[GRASS-user] P value for slope from r.series

[Daniel Victoria]

Hi Markus M,

Thanks for your input. But one thing is still confusing me. From what I
understood, the multiple comparison problem would arise if I calculated one
p-value for all the regressions in a computational region. Say I have a 100
x 100 raster, chances are one of those 10,000 pixels would yield me a
significant regression. But in my case, I'm calculating a p-value raster
that is, each pixel has it's own p-value and I'm interested in the slopes
that have a significant trend (p <= 0.05). Thus each pixel regression is
(sort of) independent.

In essence. If I generate a raster with regression slope and p-value, and I
mask out the areas with high p (above 5%), the slope values in the
remaining regions would be significant correct? What you are saying is that
I might be overestimating the area with significant slope?

Cheers and thanks
Daniel

On Wed, Oct 18, 2017 at 6:06 PM Markus Metz <markus.metz.giswork at gmail.com>
wrote:

>
>
> On Wed, Oct 18, 2017 at 7:19 PM, Daniel Victoria <
> daniel.victoria at gmail.com> wrote:
> >
> > I just read on the p-value regression ticket a comment from Markus Metz
> [1]. If I understood correctly, he mentions that the chances of getting
> small p-values at random is high and we should do a correction. But this
> would result in non-significant p-values. He concludes that it would be
> more "appropriate to make prior assumptions about slope, intercept, and
> effect size, then judge the results according to these prior assumptions".
> >
> > Does this means that I should not rely on the p-value obtained?
>
> Yes and no. The p-value needs to be interpreted correctly. Commonly used
> thresholds are alpha = 0.05 and alpha = 0.01. That means if p <= alpha, the
> result is statistically significant. Problems occur if you repeat the test
> with the same dataset several times:
> https://en.wikipedia.org/wiki/Multiple_comparisons_problem
>
> In these cases, alpha needs to be corrected in order to decide if a
> p-value is significant or not. Regarding r.series, millions of repeated
> tests might be performed (one for each cell in the current computational
> region). Any standard correction method would thus render pretty much all
> p-values non-significant. Instead, Bayesian statistics might be a solution.
>
> Markus M
>
> >
> > Where can I find more information about this? Some colleagues and I are
> in the process of finishing a paper that uses applies a regression to
> annual NDVI data and right now, we are discussing if we should (or not)
> consider the p-values obtained.
> >
> > Thanks and sorry if this is a bit of topic
> >
> > Cheers
> > Daniel
> >
> > [1] https://trac.osgeo.org/grass/ticket/2376#comment:3
> >
> >
> > On Mon, Oct 16, 2017 at 2:12 PM Daniel Victoria <
> daniel.victoria at gmail.com> wrote:
> >>
> >> Replying to self and in case helps anyone.
> >>
> >> Solved it by using R and the raster package. Here is a Stackoverflow
> post about it
> >>
> >>
> https://stackoverflow.com/questions/20262999/how-to-output-regression-summarye-g-p-value-and-coeff-into-a-rasterbrick
> >>
> >> Cheers
> >> Daniel
> >>
> >> On Wed, Oct 11, 2017 at 10:44 AM Daniel Victoria <
> daniel.victoria at gmail.com> wrote:
> >>>
> >>> OK, dumb question since I'm a bit (or very) bad at stats.
> >>>
> >>> I'm calculating the slope from a series of rasters using r.series. I
> see that I can also get the t-value and the coefficient of determination.
> Is there a way to get the p-value for the regression?
> >>>
> >>> I've seen that this question has been asked before (in 2012) [1] and
> it ended with the addition of the t-value calculation in r.series. But I
> failed to see how the p-value can be obtained.
> >>>
> >>> I also found this ticket [2], related to the p-value question.
> >>>
> >>> Thanks
> >>> Daniel
> >>>
> >>> [1] -
> http://osgeo-org.1560.x6.nabble.com/Calculate-p-value-for-regression-slope-in-r-series-td5014228.html
> >>>
> >>> [2]  https://trac.osgeo.org/grass/ticket/2376
> >>>
> >
> > _______________________________________________
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> > grass-user at lists.osgeo.org
> > https://lists.osgeo.org/mailman/listinfo/grass-user
>
>
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