R Website R Installation and Folder R Packages R Documentation R Search R Workspace Interface R Common and Important Basic Commands

Transcription

1 Table of Content R Website R Installation and Folder R Packages R Documentation R Search R Workspace Interface R Common and Important Basic Commands R Website project.org/ Download, Package CRAN R Project Search Documentation Manuals > Contributed Documentation The R Journal Books Wiki ( 1

2 R Installation and Folder [Download, Package] > [CRAN] > Choose a mirror > [Download R for Windows] or [Download R for (Mac) OS X] > base > [Download R for Windows] Double click on R win.exe It will bring you through the installation steps R Installation and Folder /Program Files (Program Files (x86))/r/r /bin/x64/rgui.exe This is your program with GUI interface /etc/rconsole This is where you can change background color, text color of your R session etc. /etc/rprofile.site This is where you can change some default stuff like mirror, site library and auto load package /library This is where all your packages are stored 2

3 R Packages R Packages are available on CRAN website where download the R installation files [Software] > [Packages] > [Table of available packages, sorted by name] Look at [vegan] package Latest version Other packages that it depends Other packages that it will install along with it Published date Authors who write the package Contact person Package homepage maintain individually by the author Help files Instruction manual Download the package and install it in Windows Download the package and install it in Mac R Documentation You will be able to find lots of documentation that helps you operate R [Manuals] are those documentation edited by the R Core Team [Contributed] are those documentation written by other people [The R Journal] is always a good source of information 3

4 R Search Another that I use very often is the R Search at the homepage You could pretty much search all the questions that you have through the mailing lists or R website Three sites that I use often Google search engine Nabble R forum ( Stackoverflow ( This one is for more general programming question R Session Interface When you start R, you will get to the R session interface There are not many user interaction function Your main interaction is the > The toolbar is on top and offers basic interface 4

5 R Workspace Interface File Source R code If you already write an R code, then you can source it here to run R functions New script Open and R editor that allows you to record your command, R codes and functions Open script Open R codes/functions, *.R Load Workspace Load your previous R work as a workspace/image, *.Rdata Save Workspace Save your current R work as a workspace/image, *.Rdata R Workspace Interface File Change dir Change your current working directory Exit Exit the current workspace 5

6 R Workspace Interface File (Tips) How to keep a record of your workflow? It is A GOOD HABIT to: Use a R editor to script your code first and then copy and paste it into the workspace to run the script Always provide good comments in your script (using symbol # ). A good script can save your time and helps to trace back your thought process after many many years. Always save your script as *.R file Built in R Editor, Tinn R, Textpad, Notepad++, Vim (I personally use Vim but it requires you to understand UNIX code) I usually don t use the History function in R to keep my record You can save a R History (*.RHistory) file to help you trace your work but it is quite messy and without comment R Workspace Interface File (Tips) How to save your workspace? It is a GOOD HABIT to always save your workspace while working as THERE IS NO AUTOSAVE feature as in WORD Ways of saving workspace [File] > [Save Workspace ] > Save as *.RData save.image( C:/ ) Remember to include the extension RData when you name the file for saving When you exit R workspace, it will always ask you whether you want to save workspace: Manually save your workspace before your exit R Choose No to NOT save your workspace when you exit R (because it will save it as another workspace (.Rdata file) and not on top of the one you name) 6

7 R Workspace Interface Edit Clear console (Ctrl + L) Give you a clean interface Data editor Open up your data frame or matrix in an spreadsheet like interface GUI preferences Change the background and text color of your interface plus many other things Any setting change and save will change the Rconsole file. I seldom use any of these functions here. R Workspace Interface Misc Stop current computation (ESC) This is handy when you are running some functions and you need to stop it for some reasons List objects R is an object oriented programming language, you assign an object to anything you do in R This helps you to list objects Remove all objects Delete all objects List search path R is a like a book with lots and lots of pages. This list out all the current pages I seldom use this tab as all can be accessed through commands 7

8 R Workspace Interface Packages This is an important tab to install extra packages not found in your R session Load package If you need to use R functions from a package that you have already installed, you need to load it first into an environment before you can access the function Install package(s) You can install R packages right away from here if you have internet access You need to first select a mirror and then select the package you want to install Update packages Important to update your packages once in a while. Process is similar to Install package(s) Install package(s) from local zip files You use this function if you manually download packages from R website and save it to a local drive You install your own packages R Workspace Interface Packages (Tips) How to install R packages to /R 3.1.2/library folder? In Windows 7 & 8, you cannot access and write the library folder So, when installing packages, R will install it to your User/Documents/R folder But I like to keep all my packages in one place (i.e., library folder) So, you need to change user permission to the library folder At library folder, right click > [Properties] > [Security] > under [Group or user names] choose [Users ( )] > click [Edit ] A new tab [Permissions for library] > click [Users ( )] > under [Allow] check the box for [Full control] > [Apply] > [OK] > [OK] > you finish changing the permission 8

9 R Workspace Interface Windows & Help Windows This is useful if you are using MDI for your R workspace Help This is useful and contain all kinds of help information I don t use it too often because help on R functions can be accessed from command line R Basic Command This is where you will type all your command Using R is not too difficult, you just need to treat it like a person and talk to it. Tips: You need add () to run a function Without it, you will see the code of the function 9

10 R Basic Command Help To look up help for a function > help([name]) >?[name] > help(ls) or?ls It will bring you to a browser and the help is displayed as an HTML help R Basic Command Help File (ls()) ls{base} It tells which package is the function belonging to Description General description of the R function and what it does Usage How to specific/use the function Arguments What are the parameters and how to specify the parameters associated with the function Details More in depth description of the function References How to cite the functions if you use it in your publication See Also Other variants of the function or other R function closely related to it Examples Some example codes on how to use the function 10

11 R Basic Command search() List search path >search() Imagine R is a like a book with many pages Each page is called an environment and each host a package.globalenv is the first page and it s what you are looking at This is where you are currently at and operate from All the objects that you create will be hosted in this environment You cannot see other environment right now because there are all behind the first page Imagine a word in a page represents a R function, Each environment host a set of functions corresponding to that package You can access functions directly in other environment from you.globalenv R Basic Command ls() List objects in an environment >ls(): list the objects in.globalenv >ls([number]): list the objects in [number] th environment >ls(2): list the objects in the package:stats environment which is the second environment 11

12 R Basic Command rm() Remove an object in the current environment > rm([name]): remove the object with the exactly matching name R Basic Command q() Exit the R session > q() Will prompt you to save the workspace It is more of my habit to save the workspace manually first Then choose not to save workspace because the problem is that it will save the workspace as.rdata and not the one that you named 12

13 Useful R Package vegan: Community Ecology Package RODBC: ODBC Database Access rpanel: simple interactive controls for R using the tcltk library tcltk2: Tcl/Tk Additions spgrass6: Interface between GRASS 6+ geographical information system and R BiodiversityR: GUI for biodiversity, suitability and community ecology analysis rgl: 3D visualization device system (OpenGL) RGtk2: R bindings for Gtk and above 13