how to import data into R and SAS

What is bio-statistics and how does it relate to me ? I am often asked this question, and now I think I may have an answer. With the advent of the Internet, we are now in the Age of Information, and when it comes to "statistical data analysis", a rather imposing mouthful, to quote a recent article in the New York Times (and I paraphrase):

In field after field, computing and the Web are creating new realms of data to explore - sensor signals, surveillance tapes, social network chatter, public records and more. We're rapidly entering a world where everything can be monitored and measured, but the big problem is going to be the ability of humans to use, analyze and make sense of the data. Strong correlations of data do not necessarily prove a cause-and-effect link. For example, in the late 1940s, before there was a polio vaccine, public health experts in America noted that polio cases increased in step with the consumption of ice cream and soft drinks. Eliminating such treats was even recommended as part of an anti-polio diet. It turned out that polio outbreaks were most common in the hot months of summer, when people naturally ate more ice cream, showing only an association. Computers do what they are good at, which is trawling these massive data sets for something that is mathematically odd, and humans do what they are good at and explain these anomalies.

To analyze statistical data, we use computer programs as tools to work with such information as biological data. Yet another recent article in the New York Times compares and contrasts two of these computer programs, R and SAS (and again I paraphrase):

SAS Institute (the privately held business software company that specializes in data analysis)'s namesake SAS has been the preferred tool of scholars and corporate managers. But the R Project has also quickly found a following because statisticians, engineers and scientists without computer programming skills find it easy to use.

Reference:
http://www.nytimes.com/2009/08/06/technology/06stats.html
http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html?pagewanted=all

So "Statistical Data Analysis" in the abstract sense is a formidable journey of a thousand miles, but the bite-size journey's first step involves importing a set of data into the tool (I'm assuming you already obtained, installed, and are running the software). For purposes of demonstration, I've created a data set using the actual previous year's receipts I had gathered and saved from each and every time I filled my car's tank with gasoline:

    18AUG2009  6 12.815 37.66
    14JUL2009 12  4.340 11.8
    28MAY2009  6  9.532 24.39
    22APR2009  4  7.348 16.01
    25MAR2009  2  5.509 11.12
    15MAR2009  7  4.230  8.62
    04MAR2009  3 11.989 25.16
    21FEB2009  7 13.298 27.91
    29JAN2009 15 13.989 27.68
    03JAN2009  6 12.620 22.70
    29NOV2008 16 11.239 20.78
    25SEP2008  8 13.929 51.80

Note that on the tail end of the second line, in the last figure, 11.8, I omitted a zero ('0') when I was typing the data in. We'll come back to that later. I decided to record the following four fields for each time I filled the gas tank (all took place at Costco in San Leandro):

1. date of purchase
2. pump number
3. quantity of gas obtained, in gallons
4. cost of the transaction

In both tools, R and SAS, we will then divide cost by quantity and generate a fifth field, price per gallon.

To import a dataset into your software, you can either read from a file, or copy and paste it in (although for R, you will copy the data set, but you won't actually paste anything). The following scripts have been tested on R versions 2.8.1, 2.9.2 and SAS version 9.1.3 Service Pack 4.

• To read data from a file within R and SAS:
  1. identify the path to the file containing your data set. Let's say the path is:
     

     G:\tpc247\petrol.txt

     if you're on Windows, the convention is to delimit or separate folders with a backslash, but this poses a problem for software that is trained to recognize tabs and carriage returns and newlines as '\t', '\r' and '\n' respectively. For reasons of cross-platform compatibility, if there are backslashes in your Windows path, add another one right next to it:
     

     G:\\tpc247\\petrol.txt

     or replace the backslash with a forward slash:
     

     G:/tpc247/petrol.txt

  2. at the command prompt, input and run the following incantations:
     • R:
       

       petrol_01 = read.table("G:/tpc247/petrol.txt", header=FALSE, col.names=c('date', 'pump', 'quantity', 'cost'))
       petrol_01$per_gallon <- petrol_01$cost / petrol_01$quantity
       petrol_01

     • SAS:

       data petrol_01;
          infile "G:/tpc247/petrol.txt";
          input date_of_sale$ 5-13 pump_number$ 16-17 quantity 20-25 cost 28-32;
          per_gallon = cost / quantity;
          proc print data=petrol_01;
          title 'Unleaded gasoline purchase history for 1 year, San Leandro, California Costco';
       run;

• To read data from computer memory in R and SAS:
  • R:
    1. copy and paste this into R, but don't actually run the incantation yet:

       petrol_01 = read.table("clipboard", col.names=c('date', 'pump', 'quantity', 'cost'))

    2. copy your data set, then run the previous incantation
    
    
    3. run the rest as you normally would:

       petrol_01$price_per_gallon <- petrol_01$cost / petrol_01$quantity
       petrol_01

  • SAS:

    data petrol_01;
      input date_of_sale$ 5-13 pump_number$ 15-16 quantity 18-23 cost 25-29;
      per_gallon = cost / quantity;
      datalines;
        18AUG2009  6 12.815 37.66
        14JUL2009 12  4.340 11.8
        28MAY2009  6  9.532 24.39
        22APR2009  4  7.348 16.01
        25MAR2009  2  5.509 11.12
        15MAR2009  7  4.230  8.62
        04MAR2009  3 11.989 25.16
        21FEB2009  7 13.298 27.91
        29JAN2009 15 13.989 27.68
        03JAN2009  6 12.620 22.70
        29NOV2008 16 11.239 20.78
        25SEP2008  8 13.929 51.80
      proc print data=petrol_01;
      title 'Unleaded gasoline purchase history for 1 year, Costco in San Leandro, California';
    run;

Coming back to the omitted zero ('0') on the second line in our last figure, 11.8, you might find it amusing how finicky R and SAS are about what they eat. Putting this tutorial together gave me the opportunity to learn some valuable things about the two tools. Just like a toddler can be very picky about the food she feels like taking in her, feeding data to R and SAS and ensuring they digest the data correctly may require some forethought and planning. When importing the dataset into both tools from a file, I noticed that in:

• R, if I didn't include in my incantation:

  header = FALSE

  I would find the first record in my dataset on file would be missing from my dataset in R
• SAS, omitting the zero ('0') when I typed the following into my dataset, for July 14, 2009:

  14JUL2009 12  4.340 11.8

  did not pose a problem, as long as I ran a previous incarnation of my SAS script:

  data petrol_01;
     infile "G:/tpc247/petrol.txt";
     input date_of_sale$ pump_number$ quantity cost;
     per_gallon = cost / quantity;
     proc print data=petrol_01;
  run;

  However, I didn't like the resulting output in SAS. I have developed a preference for a specific way of representing dates that is 9 characters long and in a format that, to my eyes, is more easy to read. However, when I ran the aforementioned script on my data set, my dates were truncated:
  
  It seemed that SAS preferred data in columns to be 8 characters or less, or else it would truncate any value greater than 8 characters. So even though running my SAS script resulted in SAS correctly reading in my data, and there was no problem with my omitting the zero ('0'), I decided to modify the incantations in my script and specify the columns so that the dates in my desired format would not be cut off. When I did this, I noticed that data in SAS was different from the data on file:
  
  As you can see, the information from the fill_the_gas_tank event for 28MAY2009 has disappeared, and the line in my dataset on file:

  14JUL2009 12  4.340 11.8

  has been replaced in SAS with

  14JUL2009 12  4.340 2.00 0.46083

  I imagine SAS would read 11.8 and then be confused because there were no more numbers and I had told it to expect one more, but I can't explain how SAS computed a cost of 2.00. However, I can explain that the price_per_gallon of around 46 cents is simply derived from dividing 2.00 dollars by 4.34 gallons. The fact that the record for May 28, 2009 is missing leads me to conclude that when reading data from file, and your SAS statement specifies columns, SAS seems to expect values for the entire range of columns you specify. I've confirmed this phenomenon, of a missing record when you specify in your SAS statement the columns where values can be found, manifests itself in SAS only when reading data from file, and not from the copy and paste of data.

Other separators and delimiters

If you have commas separating your data:

    18AUG2009,  6, 12.815, 37.66
    14JUL2009, 12,  4.340, 11.8
    28MAY2009,  6,  9.532, 24.39
    22APR2009,  4,  7.348, 16.01
    25MAR2009,  2,  5.509, 11.12
    15MAR2009,  7,  4.230,  8.62
    04MAR2009,  3, 11.989, 25.16
    21FEB2009,  7, 13.298, 27.91
    29JAN2009, 15, 13.989, 27.68
    03JAN2009,  6, 12.620, 22.70
    29NOV2008, 16, 11.239, 20.78
    25SEP2008,  8, 13.929, 51.80

In:

• R: replace read.table() with read.csv()
  Reference: http://pbil.univ-lyon1.fr/library/base/html/read.table.htm
• SAS: simply update the existing column information to reflect the new column values, or, modify your script to specify the column range for where the values can be

When importing data into R or SAS, you need to look at your dataset, and tell R or SAS exactly what to expect, or your statistical data analysis software may complain.

Reference: http://www.stat.psu.edu/online/program/stat481/01importingI/02importingI_styles.html

how to install a seat leash to prevent theft of saddle & seat post

Protect your bike from those who may see an opportunity to abscond with the valuable, quick-released perch for your peachy derriere.

a tempting target for a would-be thief	Foiled again! Thanks seat leash

Were anyone to happen upon this scene, look around and see no one watching, the thought might cross your mind to simply loosen the quick release and walk off with someone else's property like it was yours. The Great Recession created lean and mean times, changing the way Americans spend. With such general apprehension and fear, you can find some amazing bargains in the bicycle market right now. I decided to overcome my reluctance to spend and make the big purchase that, as an avid bicyclist, you might be saving for as well. My new second-hand bicycle is a lightly used 1997 Marin Team Titanium that has a quick release binder bolt for adjusting the height of the seat post.

Let's start by getting our vocabulary straight (thanks to Sheldon Brown for helping me put names to bike parts):

• saddle (also called bicycle seat)
• saddle clamp (also called seat sandwich)
• seat leash (also seat security cable)
• seatpost or seat post (also called seat mast, seat pillar, or seat pin)
• stolen (also pilfered, nicked, or made off with)
• Y hex wrench (also 3 way hex wrench. This is a tool, commonly seen in bike repair shops, that has the 3 wrench sizes to fit the socket heads on most modern bicycles. 'Hex wrench' can be used interchangeably with Allen wrench or L wrench)

Reference:
http://www.sheldonbrown.com/gloss_sa-o.html
http://en.wikipedia.org/wiki/Allen_wrench

To prevent your seatpost and saddle from being stolen, you will need:

1. seat leash
2. Y hex wrench

I tried numerous times to figure out a way to use a seat leash to secure my bicycle seat and seat-post, but the closest I got was a half-baked solution where I added the end-loop as an ingredient into the seat clamp mechanism, so that the clamp was gripping a combination of saddle rail and seat leash loop. This made for not the best grip on the saddle rails, and, while you were riding, the bicycle seat was prone to moving horizontally back and forth, a rather unpleasant event for any rider. The light bulb flashed atop my head last Sunday, September 6, at around 11:25am, when I stepped into the Missing Link repair shop and spoke with Andy Renteria, who told me it's possible to secure the saddle and seatpost to the bike with a security cable. He used his forefinger and thumb as an analog for the end-point loop of the seat security cable, and wrapped it around the saddle clamp, between the seatpost and the saddle rail. The breakthrough for me on how to secure your bike seat was using the saddle clamp itself as the focal point on which to anchor the endpoint loop:

Thanks Andy, at Missing Link repair shop


The seat security cable has end loop which uses the saddle clamp (I call it a seat sandwich) as a focal point. Also in the picture is my beloved Planet Bike Superflash Stealth Tail Rear Light







From start to finish:

1. use the Y hex wrench, or any appropriate Allen or 'L' wrench, to remove the saddle
2. insert one loop through the other and wrap your seat security cable around the seat stay, or any focal point that has stops and forms a closed area. Take care when wrapping your security cable around the seat stay that you avoid the part of the frame closest to the tire
3. with the remainder of the bike security cable in your hands, visualize the saddle clamp itself as the focal point on which to anchor the endpoint loop, and affix said loop on the clamp
4. now install (or rather, reinstall) the saddle into the seat clamp mechanism, making sure the seat leash end-point loop is between, and stopped by, the seat rail and the seat post.