[R] Log plus one transformation in R

[David Winsemius]

> On Dec 12, 2016, at 9:26 AM, John Sorkin <jsorkin at grecc.umaryland.edu> wrote:
> 
> David,
>  
> I did read the help page. All it says is
> log1p(x) computes log(1+x) accurately also for |x| << 1 (and less accurately when x is approximately -1).

Not true. You evidently did not run the examples.

-- 
David.
> 
> This gives me pause. Does it mean that log(x) does not give accurate results? If log1p gives more accurate values than log, why is the log function not written to use the more accurate computation performed by log1p. I don't believe I can look directly at the code for log and log1p, so I need to rely on the kindness of others to explain the differences between the computations performed by the functions. I guess the test I ran, log1p(0.000001)/log(0.000001+1), did not have enough precision to demonstrate a difference between the two functions.
> 
> John
> 
> 
> 
> 
> 
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> >>> David Winsemius <dwinsemius at comcast.net> 12/12/16 12:05 PM >>>
> 
> > On Dec 12, 2016, at 8:53 AM, John Sorkin <jsorkin at grecc.umaryland.edu> wrote:
> > 
> > At the risk of being flamed . . .
> > What is the difference between log1p(x) and log(x+1)?
> > The two methods appear to give the same results:
> >> log1p(0.000001)/log(0.000001+1)
> > [1] 1
> > John
> 
> Read the help page more carefully.
> 
> -- 
> David.
> > 
> > 
> > John David Sorkin M.D., Ph.D.
> > Professor of Medicine
> > Chief, Biostatistics and Informatics
> > University of Maryland School of Medicine Division of Gerontology and
> > Geriatric Medicine
> > Baltimore VA Medical Center
> > 10 North Greene Street
> > GRECC (BT/18/GR)
> > Baltimore, MD 21201-1524
> > (Phone) 410-605-7119
> > (Fax) 410-605-7913 (Please call phone number above prior to faxing) 
> >>>> William Dunlap via R-help <r-help at r-project.org> 12/12/16 11:38 AM
> >>>> 
> > log1p(x), in the base package computes log(1+x) accurately for small x
> > (and
> > large).
> > 
> > E.g.,
> >> options(digits=16)
> >> base::log1p(1e-14)
> > [1] 9.99999999999995e-15
> >> base::log1p(1e-14) - base::log(1+1e-14)
> > [1] 7.992778373591124e-18
> >> as.numeric(log(Rmpfr::mpfr(1,precBits=1000) + Rmpfr::mpfr(1e-14,
> > precBits=1000))) - log1p(1e-14)
> > [1] 0
> > 
> > 
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> > 
> > On Mon, Dec 12, 2016 at 8:23 AM, Faradj Koliev <faradj.g at gmail.com>
> > wrote:
> > 
> >> Hi all,
> >> 
> >> How do I perform log(x+1) in R?
> >> 
> >> log1p_trans() from the package ”scales" doesn’t seem to work for me.
> >> 
> >> Best,
> >> Faradj
> >> ______________________________________________
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> >> and provide commented, minimal, self-contained, reproducible code.
> > 
> > [[alternative HTML version deleted]]
> > 
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> 
> David Winsemius
> Alameda, CA, USA
> 
> 
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