       I wholeheartedly agree with the trend towards publishing 
datasets.  One way to do that is as datasets in an R package contributed 
to CRAN.


       Beyond this, there seems to be an increasing trend towards 
journals requiring authors of scientific research to publish their data 
as well.  The Public Library of Science (PLOS) has such a policy, but it 
is not enforced:  Savage and Vickers (2010) were able to get the raw 
data behind only one of ten published articles they tried, and that one 
came only after reminding the author that s/he had agreed to making the 
data available as a condition of publishing in PLOS.  (Four other 
authors refused to share their data in spite of their legal and moral 
commitment to do so as a condition of publishing in PLOS.)


       There are other venues for publishing data.  For example, much 
astronomical data is now routinely web published so anyone interested 
can test their pet algorithm on real data 
(http://sites.google.com/site/vousergroup/presentations/publishing-astronomical-data). 



       Regarding my earlier comment, I just found a Wikipedia article on 
"scientific misconduct" that mentioned the tendency to refuse to publish 
research that proves your new drug is positively harmful.  This is an 
extreme version of both types of bias I previously mentioned:  (1) only 
significant results get published.  (2) private funding provides its own 
biases.


       Spencer


#########
Savage and Vickers (2010) "Empirical Study Of Data Sharing By Authors 
Publishing In PLoS Journals", Scientific Data Sharing, added Apr. 26, 
2010 
(http://scientificdatasharing.com/medicine/empirical-study-of-data-sharing-by-authors-publishing-in-plos-journals-2 
<http://scientificdatasharing.com/medicine/empirical-study-of-data-sharing-by-authors-publishing-in-plos-journals-2/>). 




On 1/7/2011 4:08 AM, Mike Marchywka wrote:
>
>
>
>
>
>
>> Date: Thu, 6 Jan 2011 23:06:44 -0800
>> From: peter.langfelder@gmail.com
>> To: r-help@r-project.org
>> Subject: Re: [R] Waaaayy off topic...Statistical methods, pub bias, scientific validity
>>
>> > From a purely statistical and maybe somewhat naive point of view,
>> published p-values should be corrected for the multiple testing that
>> is effectively happening because of the large number of published
>> studies. My experience is also that people will often try several
>> statistical methods to get the most significant p-value but neglect to
>> share that fact with the audience and/or at least attempt to correct
>> the p-values for the selection bias.
> You see this everywhere in one form or another from medical to financial
> modelling. My solution here is simply to publish more raw data in a computer
> readable form, in this case of course something easy to get with R,
> so disinterested or adversarial parties can run their own "analysis."
> I think there was also a push to create a data base for failed drug
> trials that may contain data of some value later. The value of R with
> easily available data for a large cross section of users could be to moderate
> problems like the one cited here.
>
> I almost
> slammed a poster here earlier who wanted a simple rule for "when do I use
> this test" with something like " when your mom tells you to" since post
> hoc you do just about everything to assume you messed up and missed something
> but a priori you hope you have designed a good hypothesis. And at the end of
> the day, a given p-value is one piece of evidence in the overall objective
> of learning about some system, not appeasing a sponsor. Personally I'm a big
> fan of post hoc analysis on biotech data in some cases, especially as more pathway or other theory
> is published, but it is easy to become deluded if you have a conclusion that you
> know JUST HAS TO BE RIGHT.
>
> Also FWIW, in the few cases I've examined with FDA-sponsor rhetoric, the
> data I've been able to get tends to make me side with the FDA and I still hate the
> idea of any regulation or access restrictions but it seems to be the only way
> to keep sponsors honest to any extent. Your mileage
> may vary however, take a look at some rather loud disagreement with FDA
> over earlier DNDN panel results, possibly involving threats against critics. LOL.
>
>
>
>
>
>> That being said, it would seem that biomedical sciences do make
>> progress, so some of the published results are presumably correct :)
>>
>> Peter
>>
>> On Thu, Jan 6, 2011 at 9:13 PM, Spencer Graves
>>   wrote:
>>>       Part of the phenomenon can be explained by the natural censorship in
>>> what is accepted for publication:  Stronger results tend to have less
>>> difficulty getting published.  Therefore, given that a result is published,
>>> it is evident that the estimated magnitude of the effect is in average
>>> larger than it is in reality, just by the fact that weaker results are less
>>> likely to be published.  A study of the literature on this subject might
>>> yield an interesting and valuable estimate of the magnitude of this
>>> selection bias.
>>>
>>>
>>>       A more insidious problem, that may not affect the work of Jonah Lehrer,
>>> is political corruption in the way research is funded, with less public and
>>> more private funding of research
>>> (http://portal.unesco.org/education/en/ev.php-URL_ID=21052&URL_DO=DO_TOPIC&URL_SECTION=201.html).
>>>   For example, I've heard claims (which I cannot substantiate right now) that
>>> cell phone companies allegedly lobbied successfully to block funding for
>>> researchers they thought were likely to document health problems with their
>>> products.  Related claims have been made by scientists in the US Food and
>>> Drug Administration that certain therapies were approved on political
>>> grounds in spite of substantive questions about the validity of the research
>>> backing the request for approval (e.g.,
>>> www.naturalnews.com/025298_the_FDA_scientists.html).  Some of these
>>> accusations of political corruption may be groundless.  However, as private
>>> funding replaces tax money for basic science, we must expect an increase in
>>> research results that match the needs of the funding agency while degrading
>>> the quality of published research.  This produces more research that can not
>>> be replicated -- effects that get smaller upon replication.  (My wife and I
>>> routinely avoid certain therapies recommended by physicians, because the
>>> physicians get much of their information on recent drugs from the
>>> pharmaceuticals, who have a vested interest in presenting their products in
>>> the most positive light.)
>>>
>   		 	   		
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph:  408-655-4567


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