I want to create a grid of function values for use in `contour' or `persp'. The function is the log-likelihood for the gamma. The sample is stored as vector of length 20 called `Survival'. A single evaluation of the log-likelihood at, say, scale = 9 and shape = 10 would be obtained by sum(dgamma(Survival, scale = 9, shape = 10, log = TRUE)) (This may work only 0.99.0, I'm not sure.) I would like to evaluate such a function on a grid of scale and shape values. I don't think I can use `outer' because of the way the evaluation of the dgamma function would vectorize. Although I could write the calculation for the grid in `for' loops, I have a nagging suspicion that there is a cleaner way that I have forgotten. Can anyone remind me of a slick way of generating the grid? -- Douglas Bates bates at stat.wisc.edu Statistics Department 608/262-2598 University of Wisconsin - Madison http://www.stat.wisc.edu/~bates/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On 10 Feb 2000, Douglas Bates wrote:> I want to create a grid of function values for use in `contour' or > `persp'. The function is the log-likelihood for the gamma. The > sample is stored as vector of length 20 called `Survival'. > > A single evaluation of the log-likelihood at, say, scale = 9 and shape > = 10 would be obtained by > sum(dgamma(Survival, scale = 9, shape = 10, log = TRUE)) > (This may work only 0.99.0, I'm not sure.) > > I would like to evaluate such a function on a grid of scale and shape > values. I don't think I can use `outer' because of the way the > evaluation of the dgamma function would vectorize. Although I couldIt should vectorize correctly if we use three dimensions. Let's see: Survival <- rgamma(20, 5, 5) res <- do.call("dgamma", expand.grid(x=Survival, scale=8:12, shape=7:12, log=1)) # avoid conversion of logicals to factor here. dim(res) <- c(length(Survival), 5, 6)> apply(res, c(2,3), sum)[,1] [,2] [,3] [,4] [,5] [,6] [1,] -121.0935 -141.6717 -164.9205 -190.5250 -218.2367 -247.8546 [2,] -131.1431 -154.0770 -179.6815 -207.6417 -237.7090 -269.6826 [3,] -140.7416 -165.7827 -193.4944 -223.5618 -255.7364 -289.8171 [4,] -149.8698 -176.8171 -206.4350 -238.4086 -272.4894 -308.4764 [5,] -158.5387 -187.2262 -218.5844 -252.2982 -288.1192 -325.8464 Actually, I would use sc <- 8:12; sh <- 7:12 args <- expand.grid(scale=sc, shape=sh) matrix(apply(args, 1, function(x) sum(dgamma(Survival, scale=x[1], shape=x[2], log=T))), length(sc), dimnames=list(scale=sc, shape=sh)) shape scale 7 8 9 10 11 12 8 -121.0935 -141.6717 -164.9205 -190.5250 -218.2367 -247.8546 9 -131.1431 -154.0770 -179.6815 -207.6417 -237.7090 -269.6826 10 -140.7416 -165.7827 -193.4944 -223.5618 -255.7364 -289.8171 11 -149.8698 -176.8171 -206.4350 -238.4086 -272.4894 -308.4764 12 -158.5387 -187.2262 -218.5844 -252.2982 -288.1192 -325.8464 Brian -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
From: Douglas Bates <bates at stat.wisc.edu>
Date: 10 Feb 2000 14:28:49 -0600
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I want to create a grid of function values for use in `contour' or
`persp'. The function is the log-likelihood for the gamma. The
sample is stored as vector of length 20 called `Survival'.
A single evaluation of the log-likelihood at, say, scale = 9 and shape
= 10 would be obtained by
sum(dgamma(Survival, scale = 9, shape = 10, log = TRUE))
(This may work only 0.99.0, I'm not sure.)
I would like to evaluate such a function on a grid of scale and shape
values. I don't think I can use `outer' because of the way the
evaluation of the dgamma function would vectorize. Although I could
write the calculation for the grid in `for' loops, I have a nagging
suspicion that there is a cleaner way that I have forgotten.
Can anyone remind me of a slick way of generating the grid?
--
Douglas Bates bates at stat.wisc.edu
Statistics Department 608/262-2598
University of Wisconsin - Madison http://www.stat.wisc.edu/~bates/
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Doug,
I don't quite understand what you meant about outer. The first thing
I would try is
dgamma.grid<-function(x,y,z) sum(dgamma(z,scale=x,shape=y,log=TRUE))
outer(xgrid,ygrid,dgamma.grid,Survival)
Chong
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On 10 Feb 2000, Douglas Bates wrote:> I want to create a grid of function values for use in `contour' or > `persp'. The function is the log-likelihood for the gamma. The > sample is stored as vector of length 20 called `Survival'. > > A single evaluation of the log-likelihood at, say, scale = 9 and shape > = 10 would be obtained by > sum(dgamma(Survival, scale = 9, shape = 10, log = TRUE)) > (This may work only 0.99.0, I'm not sure.) > > I would like to evaluate such a function on a grid of scale and shape > values. I don't think I can use `outer' because of the way the > evaluation of the dgamma function would vectorize. Although I could > write the calculation for the grid in `for' loops, I have a nagging > suspicion that there is a cleaner way that I have forgotten. > > Can anyone remind me of a slick way of generating the grid? >Here's one way which avoids looping by using apply. gridS <- expand.grid(scales, shapes) survLilel <- function(ss) sum(dgamma(Survival,ss[1],ss[2])) Likel <- apply(gridS,1,survLilel) Regards, Jim Jim Robison-Cox ____________ Department of Math Sciences | | phone: (406)994-5340 2-214 Wilson Hall \ BZN, MT | FAX: (406)994-1789 Montana State University | *_______| Bozeman, MT 59717-2400 \_| e-mail: jimrc at math.montana.edu -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._