[R] Population abundance, change point

[Mike Marchywka]

> To: carusonm at gmail.com
> From: jdaily at usgs.gov
> Date: Wed, 17 Nov 2010 08:45:01 -0500
> CC: r-help at r-project.org; r-help-bounces at r-project.org
> Subject: Re: [R] Population abundance, change point
>
> There are really no set ways to determine a changepoint, since a
> changepoint depends completely on what you decide. Recursive partitioning
> will fit a best changepoint, but it will pretty much always fit one. This
If you are open to newer ideas,
have you looked at wavelets at all? these come up on googel along with R.
Also with aonly a few points, even 20-30, you coldconsider exhasiutvely
fitting slopes to all 2^n subsets and plowing throgh the histograms
looking for anything that may be publishable or illuminating about your data.
Fitting to your own model or null hypotheses would make interesting
contrasts of course, " populations remained the same after atrazine spill
or asteroid hit" etc.


> function can be found in the package rpart:
>
> > fit <- rpart(count ~ year, control = list(maxdepth = 1))
> > summary(fit)
>
> However this measure offers no level of confidence. This is where packages
> like strucchange and party come into use, as they provide measures of
> confidence. Alternatively, you could look into regression-based methods
> where the changepoint is some parameter. Piecewise regression, for
> instance, is as simple as fitting a spline of degree 1 and changepoint X:
>
> > library(splines)
> > fit <- lm(count ~ bs(year, knots = X, degree = 1))
> > plot(year, count)
> > lines(year, fitted(fit))
>
> Then you can fit a regression at each year and compare. Alternatively,
> since count data is often noisy, you could easily substitute quantile
> regression for linear regression to much of the same effect (assuming
> whatever tau you decide, I used 0.8 but this is arbitrary):
>
> > library(splines)
> > library(quantreg)
> > fit <- rq(count ~ bs(year, knots = X, degree = 1), tau = 0.8)
> > plot(year, count)
> > lines(year, fitted(fit))
> --------------------------------------
> Jonathan P. Daily
> Technician - USGS Leetown Science Center
> 11649 Leetown Road
> Kearneysville WV, 25430
> (304) 724-4480
> "Is the room still a room when its empty? Does the room,
> the thing itself have purpose? Or do we, what's the word... imbue it."
> - Jubal Early, Firefly
>
> r-help-bounces at r-project.org wrote on 11/16/2010 05:30:49 PM:
>
> > [image removed]
> >
> > [R] Population abundance, change point
> >
> > Nicholas M. Caruso
> >
> > to:
> >
> > r-help
> >
> > 11/16/2010 05:32 PM
> >
> > Sent by:
> >
> > r-help-bounces at r-project.org
> >
> > I am trying to understand my population abundance data and am looking
> into
> > analyses of change point to try and determine, at approximately what
> point
> > do populations begin to change (either decline or increasing).
> >
> > Can anyone offer suggestions on ways to go about this?
> >
> > I have looked into bcp and strucchange packages but am not completely
> > convinced that these are appropriate for my data.
> >
> > Here is an example of what type of data I have
> > Year of survey (continuous variable) 1960 - 2009 (there are gaps in the
> > surveys (e.g., there were no surveys from 2002-2004)
> > Relative abundance of salamanders during the survey periods
> >
> >
> > Thanks for your help, Nick
> >
> > --
> > Nicholas M Caruso
> > Graduate Student
> > CLFS-Biology
> > 4219 Biology-Psychology Building
> > University of Maryland, College Park, MD 20742-5815
> >
> >
> >
> >
> > ------------------------------------------------------------------
> > I learned something of myself in the woods today,
> > and walked out pleased for having made the acquaintance.
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > 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
> 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.