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Installing R & R/qtl on your Laptop or Office Computer Instructions are for Windows 7 computers (64-bit and/or 32-bit) 
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First, REMOVE any old version of R.  
  Current R version is 2016-03-10 3.2.4 (for Windows). 
  If your version is - older, go to the Windows control panel 
  & find the old R in the list, and click on Uninstall. - Now exit the Windows control panel.

Second, go to this web site: http://cran.r-project.org/ - Click on the bold-faced words Download R. - Go to USA sections and click on the Iowa State entry **NOW, click on Download R for Windows
- click on the bold-faced words install R for the first time. - Then click on the bold-face words Download R-3.2.2 for Windows. - Run the file, don't save it - Say yes to security question - In the Welcome box or installation box do the following: - Choose English and click OK
- The R for Windows Setup Window appears - click Next - Read the license details - click Next
- Relative to the next choice - STOP Here temporarily
  You do NOT want to accept the offered default directory!
  Instead, carefully delete the text:  Program Files\ 
    TO CHANGE FROM THIS:  C:\Program Files\R\R-3.2.4  
    TO THIS:              C:\R\R-3.2.4
    THEN click Next
- It is best to use the default R components - so just click Next - It is best to use the default start up options - so just click Next - It is best to use the default start menu folder - so just click Next - It is best to use  the default additional tasks - so just click Next
  Wait (!!) for setup to complete the installation - Click on the word Finish.

A Blue R icon is on your desktop (two icons if you have 64-bit Windows).   If you have 64-bit, use it instead of the 32-bit version for R/qtl.

Click the Blue R icon (64-bit one if you have it on your desktop)  - Go to the top menu tab in R entitled Packages and click on it - In the Packages menu list, select Set CRAN Mirror - Then select (HTTP mirrors) at the bottom of the list - Then page down to Choose USA(IA) and press OK **Now, go back to the Packages menu button and look at the list. - From the list, select the tab entitled Install Package(s)...... - For using Jimbo's R/qtl batch file to work with F2 and RIL pops, - you will need to install the following packages.   - Hold down Ctrl key and select (i.e., blue highlight) these packages. 

  MASS
  calibrate
  moments
  psych
  qtl
  qtlbook
  qtlc
  qtlcharts
  qtlDesign
  qtlhot
  qtlmt  
  qtlnet
  R2PPT
  rscproxy

- Now press OK, and you will then see each above package downloaded.
  Other packages will also be downloaded automatically. 
  Feedback will stated package ‘xxxxx’ successfully unpacked and 
   MD5 sums checked. WAIT PATIENTLY for the R red > carot (=done) - There is no need to save R at this time. To exit R, simply click on  
  File (upper left), then Exit.  Or click on the upper right X to close R.
  Click on NO when asked to save. Now continue on below

Next, you need to make your R/qtl sesions functionally utilitarian.
  Go to your C:\directory and use NotePad to create there two files, 
  and when done, save each of these two files in an All Files format
  (NOT a *.txt format). Yes, names of those files begin with a dot!

- One file will be titled .Renviron - type in these two lines of text:
  R_PAPERSIZE=letter
  R_PRINTCMD lpr

- Other file will be titled .Rprofile and needs the below text lines
  (these packages are then auto-called each time you use R for Rqtl)  

options(htmlhelp=TRUE, show.signif.stars=FALSE) library(MASS)
library(calibrate)
library(moments)
library(psych)
library(qtl)
library(qtlbook)
library(qtlDesign)
library(qtlhot)
library(qtlmt)
library(qtlnet)
library(QTLRel)
library(R2PPT)
library(rscproxy)

- Recheck your C:\ directory to see if the .Renviron and .Rprofile files 
  are there. They will have NO filestem name or.txt extension.  

Now, create a C:\WorkName directory into which the files you will be  outputting when you use the R/qtl program. Putting all of your Rqtl  output files into one directory is handy. You can later move outputted files of a specific project to subdirectories within tis main directory.  For example, create a directory named: WorkRqtl like this C:\WorkRqtl 
 
*****Finally, go to the R/qtl website:  http://www.rqtl.org/ The current R/qtl version is 1.39-5 (2016-03-04) but you get it that version autmatically when you issue the r command library(qtl). This  comman is already in my Jimbo RqtL batchfiles for F2 or RIL populations.  It is useful to a put pdf copy of the 03/04/2016 Rqtl Manual on the desktop. 

The book titled "A guide to QTL Mapping with Rqtl" is a good one to buy. However, if you are a penny-pincher, you can go to this website to get an online version of Broman & Sen book, and put that pdf on your desktop:

http://www.leg.ufpr.br/~eder/ebooksclub.org__A_Guide_to_QTL_Mapping_with_R_qtl__Statistics_for_Biology_and_Health_.pdf