[R] plot representation of calculated value known to be 7.4
Troels Ring
tring at gvdnet.dk
Tue Dec 26 18:31:10 CET 2017
Thanks a lot -- yes it is amazing how much coherent detail has been put
into this and kept integrated :-)
Best wishes
Troels
Den 26-12-2017 kl. 16:35 skrev Bert Gunter:
> Inline.
>
> -- Bert
>
>> Thanks a lot - formatting the ordinate as ylim=c(4,10) before plotting pH also removed the problem, and options(digits=10) confirmed that pH was not all exactly 7.4 - as I knew. Still I wonder just why R chooses to plot(ATOT,pH) as shown with repeated "7.4" instead of some more detailed representation. Thanks a gain and happy New Year!
> --------------------
> There is no need to wonder if you just follow the docs in detail:
>
> Your first stop should be ?plot.default. If you read carefully through
> it, you will find in the examples:
>
> ##--- Log-Log Plot with custom axes
>
> In this example, you will find the use of the axis() function to
> create the custom axes. So this suggests, to me anyway, that ?axis
> should be the next port of call.
>
> ?axis reveals that axis() has a "labels" argument. The details section
> of the docs say:
>
> "If labels is not specified, the numeric values supplied or calculated
> for at are converted to character strings as if they were a numeric
> vector printed by print.default(digits = 7)."
>
> So -- aha! -- that looks like the explanation you sought. And, indeed,
> checking ?print.default, it says in "Details":
>
> "The same number of decimal places is used throughout a vector. This
> means that digits specifies the minimum number of significant digits
> to be used, and that at least one entry will be encoded with that
> minimum number. However, if all the encoded elements then have
> trailing zeroes, the number of decimal places is reduced until at
> least one element has a non-zero final digit."
>
> So, yes, it's a bit of a "Long Day's Journey...," but if you expend
> the effort to follow it all through carefully, especially for R's base
> functionality (it gets much more chancy with user-contributed
> packages, of course) it almost aways **is** all there.
>
> Cheers,
> Bert
>
>
>
>
>
>> Troels
>>
>>
>> Den 26-12-2017 kl. 01:03 skrev Bert Gunter:
>>
>> Note that ?all.equal clearly says that it tests for **approximate equality only** with tolerance "close to 1.5 e-8.
>>
>> So..
>>
>>> all.equal(z,pH, tol = 1e-15)
>> [1] "Mean relative difference: 6.732527e-11"
>>
>> and
>>
>>> print(pH, digits =15)
>> ## output omitted
>>
>> Shows you what's going on.
>>
>> Cheers,
>> Bert
>>
>>
>>
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming along and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>
>> On Mon, Dec 25, 2017 at 11:00 AM, Troels Ring <tring at gvdnet.dk> wrote:
>>> Dear friends - copy paste missed
>>>
>>> SID <- c() before the first loop - sorry
>>>
>>> BW Troels
>>>
>>>
>>>
>>> Den 25-12-2017 kl. 19:12 skrev Troels Ring:
>>>>
>>>> Dear friends - merry Christmas and thanks a lot for much help during the year!
>>>>
>>>> In the example below I fail to understand how the calculated value pH is represented in a simple plot - also included. The calculations are useful in practice and likely to be right in principle but I cannot see how this occurs: why a calculated value of 7.4 known as numeric is not simply plotted as such. It happened on Windows both 7 and 10 with R version 3.4.1.
>>>>
>>>> All best wishes
>>>>
>>>> Troels
>>>>
>>>> ff <- function(H,SID,ATOT,ka) H + SID - kw/H - ka*ATOT/(H+ka)
>>>> ka <- 1e-7
>>>> kw <- 1e-14
>>>> ATOT <- seq(0,0.3,length=100)*1e-3
>>>>
>>>> for (i in 1:length(ATOT)) {
>>>> SID[i] <- uniroot(ff,c(-1,1),tol=.Machine$double.eps,maxiter=100000,ka=ka,
>>>> ATOT=ATOT[i], H = 10^-7.4)$root}
>>>> ATOT
>>>>
>>>> #confirm pH 0 7.4
>>>>
>>>> H <- c()
>>>> for (i in 1:length(ATOT)) {
>>>> H[i] <- uniroot(ff,c(1e-19,1),tol=.Machine$double.eps,maxiter=100000,ka=ka,
>>>> ATOT=ATOT[i], SID = SID[i])$root}
>>>>
>>>> (pH <- -log10(H))
>>>> plot(pH)
>>>> str(pH)
>>>> # num [1:100] 7.4 7.4 7.4 7.4 7.4 ...
>>>> z <- rep(7.4,length(ATOT))
>>>> all.equal(z,pH)
>>>> #TRUE
>>>> points(z,col="red")
>>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>>
>>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
More information about the R-help
mailing list