https://www.r-phylo.org/w/index.php?action=history&feed=atom&title=HowTo%2FHelpWiki 2026-06-10T01:58:41Z Revision history for this page on the wiki MediaWiki 1.41.1 https://www.r-phylo.org/w/index.php?title=HowTo/HelpWiki&diff=428&oldid=prev 2008-02-06T18:52:27Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:52, 6 February 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l77">Line 77:</td> <td colspan="2" class="diff-lineno">Line 77:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:HowTo]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:HowTo]]</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:R Help]]</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:Comparative Methods Help]]</ins></div></td></tr> </table>

Hilmar https://www.r-phylo.org/w/index.php?title=HowTo/HelpWiki&diff=427&oldid=prev 2008-01-04T18:46:44Z

<p><a href="/w/index.php?title=R_Hackathon1/HelpWiki&amp;action=edit&amp;redlink=1" class="new" title="R Hackathon1/HelpWiki (page does not exist)">R Hackathon1/HelpWiki</a> moved to <a href="/wiki/HowTo/HelpWiki" title="HowTo/HelpWiki">HowTo/HelpWiki</a>: Fixing the name</p> <p><b>New page</b></p><div>&lt;h2&gt;Beginners HowTo (draft)&lt;/h2&gt;<br /> <br /> These pages are intended to be eventually moved to a more permanent location...<br /> <br /> ==Contents==<br /> * [[R_Hackathon/GettingStarted|Getting Started]] - Smith<br /> ** Downloading R (for Mac &amp; PC)<br /> ** Packages (for comparative methods) - w/ pointers to relevant R documents<br /> *** Which ones - pointer to task view?<br /> *** How to install<br /> *** Checking for updates<br /> <br /> * [[R_Hackathon/Basics|Basics of Using R]]<br /> ** Setting up your workspace - eg using library(package)<br /> ** How to Access Help<br /> *** help.search(&quot;x&quot;)<br /> *** ?x<br /> ** Changing your working directory<br /> ** Saving your work<br /> *** Saving the workspace<br /> *** Saving a script<br /> <br /> * [http://www.bio.unc.edu/faculty/vision/lab/CPM_taskview.html CRAN Task View Comparative Phylogenetic Methods] - Price &amp; Vision<br /> <br /> * [[R_Hackathon/UsingVignettes|Using Vignettes]] - Vision<br /> <br /> *[[R_Hackathon/InputtingTrees|Inputting Trees]] - Sidlauskas<br /> ** Inputting trees<br /> *** Taxon names without spaces or quotes<br /> *** Nexus (translation table or names)<br /> *** Newick (names only)<br /> ** Exporting trees<br /> ** Working with multi tree files<br /> ** Example files<br /> <br /> * [[R_Hackathon/InputtingData|Inputting and Exporting Data]] - Sidlauskas<br /> ** Tab-delimited tables<br /> ** Taxon names should appear in first column for translation to rownames<br /> <br /> *[[R_Hackathon/DataTreeManipulation|Basic Tree and Data Manipulation]] - Sidlauskas<br /> ** Rooting<br /> ** Resolving polytomies<br /> ** Setting branch lengths<br /> ** Identifying subgroups<br /> ** Identifying most recent common ancestors<br /> ** Culling taxa<br /> ** Calculating patristic distances<br /> ** Plotting trees<br /> <br /> *[[R_Hackathon/TransitionProbability|Modeling Discrete Character Evolution in R]] - Smith<br /> ** Formatting discrete data for analysis<br /> ** Model fitting<br /> ** Comparisons with the likelihood ratio test<br /> <br /> *[[R_Hackathon/CorrelatedDiscrete|Testing for Correlated Evolution among Discrete Characters in R]] <br /> <br /> *[[R_Hackathon/ContinuousData|Modeling Continuous Character Evolution in R]] - Hunt<br /> <br /> * [[R_Hackathon/PhylogeneticIndependentContrasts| How to do I run Phylogenetic Independent Contrasts in R?]] - Price<br /> **Calculating contrasts<br /> **Plotting contrasts<br /> **Calculating and plotting correlated trait evolution<br /> <br /> * [[R_Hackathon/Diversification | How do I run analyses of diversification in R?]] - Price<br /> <br /> * [[R_Hackathon/PGLS| Testing for Correlated Evolution among Continuous Characters with PGLS in R]] - Smith<br /> ** Assuming a Brownian Motion correlation structure<br /> ** Assuming an Ornstein-Uhlenbeck correlation structure<br /> <br /> * [[R_Hackathon/Ancestral State Reconstruction| How do I Reconstruct Ancestral States in R?]] - Sidlauskas<br /> ** Continuous Data<br /> ** Discrete Data<br /> <br /> * [[R_Hackathon/Divergence Time Estimation| How do I estimate divergence times in R?]] - Bell<br /> <br /> * [[R_Hackathon/Mesquite In R| Using Mesquite in R]]<br /> <br /> [[Category:HowTo]]</div>

Hilmar