R help - Aug 2004 - Is R good for not-professional-statistician, un-mathematical clinical researchers?

Alternate title: How can I persuade my students that R is for them?

Alternate title: Can R replace SAS, SPSS or Stata for clinicians?

I am teaching introductory statistics to twelve physicians and two veterinarians
who have enrolled in a Mentored Clinical Research Training Program.  My course
is the
first in a sequence of three.  We (the instructors of this sequence) chose to
teach
R rather than some other computing environment.

My (highly motivated) students have never encountered anything like R.  One
frankly
asked:

"Do you feel (honestly) that a group of physicians (with two vets)
clinicians will
be able to effectively use and actually understand R? If so, I will happily call
this
bookstore and order this book [Venables and Ripley] tomorrow."

I am heavily biased toward R/S because I have used it since the first applied
statistics
course I took.  But I would love to give these students some kind of objective
information
about the usability of R by non-statisticians--not just my own bias.

Could anyone suggest any such information?  Or does anyone on this list use R
who is
a clinician and not really mathematically savvy?  For instance, someone who
doesn't
remember any math beyond algebra and doesn't think in terms of P(A|B)?

Or have we done a disservice to our students by choosing to make them
learn R, rather than making ourselves learn SAS, Stata or SPSS?

Thank you for any ideas

Jake Wegelin

One thought -- the first course I took, I taught physicians
XLispStat.  They appreciated it since it allowed them to do logistic
regression without spending large $$$.....

Now, that isn't quite true any more.  So might depend on how times
have changed.



Jacob Wegelin <jawegelin at ucdavis.edu> writes:
> Alternate title: How can I persuade my students that R is for them?
>
> Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
>
> I am teaching introductory statistics to twelve physicians and two
veterinarians
> who have enrolled in a Mentored Clinical Research Training Program.  My
course is the
> first in a sequence of three.  We (the instructors of this sequence) chose
to teach
> R rather than some other computing environment.
>
> My (highly motivated) students have never encountered anything like R.  One
frankly
> asked:
>
> "Do you feel (honestly) that a group of physicians (with two vets)
clinicians will
> be able to effectively use and actually understand R? If so, I will happily
call this
> bookstore and order this book [Venables and Ripley] tomorrow."
>
> I am heavily biased toward R/S because I have used it since the first
applied statistics
> course I took.  But I would love to give these students some kind of
objective information
> about the usability of R by non-statisticians--not just my own bias.
>
> Could anyone suggest any such information?  Or does anyone on this list use
R who is
> a clinician and not really mathematically savvy?  For instance, someone who
doesn't
> remember any math beyond algebra and doesn't think in terms of P(A|B)?
>
> Or have we done a disservice to our students by choosing to make them
> learn R, rather than making ourselves learn SAS, Stata or SPSS?
>
> Thank you for any ideas
>
> Jake Wegelin
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
-- 
Anthony Rossini			    Research Associate Professor
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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On Thu, 2004-08-19 at 07:45, Jacob Wegelin wrote:
> Alternate title: How can I persuade my students that R is for them?
> 
> Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
> 
> I am teaching introductory statistics to twelve physicians and two
veterinarians
> who have enrolled in a Mentored Clinical Research Training Program.  My
course is the
> first in a sequence of three.  We (the instructors of this sequence) chose
to teach
> R rather than some other computing environment.
> 
> My (highly motivated) students have never encountered anything like R.  One
frankly
> asked:
> 
> "Do you feel (honestly) that a group of physicians (with two vets)
clinicians will
> be able to effectively use and actually understand R? If so, I will happily
call this
> bookstore and order this book [Venables and Ripley] tomorrow."
> 
> I am heavily biased toward R/S because I have used it since the first
applied statistics
> course I took.  But I would love to give these students some kind of
objective information
> about the usability of R by non-statisticians--not just my own bias.
> 
> Could anyone suggest any such information?  Or does anyone on this list use
R who is
> a clinician and not really mathematically savvy?  For instance, someone who
doesn't
> remember any math beyond algebra and doesn't think in terms of P(A|B)?
> 
> Or have we done a disservice to our students by choosing to make them
> learn R, rather than making ourselves learn SAS, Stata or SPSS?
> 
> Thank you for any ideas
> 
> Jake Wegelin
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Hi Jake,

I can give you my experience on this subject. First of all I am not a
Stats/Maths professional, I'm a Marine Biologist working in fisheries,
although with a MSc in Stats ... but I've started using R before I did
the MSc.

In the Fisheries Scientists Community R is becoming broadly used and
most scientists have backgrounds in Biology or similars.

I think the most important question is "are they afraid of the command
line ?" if yes forget about R, otherwise I guess they will love it when
they'll find how much they can do with it.

Hope it helps

Best regards

EJ

I'm not in your target audience but I consult with and teach to your target
audience, so I'll chime in anyway.

1. Look at the "user friendliness" of the alternatives you offered to
R. I haven't used SPSS recently or Stata at all but I know SAS is NOT that
user friendly. Note that my institute has historically used Minitab for teaching
our introductory course in biostatistics.
2. Look for "user friendly" front ends to R. Professor John Fox has
late beta software for teaching introductory statistics (see:
http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/). If you would like to add
procedures to those provided by the basic front end, Rcmdr is written so that
you can. I plan to do that and teach a stand alone seminar on R through Rcmdr in
the late fall or early winter.
3. Last year, outside of our biostatistics class, I taught a seminar on
installing and basic use of command line R. At first, I was concerned that I
wouldn't be able to fill the 20 seats in our computer lab. In response to my
advertisement within WRAIR, I actually had to add three more sections. Classes
were received enthusiastically and students stayed after each seminar for
continued discussion. Unfortunately, the small number of students I consulted
with subsequently indicated that they never used R after my seminar.

Chuck 

Charles E. White, Senior Biostatistician, MS
Walter Reed Army Institute of Research
503 Robert Grant Ave., Room 1w102
Silver Spring, MD 20910-1557
301 319-9781
Personal/Professional Site: http://users.starpower.net/cwhite571/professional/

On Thu, 2004-08-19 at 01:45, Jacob Wegelin wrote:
> Alternate title: How can I persuade my students that R is for them?
> 
> Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
> 
> I am teaching introductory statistics to twelve physicians and two
veterinarians
> who have enrolled in a Mentored Clinical Research Training Program.  My
course is the
> first in a sequence of three.  We (the instructors of this sequence) chose
to teach
> R rather than some other computing environment.
> 
> My (highly motivated) students have never encountered anything like R.  One
frankly
> asked:
> 
> "Do you feel (honestly) that a group of physicians (with two vets)
clinicians will
> be able to effectively use and actually understand R? If so, I will happily
call this
> bookstore and order this book [Venables and Ripley] tomorrow."
> 
> I am heavily biased toward R/S because I have used it since the first
applied statistics
> course I took.  But I would love to give these students some kind of
objective information
> about the usability of R by non-statisticians--not just my own bias.
> 
> Could anyone suggest any such information?  Or does anyone on this list use
R who is
> a clinician and not really mathematically savvy?  For instance, someone who
doesn't
> remember any math beyond algebra and doesn't think in terms of P(A|B)?
> 
> Or have we done a disservice to our students by choosing to make them
> learn R, rather than making ourselves learn SAS, Stata or SPSS?
> 
> Thank you for any ideas
> 
> Jake Wegelin

A couple of questions:

1. What is the intended goal of the series of classes?

2. What are the expectations of the clinicians for themselves and what
is their likely career path?


Possible answers to the questions:

1. Provide the clinicians a reasonable (and perhaps broad) foundation of
statistical knowledge.

2. To be able to have a reasonable comprehension of statistical concepts
and methods so that in the future, as they are busy with patients
(animals for the vets) in a clinical practice, they can intelligently
interact with formally trained statisticians when engaged in clinical
research in a multi-disciplinary team environment.


If the above is close to reality, then let me suggest that you consider
Peter's book "Introductory Statistics with R" rather than MASS, at
least
for the first class in the series. I cannot think of a more gentle,
broad and competent way to introduce clinicians to both statistics and R
at the same time.

If these clinicians are likely to move on to busy clinical practices, in
my experience having come out of the clinical environment, they will not
have the time to sit at a computer and grind out analyses, much less
maintain their proficiency with a programming language (R, Stata or SAS)
or the broad range of statistical methodologies that they would likely
encounter over their careers.

They will however, need to be able to sit and interact with
statisticians, bringing the significant value of their clinical training
and knowledge, to the process of designing clinical research projects
and effectively comprehend the multitude of issues in that endeavor.
They will need to have an understanding of the complex processes by
which data are collected, managed, manipulated and analyzed in the
course of obtaining the resultant analyses. 

In other words, it is important that they realize that it is more than
just a "point and click" process where voila, you have logistic
regression model. They need to appreciate both the subtleties and
complexities of dealing with real world research, incomplete data, etc.
Many clinicians do not and this results in mis-matched expectations in
the future as they deal with real world situations.

There are certainly physicians who have made the decision to focus their
careers on the statistical part of the research process, forsaking any
significant clinical patient care role. They are far and few between, to
my experience, though two or three immediately come to mind. They have
also generally made the commitment to formal graduate level education in
math/statistics securing advanced degrees.

Short of that, there is typically a future dependence upon trained
statisticians, either within an academic medical environment or via
contracted services.

The above is based upon my own experience, which is largely in
sub-specialty clinical areas. Others may and perhaps will differ, based
upon their own bias.

HTH,

Marc Schwartz

Jake,

this is a great question.

I have experience teaching R to forestry and natural resources graduate and
undergraduate students.  These students are amongst the least numerically
comfortable students I've taught.  I have found that the numerically
comfortable among them leap into the challenge, and the remainder reject it (and
usually me) as irrelevant and deliberately obtuse.  I am heavily biased towards
R because every once in a while I find myself writing code with a big happy
smile.  It's just fun.  There are some things that it does, that it does
just beautifully.  Oh, and I'm addicted to Sweave :).

R, by its nature, exposes the seamy underbelly of statistical reasoning, and
this creates various degrees of empowerment and fear, depending on the student. 
R requires us to create the syntax of our commands, and to think through the
process of analysis before its execution, at least enough to compose a coherent
statement.  Of course, this is educationally a very good thing, but also very
challenging.

I would suggest that it's just as plausible to teach R in a pre-packaged way
as it is to teach the other applications in a pre-packaged way.  The problem
arises when the students have to do their own analyses.  R has many elements
that require confidence and experience to overcome efficiently.

For example, let's take error reporting: one really has to have at least a
grasp of matrix algebra to know what singularities are.  Yet, singularities will
be reported in errors for tools that, prima facie, have no necessary obvious
relation with matrices.  Or another example is: we don't need to know
qr-decomposition or svd in order to be able to understand the statistical
elements of a multiple regression.  But, sometimes (NOT in those cases, I hasten
to add, but they're a good example of the kind of thing I mean) these
details bleed through.  So, our error messages sometimes, lack obvious
statistical relation to the problem at hand for the neophyte.  They can seem
cryptic and obscure.

Ok, this is inevitable, in a community-generated product like R, but it is a
hurdle that students will find frustrating, and will take them a long time to
overcome, regardless of their good intentions.  Many of the help files include
references to further reading, which is excellent and essential, but some do
not.

Now, I argue that student will certainly benefit from adopting the hacker-style
can-do attitude necessary to plough forwards.  But they rightly ask: is this the
most appropriate medium for that approach to be encouraged, for us?  A problem
is that for success, they not only require the hacker-style can-do attitude,
they also require technical background, which they do not intend to develop. 
Googling alone is not the answer, nor is R-help.  So it depends on the student.

In general, though, I don't think that R by itself can be considered
adequate for not-professional-statistician, un-mathematical clinical
researchers.  I don't think that it wants to be, or that we want it to be,
enough.  So, increasingly, I do think that we should learn another language, and
offer such students the option of a more unified approach.

Thanks for a very thought-provoking question.

Andrew

----- Original Message -----
From: Jacob Wegelin <jawegelin at ucdavis.edu>
Date: Thursday, August 19, 2004 4:45 pm
Subject: [R] Is R good for not-professional-statistician, un-mathematical
clinical researchers?
> 
> Alternate title: How can I persuade my students that R is for them?
> 
> Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
> 
> I am teaching introductory statistics to twelve physicians and two 
> veterinarianswho have enrolled in a Mentored Clinical Research 
> Training Program.  My course is the
> first in a sequence of three.  We (the instructors of this 
> sequence) chose to teach
> R rather than some other computing environment.
> 
> My (highly motivated) students have never encountered anything 
> like R.  One frankly  asked:
> 
> "Do you feel (honestly) that a group of physicians (with two vets) 
> clinicians will
> be able to effectively use and actually understand R? If so, I 
> will happily call this
> bookstore and order this book [Venables and Ripley] tomorrow."
> 
> I am heavily biased toward R/S because I have used it since the 
> first applied statistics
> course I took.  But I would love to give these students some kind 
> of objective information
> about the usability of R by non-statisticians--not just my own bias.
> 
> Could anyone suggest any such information?  Or does anyone on this 
> list use R who is
> a clinician and not really mathematically savvy?  For instance, 
> someone who doesn't
> remember any math beyond algebra and doesn't think in terms of P(A|B)?
> 
> Or have we done a disservice to our students by choosing to make them
> learn R, rather than making ourselves learn SAS, Stata or SPSS?
> 
> Thank you for any ideas
> 
> Jake Wegelin
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-
> guide.html

I am a clinician turned epidemiologist. I just taught R in an intro epi
course. Here are some tips:

- encourage them to use R as their calculator
- encourage them to use R as their spreadsheet
- provide them with exercises to work this functionality
- we started a Yahoo help group for beginner questions (see
http://www.ucbcidp.org/epitools.html)

I have some exercises at http://www.medepi.net/epitools/lab/

If you only show how to do things that can be done is any statistical
package, then they'll choose the "user-friendly" statistical
package
(e.g., stata).

For any additional question, please contact me.
Good luck!

Tomas Aragon
http://www.idready.org

 
--- Jacob Wegelin <jawegelin at ucdavis.edu> wrote:
> 
> Alternate title: How can I persuade my students that R is for them?
> 
> Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
> 
> I am teaching introductory statistics to twelve physicians and two
> veterinarians
> who have enrolled in a Mentored Clinical Research Training Program. 
> My course is the
> first in a sequence of three.  We (the instructors of this sequence)
> chose to teach
> R rather than some other computing environment.
> 
> My (highly motivated) students have never encountered anything like
> R.  One frankly
> asked:
> 
> "Do you feel (honestly) that a group of physicians (with two vets)
> clinicians will
> be able to effectively use and actually understand R? If so, I will
> happily call this
> bookstore and order this book [Venables and Ripley] tomorrow."
> 
> I am heavily biased toward R/S because I have used it since the first
> applied statistics
> course I took.  But I would love to give these students some kind of
> objective information
> about the usability of R by non-statisticians--not just my own bias.
> 
> Could anyone suggest any such information?  Or does anyone on this
> list use R who is
> a clinician and not really mathematically savvy?  For instance,
> someone who doesn't
> remember any math beyond algebra and doesn't think in terms of
> P(A|B)?
> 
> Or have we done a disservice to our students by choosing to make them
> learn R, rather than making ourselves learn SAS, Stata or SPSS?
> 
> Thank you for any ideas
> 
> Jake Wegelin
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> 

====Tomas Aragon, MD, DrPH, Director
Center for Infectious Disease Preparedness
UC Berkeley School of Public Health
1918 University Ave., 4th Fl., MC-7350
Berkeley, CA 94720-7350
http://www.idready.org