![]() Here's how to get relative paths working: If you're using Post Haste to create templates for your Adobe project files, you may have run into an issue where the project file still points to assets in their original location on disk, not relative to the template path. Retrieved from ”įound this document useful? Have any questions? Want to do research on phylogenetic community structure? Contact me at smvamosi+ucalgary.Making relative Adobe asset paths work in Post Haste templates Instructions for running the Analysis of Traits module of To cite this document (e.g., for a class project), perhaps use: “Vamosi, S.M. For example, if you scroll down towards the bottom of the results.xls file, you will encounterĪ section titled “Output of independent contrast values by node” - for my purposes, I would select the data in the “Contrast2”Ĭolumn, and run a Wilcoxon rank test on the data to ask whether state 1 of the independent variable is typically associated with larger/smaller values of the Soak up/interpret what the Phylocom analysis has output for you. This will facilitate opening it later in Excel just by clicking on theįile name AND will prevent you from writing over the results file sitting in the Phylocom directory.ġ5. In Excel, save the file as “results.xls” in your current data directory. Once that is complete, type “open -a Microsoft\ Excel results.txt” to have the “results.txt” file open in Excel (muchĮasier than importing the file into Excel manually).ġ4. Type “./phylocom aotf > results.txt” to run a full AOT (Analysis of Traits).ġ3. Now you're ready for your Phylocom analysis. For this and the nextįew commands, hit enter after typing the indicated command.ġ2. “cd /Applications/Phylocom/phylocom-3.41” or simply drag the appropriate folder from Finder into my iTerm window. ![]() ![]() Get into the directory that houses Phylocom in my case, I would type “phylo”, “traits”, and “results.txt” files.ġ0. For subsequent runs of Phylocom, I like to first delete the preceding Copy and paste “phylo” and “traits” files into your Phylocom directory (e.g., Now save this file as your “traits” file in your current data directory using “Save As.”ĩ. Ensure that there is a hard RET after the last line of data, and that line endings are Twice (yes, Excel, I really want to do this!).Ĩ. Save file as “traits.txt” using “File” -> “Save As.” -> “Text (Tab delimited)”. Of Trait 1 data (e.g., “breedsys”), and name of Trait 2 data (e.g., “seedsize”) in the first three columns.ħ. In row 1, enter type, 0, and 3 in the first three columns (assuming that Trait 1 is binary and Trait 2 is continuous). Copy and paste into the third row of a new Excel file. Go back to Excel file, select the data in the Genus_species, Trait 1, and Trait 2 columns. Save thisĪs your “phylo” file (i.e., with no extension) in your current data directory.Ħ. Of the tree and a corresponding “(” from the beginning of the tree. As of the current tree, you may need to remove “euphyllophyte” from the end Select all, copy and paste the phylogeny into TextWrangler. Copy and paste the community list into Phylomatic, making sure that there is a hard RET after the last line.ĥ. List into TextWrangler, and save it as a “taxa” file, in the current data directoryģ. To begin to make the phylogeny in Phylomatic, select Family, Genus, Genus_species columns,Ĭopy and paste into Word. * I expect that you would follow similar steps if you instead use NeoOffice orĢ. Outline a two trait scenario (1 = binary, 2 = continuous). For the rest of these instructions, I will Is often the case with my analyses), then convert values to “0”s and “1”s at this point. Start with an Excel* file containing the following columns: Family, Genus, Genus_species, Trait 1, Trait 2. "Analysis of Traits" (or 'AOT') module for a phylogenetic community structure analysis, you should also check out the excellentīodega Phylogenetics Wiki by Sharon Strauss and Jean Burns.ġ. Finally, these instructions are most relevant to the Phylocom manual before attempting these analyses. Obviously, you should thoroughly read the I make no guarantees that every step will work on your computer, nor do IĪccept any responsibility for anything that might happen to your computer if you do follow these instructions. Preamble: These instructions were written with Mac OS X in mind.
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