# plot representation of calculated value known to be 7.4

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## plot representation of calculated value known to be 7.4

 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") ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: plot representation of calculated value known to be 7.4

 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") > ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: plot representation of calculated value known to be 7.4

 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 <[hidden email]> 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") >> >> > ______________________________________________ > [hidden email] 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/posti> ng-guide.html > and provide commented, minimal, self-contained, reproducible code. >         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: plot representation of calculated value known to be 7.4

 In reply to this post by tring 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! 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 <[hidden email] > > 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") > > >     ______________________________________________ >     [hidden email] 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. > >         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: plot representation of calculated value known to be 7.4

 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 <[hidden email]> 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") >>> >> >> ______________________________________________ >> [hidden email] 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. > > > ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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