[R] Verify that a grid is uniform

Tue Apr 7 10:24:38 CEST 2015

Yes, it could be a reasonable choice but I am not sure in general. If
min(abs(diff(z))) is significant (global minimum or accentuated local
minimum) my abscissa is not uniform a priori without performing the control.

2015-04-07 0:55 GMT+02:00 Bert Gunter <gunter.berton at gene.com>:

> Does not min(abs(diff(z))) give you the scaling you need to set a
> tolerance?
>
> -- Bert
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
> (650) 467-7374
>
> "Data is not information. Information is not knowledge. And knowledge
> is certainly not wisdom."
> Clifford Stoll
>
>
>
>
> On Mon, Apr 6, 2015 at 2:55 PM, Marc Lamblin <marcgg.lamblin at gmail.com>
> wrote:
> > The first solution with diff works for uniform abscissa only with integer
> > values.
> >
> > z <- seq(0, 10, length=100)
> > all(diff(z) == z[2] - z[1] )
> > ## FALSE
> >
> > In this case, as you recommended, I could use signif or round or a
> tolerance
> > for real numbers. In my particular case, in order to set a tolerance, I
> need
> > the scale used and I don't have this information. I prefer to test the
> "near
> > uniformity".
> > I didn't know the function zapsmall. It could be useful!
> > Thanks Sarah and Bert!!!
> >
> > Marc
> >
> >
> >
> >
> >
> > 2015-04-06 19:51 GMT+02:00 Bert Gunter <gunter.berton at gene.com>:
> >>
> >> ... correction: you need to use absolute value for the comparison, of
> >> course.
> >>
> >> all(abs(diff(z) - z[2] + z[1]) < tol)
> >>
> >> -- Bert
> >>
> >> Bert Gunter
> >> Genentech Nonclinical Biostatistics
> >> (650) 467-7374
> >>
> >> "Data is not information. Information is not knowledge. And knowledge
> >> is certainly not wisdom."
> >> Clifford Stoll
> >>
> >>
> >>
> >>
> >> On Mon, Apr 6, 2015 at 10:47 AM, Bert Gunter <bgunter at gene.com> wrote:
> >> > Perhaps ?diff might be useful here:
> >> >
> >> > z <- runif(20)
> >> > all(diff(z) == z[2] - z[1] )
> >> > ## FALSE
> >> >
> >> > z <- seq_len(10)
> >> > all(diff(z) == z[2] - z[1] )
> >> > ##TRUE
> >> >
> >> > You can use signif or round as before to allow for "near uniformity"
> >> > or use ?zapsmall or an explicit comparison with a tolerancec instead
> >> > of ==, e.g. all(diff(z) - z[2] + z[1] < tol)
> >> >
> >> > Cheers,
> >> > Bert
> >> >
> >> > Bert Gunter
> >> > Genentech Nonclinical Biostatistics
> >> > (650) 467-7374
> >> >
> >> > "Data is not information. Information is not knowledge. And knowledge
> >> > is certainly not wisdom."
> >> > Clifford Stoll
> >> >
> >> >
> >> >
> >> >
> >> > On Mon, Apr 6, 2015 at 10:11 AM, Marc Lamblin <
> marcgg.lamblin at gmail.com>
> >> > wrote:
> >> >> The aim is to control if a given abscissa/grid is uniform or not.
> >> >> Abscissa
> >> >> in generic vector of real ordered numbers.
> >> >>
> >> >> Here a reproducibile code:
> >> >>
> >> >> # uniform abscissa/grid
> >> >> abscissa1 <- seq(0, 1, length=100)
> >> >> # non-uniform abscissa/grid
> >> >> abscissa2 <- sort(runif(100))
> >> >>
> >> >> control1 <- all(signif(abscissa1[1:(length(abscissa1) - 1) + 1] -
> >> >> abscissa1[1:(length(abscissa1) - 1)]) ==
> >> >> signif(rep((range(abscissa1)[2] -
> >> >> range(abscissa1)[1])/(length(abscissa1) - 1), length(abscissa1) -
> 1)))
> >> >> control2 <- all(signif(abscissa2[1:(length(abscissa2) - 1) + 1] -
> >> >> abscissa2[1:(length(abscissa2) - 1)]) ==
> >> >> signif(rep((range(abscissa2)[2] -
> >> >> range(abscissa2)[1])/(length(abscissa2) - 1), length(abscissa2) -
> 1)))
> >> >>
> >> >> control1
> >> >> control2
> >> >>
> >> >> As expected control1 is TRUE and control2 is FALSE. Actually in this
> >> >> code
> >> >> it is possible also to use
> >> >> diff inside signif.
> >> >> Do you mean that the control to perform can be done in this manner
> >> >>
> >> >> if (length(unique(diff(vec))) == 1) {
> >> >>   control <- TRUE
> >> >> } else {
> >> >>   control <- FALSE
> >> >> }
> >> >>
> >> >> I have tried to apply this control on abscissa1 which is uniform but
> >> >> length(unique(diff(abscissa1))) was greater than one; probably, as
> you
> >> >> said, this is due to the fact that in this way I don't take into
> >> >> account
> >> >> the machine precision.
> >> >> What I want to understand is if there is a SAFE solution, even if
> until
> >> >> now
> >> >> this control is working correctly. I have seen in the documentation
> of
> >> >> signif that by default the number of digits considered are 6. The
> >> >> number of
> >> >> digits to consider depends on the scale used. It doesn't make sense
> to
> >> >> increase the number of digits with respect to default because, in
> this
> >> >> case, you are not using an handy scale.
> >> >> Maybe it could be better directly to ask user if the abscissa passed
> as
> >> >> argument is uniform or not.
> >> >> Thanks a lot for the link!!!
> >> >>
> >> >> Marc
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> 2015-04-06 16:32 GMT+02:00 Sarah Goslee <sarah.goslee at gmail.com>:
> >> >>
> >> >>> Without a reproducible example that includes some sample data (fake
> is
> >> >>> fine), the code you used (NOT in HTML format), and some clear idea
> of
> >> >>> what output you expect, it's impossible to figure out how to help
> you.
> >> >>> Here are some suggestions for creating a good reproducible example:
> >> >>>
> >> >>>
> >> >>>
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> >> >>>
> >> >>> Without knowing what you want, it looks like abscissa is a vector,
> and
> >> >>> so I'm not sure how this defines a grid, but
> >> >>> length(unique(diff(vec)))
> >> >>> might help. Note that this DOES NOT account for machine precision in
> >> >>> any
> >> >>> way.
> >> >>>
> >> >>> Sarah
> >> >>>
> >> >>> On Mon, Apr 6, 2015 at 7:50 AM, Marc Lamblin
> >> >>> <marcgg.lamblin at gmail.com>
> >> >>> wrote:
> >> >>> > I need to control of a given grid is uniform. This control using
> >> >>> > signif
> >> >>> > until now works:
> >> >>> >
> >> >>> > if (all(signif(abscissa[1:(length(abscissa) - 1) + 1] -
> >> >>> > abscissa[1:(length(abscissa) - 1)]) ==
> >> >>> > signif(rep((range(abscissa)[2] -
> >> >>> >          range(abscissa)[1])/(length(abscissa) - 1),
> >> >>> > length(abscissa) -
> >> >>> > 1)))) {
> >> >>> > # other stuff
> >> >>> > }
> >> >>> >
> >> >>> > Does someone have some suggestions to improve this control? Thanks
> >> >>> > in
> >> >>> > advance!! :)
> >> >>> >
> >> >>> > Marc
> >> >>> >
> >> >>> >         [[alternative HTML version deleted]]
> >> >>> >
> >> >>>
> >> >>>
> >> >>> --
> >> >>> Sarah Goslee
> >> >>> http://www.functionaldiversity.org
> >> >>>
> >> >>
> >> >>         [[alternative HTML version deleted]]
> >> >>
> >> >> ______________________________________________
> >> >> 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.
> >
> >
>

	[[alternative HTML version deleted]]