===================== INSTRUCTIONS ============================== This document contains instructions for installing and using the GrammR package for R. 1. Install For Linux users, download the compiled R package file: Gramma_1.0.0.tar.gz Then use the following function in R to install the package >install.packages(pkgs=filename,repos=NULL) where "filename" should be replaced with the corresponding file name (GrammR_1.0,0.tar.gz) with the correct path. Alternatively, at the Linux command line, you may type "R CMD INSTALL PACKAGE_DIRECTORY/GrammR_1.0.0.tar.gz" where PACKAGE_DIRECTORY is the folder containing GrammR_1.0.0.tar.gz. GrammR depends on several other packages (gWidgetsRGtk2, RGtk2, gWidgets), which need to be installed before running GrammR. 2. Usage #Load the packages into R >library(GrammR) #Read the details about the package >?GrammR #Rad the details about the main functions >?GrammRGUI >?GrammRServ 3. Example > GrammRGUI() To run the example using GrammRGUI(), you will need to first download the example data files contained in Sample Data. The pop-up windown should be self-explanatory for carrying out the analysis using the example data. The results can be viewed online. > data(metagencounts) > GrammRServ(metagencounts$Counts) The results will be stored in files for viewing. Note: For running the example with the UniFrac option, the Tree.txt is a randomly generated tree (not a real phylogenetic tree) for demonstration purpose only. Further details can be found in the manual.