<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hilmar Lapp wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Mar 5, 2008, at 3:14 AM, Steve Kembel wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Are there any more decisions to be made about what to call things?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Tips, internals, nodes, edges</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Descendant, ancestor, sister</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I wouldn't use sister, use the more neutral 'sibling' instead.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">There is also typically a distinction between parents versus<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ancestors, and children (or daughters) versus descendants (the <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">first<span class="Apple-converted-space"> </span>ones being in direct relationship, and the latter ones <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">direct or via<span class="Apple-converted-space"> </span>transitivity).</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span>-hilmar</div> </blockquote><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; "><span class="Apple-converted-space"> </span>that's useful.<span class="Apple-converted-space"> </span>so my functions (ancestor, descendants,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">alldescendants, allancestors) could be (parent, children,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">descendants, ancestors) ... ?</div> </blockquote><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; ">That's right. allancestors() sounds confusing, for the above reasons.</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; ">Obviously you could just have ancestors(), with an option direct=TRUE|<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FALSE. You could also still have parents() and have it just delegate <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to ancestors(direct=TRUE). Personally that's probably what I would go <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">with implementation-wise, but it may be more a matter of taste than <span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">anything else.</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; "><span class="Apple-tab-span" style="white-space:pre"> </span>-hilmar</div></blockquote><div><br class="webkit-block-placeholder"></div>Woa guys! As far as I know, people who use comparative methods think of ancestor and descendant as the direct relationship. </div><div><br class="webkit-block-placeholder"></div><div>It may be because when students are being taught systematics, this is the terminology that we use to talk about character evolution on trees (especially when introducing synapomorphy, homology, homoplasy, etc). Which way the ancestor - descendant relationship goes matters a great deal when you are trying to figure out character polarity (which is the new vs. ancestral character state)</div><div><br class="webkit-block-placeholder"></div><div>Also, there might be stuff floating around. Years ago, Wayne Maddison made a tree programming tutorial in Pascal, and he used ancestor-descendant to talk about linking nodes together via pointers. I am pretty sure that Joe Felsenstein used this terminology too in an short document in his Phylip package (all written in ascii!)</div><div><br class="webkit-block-placeholder"></div><div>So, please don't use parent to mean ancestor and descendant() to mean grab the entire clade! That will be very confusing. I would prefer the single function, but with the default indicated this way:</div><div><br class="webkit-block-placeholder"></div><div>ancestor(all=FALSE) </div><div>descendant(all=FALSE)</div><div><br></div>If you are coming from the point of view that descendant means direct descendant and ancestor means direct ancestor, this might be more intuitive.<div><br class="webkit-block-placeholder"></div><div>Marguerite<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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