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<br><div><div>On Feb 28, 2008, at 1:11 AM, Thibaut Jombart wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi phylobasists,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1) considering the current implementation of labels() labels(x) returns<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the tip labels of 'x'), I was thinking that I would prefer to have it<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">return the labels of all nodes and tips, that is, associating a label to<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">each number in @edge.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Anyony voting against this modification, or having an advice?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote><div><br class="webkit-block-placeholder"></div><div>YES! A strong vote in favor of returning all node labels (internal + tip). I personally get very confused about the numbering of nodes on the tree, and this would help avoid a serious mistake. I would really like to avoid breaking up the structure of the data object into pieces, it's safer to keep it whole. Especially since labels() is so generic.. it's not tip.labels() after all, so I would expect the default behavior to return all labels anyway.</div><div><br class="webkit-block-placeholder"></div><div>Perhaps one solution would be to have an option labels( tree, tips.only=FALSE) or a type="tips", "internal", etc.?</div><div><br class="webkit-block-placeholder"></div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2) Another small concern I have is about the way functions returning a<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">component or a simple information about a phylo4/phylo4d are named:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">we have a "hasNodeLabels", a "nTips", or a "rootNode" but we have<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">"NodeLabels" and "EdgeLength" (not "nodeLabels" and "edgeLength") to<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">give a few examples. This is annoying when looking for a function...<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">like typing "node" then [tab][tab] does not list all 'node' functions.<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Another related issue is about already existing functions, i.e. from the<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">required packages. Looking for node labels, I was mislead by ape's<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">functions "tiplabels", "nodelabels" and "edgelabels" which actually do a<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">different job (add labels to a plot).</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In an ideal world, I guess, we would be using a generic<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">way-of-naming-functions... any idea about what we can do in the real world?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote><div><br class="webkit-block-placeholder"></div><div>We definitely need some consistency. It is not obvious to me what the scheme should be however. The lower case form looks more like conventional R code, but I don't have a strong feeling as long as it is a coherent system.</div><div><br class="webkit-block-placeholder"></div><div>We should probably fix this before it goes further and gets more out of hand, though.</div><div><br class="webkit-block-placeholder"></div><div>Marguerite</div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cheers,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thibaut.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Phylobase-devl mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:Phylobase-devl@lists.r-forge.r-project.org">Phylobase-devl@lists.r-forge.r-project.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl</a></div> </blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Lucida Grande; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">____________________________________________</span></span></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-size: 12px; ; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Marguerite A. 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