<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Thibaut and Everyone,</div><div><br class="webkit-block-placeholder"></div><div>Hope I'm not too late in joining the discussion.</div><div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; "></span></div></blockquote><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">I am still wondering about distinguishing node/internal. I think a </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">former ape user would understand 'nodes' as internal nodes. You may find<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">another terminology for the print method. Does 'node' refer to any node<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(tips+internal nodes) elsewhere in the packge (or other required<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">packages?). I may be insisting, but as the changes are going to affect<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the whole package...</div></blockquote><br><div>I'm probably responsible for the creeping in of the node terminology. For me, it is a design issue. The fundamental unit of the phylogenetic object is the node (this is how I think about abstracting the data). Everything is associated with the node, the links to the connecting nodes, the phenotypic data, branch length (or time depth), etc. </div><div><br></div><div>Tips are in fact nodes (although they are special in the sense that they have no descendants and all occur at the same time -- otherwise extinct taxa are tips too). </div><div><br class="webkit-block-placeholder"></div><div>When you think about tree recursion, or tree traversal, it is through the nodes. </div><div><br class="webkit-block-placeholder"></div><div>I understand that there might be some confusion with ape users, but I would still rather have the terminology changed to nodes for all nodes. Names are important here because it affects the way you think about the object, it's special properties, etc. Besides, I think it will be a one time thing, people might be temporarily confused, but they will quickly figure it out once they see the tree structure or the documentation, etc. </div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To recap with the nomenclature:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- "tips", "edges": seems to have a consensus on that</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>I would prefer "branches", only because that's the most commonly terminology that we use in the phylogenetics literature, so I think that's what users will be most familiar with. I know that programmers, mathematicians, and ecologists often use "edges", though.</div><div><br class="webkit-block-placeholder"></div><div>But this is not a big deal (compared to the nodes issue). </div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- "nodes": equals 'internal nodes' (has my vote) /vs/ all nodes (tips +<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">internal)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote><div>Vote for all nodes.</div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- "NexusToPhylo4" (and related IO functions): there seems to be a<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">consensus for changing the name, and using an argument to specify the<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">output; "read.nexus" would conflict with ape, but this may be solved by<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">using a namespace (is this overkill?); Hilmar suggested naming the<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">function from the content read (phylogeny / comparative data) rather<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">than from the format (newick, nexus, ...). I think content is more<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">generic, but I find it more visible to have a read.[format].</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>Namespace is a good idea. This package is going to get bigger....</div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- naming functions: there seems to be a consensus about the "camelCase"<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(i.e. "lowerCamelCase" rather than "UpperCamelCase").</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote>Doesn't matter to me, as long as it's written somewhere (a phylobase style guide?)</div><div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Appart from this, one colleague here is presently using/crash-testing<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phylobase - as an enduser -, and I begin to receive good feedback (among<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">bunches of "why is this not working?!?"). A good point for us all, I guess.</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>cool!</div><div><br class="webkit-block-placeholder"></div><div>Marguerite<br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></blockquote></div><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. Butler</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; ">Department of Zoology</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; ">University of Hawaii</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; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px;; font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; ">2538 McCarthy Mall, Edmondson 259</span></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; ; font-family: Helvetica; ; font-size: 12px; "><span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; "><span class="Apple-style-span" style="font-family: Helvetica; font-size: 12px; ">Honolulu, HI 96822</span></span><br style="; font-family: Helvetica; ; font-size: 12px; "></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; font-family: Helvetica; ; font-family: Helvetica; ; font-size: 12px; "><br class="khtml-block-placeholder"></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; ">Phone: 808-956-4713</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; ">FAX: 808-956-9812</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-family: Lucida Grande; ">Dept: 808-956-8617</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; "><a href="http://www2.hawaii.edu/~mbutler">http://www2.hawaii.edu/~mbutler</a></span></span></span></div><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; "><a href="http://www.hawaii.edu/zoology/">http://www.hawaii.edu/zoology/</a></span><br class="Apple-interchange-newline"></span></span></span> </div><br></body></html>