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<br><div><html>On Mar 23, 2008, at 12:07 PM, Ben Bolker wrote:</html><br class="Apple-interchange-newline"><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 22, 2008, at 2:56 PM, Peter Cowan wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ancestors(..., which = c("all", "parent")) # default to "all" since ancestor() exists</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; ">descendants(..., which = c("children", "tips", "all")) # first option calls children()</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Does that mean the default for descendants() is which="children", meaning only direct children? Isn't that inconsistent with the default of ancestors()?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </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; "><span class="Apple-converted-space"> </span>Yes, it is.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>The problem is that I think people will frequently want to access direct ancestors and descendants (parents/children).<span class="Apple-converted-space"> </span>"ancestor" is</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">a nice short term for "only direct ancestors", because there is by</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">definition only one of them.<span class="Apple-converted-space"> </span>There are (usually) multiple descendants,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">so this shortcut doesn't work for descendants.</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>(1) we could leave it this way (too confusing?)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>(2) we could switch the default to "tips" (probably the second</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">most common request), and indicate that children() is available if</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">one wants a shortcut for descendants(tree,which="children")</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>votes?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote><div><br></div><div>I vote for ancestor() = direct ancestor, and descendant() = direct descendant. </div><div>ancestors() = all ancestors by default, descendants() = all descendants by default. </div><div>descendants(some option for tips only) = tip descendants only.</div><div><br></div><div>I know that grammatically it is not corrrect to use the singular form when there could be more than one, but it could simply be explained in the help file that this is to make it logically consistent (which I think is more important). </div><div><br></div><div>I don't have any feeling for whether users will want tips only more often than all descendants. But if someone is sophisticated enough to be editing the trees in this fashion (or subsetting the data), then I think it's simple enough for them to learn to set an option. </div><div><br></div><div>Marguerite</div><div><br></div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>Ben</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: 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: 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 class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">____________________________________________</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Marguerite A. Butler</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Department of Zoology</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">University of Hawaii</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; "><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; ">2538 McCarthy Mall, Edmondson 259</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Phone: 808-956-4713</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Lab: 808-956-5867</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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">FAX: 808-956-9812</span></span></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; "><span class="Apple-style-span" style="font-family: Lucida Grande; "><span class="Apple-style-span" style="font-family: Lucida Grande; ">Dept: 808-956-8617</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; "><a href="http://www.hawaii.edu/zoology/faculty/butler.html">http://www.hawaii.edu/zoology/faculty/butler.html</a></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; "><span class="Apple-style-span" style="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></span></span></div><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; "></span></span></span></span></span><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: 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; "><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; "><span class="Apple-style-span" style="font-family: Lucida Grande; font-size: 13px; "><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></span></span></span></span></span></span></div><br class="Apple-interchange-newline"></span> </div><br></body></html>