Re: [R] Constrain density to 0 at 0?
Look at the logspline package. This is a different approach to density estimation from the kernel densities used by 'density', but does allow you to set fixed boundaries. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Farley, Robert Sent: Monday, July 19, 2010 7:57 PM To: r-help@r-project.org Subject: [R] Constrain density to 0 at 0? I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Thanks Robert Farley Metro 1 Gateway Plaza Mail Stop 99-23-7 Los Angeles, CA 90012-2952 Voice: (213)922-2532 Fax:(213)922-2868 www.Metro.net [[alternative HTML version deleted]] __ R-help@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@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.
Re: [R] Constrain density to 0 at 0?
This is the boundary problem in density estimation. One simple trick is to use the idea of reflection. If your data is (y1, y2, ...,yn), you create a reflected data by appending `n' negative values to your data, call this y*. Estimate the kernel density for this as fhat(y*). Redefine this estimate so that it is zero for all y 0, and is equal to 2 * fhat(y*). Here is an example: y - rexp(100, rate=10) yref - c(-y, y) fref - density(yref) sel - fref$x = 0 fref$y[sel] - 2 * fref$y[sel] par(mfrow=c(2,1)) plot(density(y)) plot(fref$x[sel], fref$y[sel], type=l) This approach assumes that the density has 0 gradient at the boundary (gradient defined from the right hand side). There are other (better) approaches as well. Look at a book on density estimation. Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Farley, Robert farl...@metro.net Date: Tuesday, July 20, 2010 2:47 pm Subject: Re: [R] Constrain density to 0 at 0? To: r-help@r-project.org r-help@r-project.org Read the help page for density more carefully. Especially the bw and from arguments. Yes, it was my inability to make sense of the help page that motivated my email. My distances range from 0.4 to 7.6 but the density plot ranges from -2 to 10. from=0 seems to hide the negative portion of the density without setting it to 0. I've tried adjust, but it requires a value of 0.2, which results in a very, very spiky plot. I was hoping for a process that could forbid impossible (negative) values, yet allow the density plot to blend the individual measurements. Is there a variable bw that could be set small at the extrema, and larger in the range of the data? Robert Farley Metro www.Metro.net -Original Message- From: David Winsemius [ Sent: Monday, July 19, 2010 19:31 To: Farley, Robert Cc: r-help@r-project.org Subject: Re: [R] Constrain density to 0 at 0? On Jul 19, 2010, at 9:57 PM, Farley, Robert wrote: I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Yes. (Assuming it can be zero, given the data.) Read the help page for density more carefully. Especially the bw and from arguments. -- David. __ R-help@r-project.org mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constrain density to 0 at 0?
Read the help page for density more carefully. Especially the bw and from arguments. Yes, it was my inability to make sense of the help page that motivated my email. My distances range from 0.4 to 7.6 but the density plot ranges from -2 to 10. from=0 seems to hide the negative portion of the density without setting it to 0. I've tried adjust, but it requires a value of 0.2, which results in a very, very spiky plot. I was hoping for a process that could forbid impossible (negative) values, yet allow the density plot to blend the individual measurements. Is there a variable bw that could be set small at the extrema, and larger in the range of the data? Robert Farley Metro www.Metro.net -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Monday, July 19, 2010 19:31 To: Farley, Robert Cc: r-help@r-project.org Subject: Re: [R] Constrain density to 0 at 0? On Jul 19, 2010, at 9:57 PM, Farley, Robert wrote: I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Yes. (Assuming it can be zero, given the data.) Read the help page for density more carefully. Especially the bw and from arguments. -- David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constrain density to 0 at 0?
On Jul 20, 2010, at 2:45 PM, Farley, Robert wrote: Read the help page for density more carefully. Especially the bw and from arguments. Yes, it was my inability to make sense of the help page that motivated my email. My distances range from 0.4 to 7.6 but the density plot ranges from -2 to 10. from=0 seems to hide the negative portion of the density without setting it to 0. I've tried adjust, but it requires a value of 0.2, which results in a very, very spiky plot. I was hoping for a process that could forbid impossible (negative) values, yet allow the density plot to blend the individual measurements. Is there a variable bw that could be set small at the extrema, and larger in the range of the data? The best answer may depend on what your (unstated) goals are. Have you considered fitting a log-Normal or Gamma distribution to the data? You could plot the histogram and then overlay a smooth fitted distribution curve. ?hist require(MASS) ?fitdistr -- David. -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Monday, July 19, 2010 19:31 To: Farley, Robert Cc: r-help@r-project.org Subject: Re: [R] Constrain density to 0 at 0? On Jul 19, 2010, at 9:57 PM, Farley, Robert wrote: I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Yes. (Assuming it can be zero, given the data.) Read the help page for density more carefully. Especially the bw and from arguments. -- David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Constrain density to 0 at 0?
I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Thanks Robert Farley Metro 1 Gateway Plaza Mail Stop 99-23-7 Los Angeles, CA 90012-2952 Voice: (213)922-2532 Fax:(213)922-2868 www.Metro.net [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constrain density to 0 at 0?
On Jul 19, 2010, at 9:57 PM, Farley, Robert wrote: I'm plotting some trip length frequencies using the following code: plot( density(zTestData$Distance, weights=zTestData$Actual), xlim=c(0,10), main=Test TLFD, xlab=Distance, col=6 ) lines(density(zTestData$Distance, weights=zTestData$FlatWeight), col=2) lines(density(zTestData$Distance, weights=zTestData$BrdWeight ), col=3) which works fine except the distances are all positive, but the densities don't drop to 0 until around -2 or -3. Is there a way for me to force the density plot to 0 at 0? Yes. (Assuming it can be zero, given the data.) Read the help page for density more carefully. Especially the bw and from arguments. -- David. __ R-help@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.
