From j|ox @end|ng |rom mcm@@ter@c@  Thu Mar 28 17:18:40 2019
From: j|ox @end|ng |rom mcm@@ter@c@ (Fox, John)
Date: Thu, 28 Mar 2019 16:18:40 +0000
Subject: [Rd] default for 'signif.stars'
Message-ID: <ACD1644AA6C67E4FBD0C350625508EC836B2CD34@FHSDB2D11-2.csu.mcmaster.ca>

Dear all,

I agree with both Russ and Terry that the significance stars option should default to FALSE. Here's what Sandy Weisberg and I say about significance starts in the current edition of the R Companion to Applied Regression:

	'If you find the ?statistical-significance? asterisks that R prints to the right of the p-values annoying, as we do, you can suppress them, as we will in the remainder of the R Companion, by entering the command: options(show.signif.stars=FALSE).'

This is a rare case in which I find myself disagreeing with Martin, whose arguments are almost invariably careful and considered. In particular, the crude discretization of p-values into several categories seems a poor visualization to me, and in any event "scanning" many p-values quickly, which is the use-case that Martin cites, avoids serious issues of simultaneous inference.

Best,
 John

> -----Original Message-----
> From: R-devel [mailto:r-devel-bounces at r-project.org] On Behalf Of 
> Therneau, Terry M., Ph.D. via R-devel
> Sent: Thursday, March 28, 2019 9:28 AM
> To: r-devel at r-project.org
> Subject: Re: [Rd] default for 'signif.stars'
> 
> The addition of significant stars was, in my opinion, one of the worst 
> defaults ever added to R.?? I would be delighted to see it removed, or 
> at least change the default.? It is one of the few overrides that I 
> have argued to add to our site- wide defaults file.
> 
> My bias comes from 30+ years in a medical statistics career where 
> fighting the disease of "dichotomania" has been an eternal struggle.? 
> Continuous covariates are split in two, nuanced risk scores are 
> thresholded, decisions become yes/no, ....??? Adding stars to output 
> is, to me, simply a gateway drug to this pernicous addiction.?? We shouldn't encourage it.
> 
> Wrt Abe's rant about the Nature article:? I've read the article and 
> found it to be well reasoned, and I can't say the same about the rant.?? 
> The issue in biomedical science is that the p-value has fallen victim to Goodhart's law:
> "When a measure becomes a target, it ceases to be a good measure."? 
> The article argues, and I would agree, that the .05 yes/no decision 
> rule is currently doing more harm than good in biomedical research.?? 
> What to do instead of this is a tough question, but it is fairly clear 
> that the current plan isn't working.?? I have seen many cases of two 
> papers which both found a risk increase of 1.9 for something where one 
> paper claimed "smoking gun" and the other "completely exonerated".?? 
> Do YOU want to take a drug with 2x risk and a p= 0.2 'proof' that it 
> is okay??? Of course, if there is too much to do and too little time, 
> people will find a way to create a shortcut yes/no rule no matter what 
> we preach.?? (We statisticians will do it
> too.)
> 
> Terry T.
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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[Rd] default for 'signif.stars'
Fox, John