</td>
<td style="text-align: left;">window size. Default is to use a pct of 100% of n</td>
</tr>
<tr class="even">
<td style="text-align: right;">pct</td>
<td>100</td>
<td style="text-align: left;">pct</td>
<td style="text-align: left;">100</td>
<td style="text-align: left;">specify w as a percentage of n in (0,100]</td>
</tr>
<tr class="odd">
<td style="text-align: right;">relative</td>
<td>TRUE</td>
<td style="text-align: left;">relative</td>
<td style="text-align: left;">TRUE</td>
<td style="text-align: left;">set to FALSE to get the GAR, i.e., the absolute number of AR events in the window.</td>
</tr>
</tbody>
</table></li>
</ul>
</table>
</section>
<section id="rho" class="level3">
<h3 class="anchored" data-anchor-id="rho">Rho</h3>
Expand All @@ -382,37 +392,42 @@ <h3 class="anchored" data-anchor-id="rho">Rho</h3>
<h3 class="anchored" data-anchor-id="smacof_stress0">smacof_stress0</h3>
<p>Stress0 calculated for different transformation types from package smacof.</p>
<ul>
<li><p>merit: FALSE</p></li>
<li><p>optimized by: <a href="seriation_methods.html#mds_smacof">MDS_smacof</a></p></li>
<li><p>registered by: register_smacof()</p></li>
<li><p>additional parameters:</p>
<li>merit: FALSE</li>
<li>optimized by: <a href="seriation_methods.html#mds_smacof">MDS_smacof</a></li>
<li>registered by: register_smacof()</li>
<li>additional parameters:</li>
</ul>
<table class="table">
<colgroup>
<col style="width: 4%">
<col style="width: 7%">
<col style="width: 88%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: right;">de</th>
<th>fault values he</th>
<th style="text-align: left;">lp</th>
<th style="text-align: left;"></th>
<th style="text-align: left;">default</th>
<th style="text-align: left;">help</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right;">type</td>
<td>“ratio”</td>
<td style="text-align: left;">type</td>
<td style="text-align: left;">“ratio”</td>
<td style="text-align: left;">MDS type (see ? smacof::stress0)</td>
</tr>
<tr class="even">
<td style="text-align: right;">warn</td>
<td>FALSE</td>
<td style="text-align: left;">warn</td>
<td style="text-align: left;">FALSE</td>
<td style="text-align: left;">produce a warning if the 1D MDS fit does not preserve the given order (see ? seriation::uniscale).</td>
</tr>
<tr class="odd">
<td style="text-align: right;">more</td>
<td>NA</td>
<td style="text-align: left;">more</td>
<td style="text-align: left;">NA</td>
<td style="text-align: left;">more arguments are passed on to smacof::stress0.</td>
</tr>
</tbody>
</table></li>
</ul>
</table>
</section>
</section>
<section id="criteria-for-data-matrices-tables-and-data.frames" class="level2">
Expand Down
5 changes: 2 additions & 3 deletions docs/seriation_criteria.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ packageVersion('seriation')

```{r, echo = FALSE}
.print_control <- function(control,
label = "default values",
help = TRUE,
trim_values = 30L) {
if (length(control) < 1L) {
Expand All @@ -31,7 +30,7 @@ packageVersion('seriation')
)
contr <- as.data.frame(t(as.data.frame(contr)))
colnames(contr) <- c(label)
colnames(contr) <- "default"
contr <- cbind(contr, help = "N/A")
if (!is.null(attr(control, "help")))
Expand All @@ -41,7 +40,7 @@ packageVersion('seriation')
contr[["help"]][i] <- hlp
}
print(knitr::kable(contr, format = "simple"))
print(knitr::kable(contr))
}
}
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