1. Install R with Plugins (Math 160 and Biology 211). Use the Following Install Files

Installing R on Windows 7 (August 2015)

1. Install R with Plugins (Math 160 and Biology 211). Use the following install files:

R-3.2.2-win.exe

(

RcmdrPlugin.Bio211_1.0.tar.gz

RcmdrPlugin.Math160_1.0.tar.gz

The current version of R, as of this writing (August 2015) is 3.2.2 and this process below has been tested with this version.

Install R on the computer using the link above. Only install the 32-bit version. (Uncheck the 64 bit at the “Select Components” screen.)
For R Commander to work properly, you will first need to make some minor adjustments. More specifically, right-click on the R shortcut that was created on the desktop and selectPropertiesfrom the menu that appears. In the Properties window that opens, select theShortcuttab if it is not already selected. TheTargettextbox should contain something like"C:\Program Files\R\R-3.1.2\bin\Rgui.exe"in it, although this might be slightly different on your computer. Add--sdito the end of this (preceded by a space), so that it reads something like: "C:\Program Files\R\R-3.2.2\bin\Rgui.exe" –sdi
Install the R Commander package as follows. If you are using Windows 7, first start R as administrator by right-clicking the shortcut that you just edited and selecting Run as administrator. If you are not using Windows 7, run R by double-clicking on the shortcut that you just edited. In either case, when the > appears with the cursor after it, type

install.packages("Rcmdr", dependencies=TRUE)

You will be asked to choose a mirror site. For the fastest download, select one of the mirrors in Oregon, which are at the bottom of the list of mirrors. With the current version of R a few dependencies don’t get installed, so run these two commands to install the dependencies:

install.packages("rpanel", dependencies=TRUE)

install.packages("XLConnect", dependencies=TRUE)

Download the install file for the Bio 211 and/or Math 160 plugins using the link(s) on the top of the page. Note where it was saved onto your computer. You will need to find this file in Step f and/or Step g.

Next, enter the following command at the > prompt in R:

.libPaths()

This will output one or more file folder names. The“myLibraryFolder” that you will need for the next step is the one that contains Program Files/R (or some abbreviated version of that) in it.

Note: do this step for Bio 211 and ignore for Math 160.Enter the following command at the > prompt in R, filling in your library folder in place of myLibraryFolder inside the quotes (keeping the quotes):

install.packages(file.choose(), lib="myLibraryFolder", repos=NULL, type="source",dependencies=TRUE)

This will open a dialog box for you to choose a file. Select the file that you downloaded in Step d onto your computer. The computer will then install the Bio 211 menu package. (RcmdrPlugin.Bio211_1.0.tar.gz)

Note: do this step for Math 160 and ignore for Bio 211.Enter the following command at the > prompt in R, filling in your library folder in place of myLibraryFolder inside the quotes (keeping the quotes):

install.packages(file.choose(), lib="myLibraryFolder", repos=NULL, type="source",dependencies=TRUE)

This will open a dialog box for you to choose a file. Select the file that you downloaded in Step d onto your computer. The computer will then install the Math160 menu package. (RcmdrPlugin.Math160_1.0.tar.gz)

When the steps above are complete, you may exit R by entering

quit(save="no")

at the > prompt.

These steps will install R Commander with the Bio 211 menu and the Math 160 menu items on your computer. Once this is installed, you can use it by running R and entering

library(Rcmdr)[SW1]

at the > prompt. To make sure the plugin’s installed correctly, go to “Tools-Load Rcmdr Plug-in(s) menu” and the list should have RcmdrPlugin.Bio211 and RcmdrPlugin.Math160 listed. Select one or both and then Rcmdr will want to restart. Once it has restarted, there will be a menu at the top called Bio 211 and/or Math 160.

To exit R commander, use the File/Exit/From Commander and R menu option. You will be asked Exit?, and you should answer OK. Then you will be asked Save script file?, and you should answer No. You will then be asked Save output file?, which you should also answer No. After these questions, R Commander and R will both be closed.

If for some reason you accidentally exit R Commander but not R, you can exit R by typing

quit(save="no")

at the > prompt, or by many of the usual ways of closing programs. If you are asked Save workspace image? in the process, you should answer No.

*Please note that due to the nature of open source software and the number of dependent files and the various configurations of machines, these instructions may not work. The software is always installed on vDesk at:
vdesk.pugetsound.edu

Installing R on Mac OS 10.10 Yosemite (August 2015)

1. Install R with Plugins (Math 160 and Biology 211). Use the following install files:

R-3.2.2-win.exe

(

Xquartz

(

RcmdrPlugin.Bio211_1.0.tar.gz

(

RcmdrPlugin.Math160_1.0.tar.gz

(

The current version of R, as of this writing (August 2015) is 3.2.2 and this process below has been tested with this version.

Install R on the computer using the link above. Use all the defaults. (You will need to know your Mac password.)
Double-click on the “R” icon in Applications to launch R. When the > appears with the cursor after it, type (Make sure to have the quotes and capitation exactly as written below.)

install.packages("Rcmdr", dependencies=TRUE)

You will be asked to choose a mirror site. For the fastest download, select one of the mirrors in Oregon or Washington, which are at the bottom of the list of mirrors.(These are constantly changing, so try Oregon first if there is one, then one in Washington second.) With the current version of R a few dependencies don’t get installed, so run these two commands to install the dependencies:

If at any point it asked this question: “Do you want to install from sources the package that require compilation?” select no.

install.packages("rpanel", dependencies=TRUE)

install.packages("XLConnect", dependencies=TRUE)

Enter the following command at the > prompt in R.

install.packages(file.choose(),repos=NULL, type="source",dependencies=TRUE)

This will open a dialog box for you to choose a file. Select the fileRcmdrPlugin.Bio211_1.0.tar.gz that you just downloaded onto your computer. The computer will then install the Bio 211 menu package. (RcmdrPlugin.Bio211_1.0.tar.gz) If you are also installing the Math 160 plugin, repeat the above command and select the file RcmdrPlugin.Math160_1.0.tar.gz.

Once done type the following command to launch R commander:

library(Rcmdr)

at the > prompt.

You may get a prompt to install oTools and Xcode. If that happens then select download and it should automatically go out to the internet and install the tools necessary and put a prompt when it is done.

Once Xcode is installed you will need to type this again:

library(Rcmdr)

at the > prompt.

If you get an error that X11 library is missing, you will need to download and install XQuartz from the link above. Launch the XQuartz installer and follow the prompts. (This install may take several minutes and may look like it is stuck.) Once XQuartz is done you will need to logout of your machine and log back in. (or simply reboot it) Once you have logged back in start R and type:

library(Rcmdr)

at the > prompt.

This may take a moment because XQuartz will also need to launch in the background. The R commander screen should come up on the screen. You now have R Commander installed.

These steps will install R Commander with the Bio 211 menu and the Math 160 menu items on your computer. Once this is installed, you can use it by running R and entering

library(Rcmdr)

If for some reason you accidentally exit R Commander but not R, you can exit R by typing

quit(save="no")

at the > prompt, or by many of the usual ways of closing programs. If you are asked Save workspace image? in the process, you should answer No.

You will also want to make sure to quit out of XQuartz, which is a separate program and if left open can cause your computer to slow.

[SW1]I got an error that the package RODBC was missing. No problem to install it, but FYI.