On Jul 22, 2010, at 5:34 PM, David Winsemius wrote:
On Jul 22, 2010, at 5:27 PM, Daniel Hocking wrote:
I am sorry if this question is vague or uninformed. I am just
learning R and struggling. I am using the book Hierarchical Modeling
and Inference in Ecology and they provide examples of R code. I have
the following code from the book but when I run it I don't get any
output. I cannot get the values of 'out' to show up. Basically, I
just want to see my estimates for b0, b1, b2, and b3. Any time
that I
have used or see function( ) there have been arguments and I just
call
for the value of the function. In this case there doesn't seem to be
a value for the function. Any help would be appreciated.
You have defined a function that has no arguments. You should be
typing this at the console:
panel3pt1.fn()
I get an error because there is no such file on my machine and you
have not provided a link to an accessible copy.
If you go to their website
http://www.mbr-pwrc.usgs.gov/pubanalysis/roylebook/chapters.htm
... and:
a) download the .Rd file and the similarly named .csv file referenced
by that function to your working directory
b) change the extension of the .csv file to match the function reference
c) add , sep="," to the read.table call
d) then do what I said above ....
> panel3pt1.fn() # Voilà !!
$minimum
[1] 100.887223663
$estimate
[1] -0.542213281782 1.847343506809 -1.060864239423 0.646910762031
$gradient
[1] 2.34905428442e-05 3.14549972521e-05 6.51961177771e-05
4.88853402203e-05
$hessian
[,1] [,2] [,3] [,4]
[1,] 33.38181500113 15.26441629493 27.8670270859 6.61193837459
[2,] 15.26441629493 27.86699589010 30.5057286674 -9.66977848175
[3,] 27.86702708591 30.50572866744 52.5892374981 -12.50448633528
[4,] 6.61193837459 -9.66977848175 -12.5044863353 34.09027300450
$code
[1] 1
$iterations
[1] 16
--
David.
Thanks,
Dan
`panel3pt1.fn` <-
function(){
source("utilfns.Rd")
data<- read.table("wtmatrix.txt",header=T,na.strings=T)
elev<-data[,"elev"]
forest<-data[,"forest"]
elev<-scale(elev,center=TRUE)
forest<-scale(forest,center=TRUE)
pamat<-data[,c("y.1","y.2","y.3")]
z<-pamat[,1]
M<-length(z)
lik<-function(parms){
b0<-parms[1]
b1<-parms[2]
b2<-parms[3]
b3<-parms[4]
ones<-rep(1,M)
### Compute binomial success probabilities
probs<-expit(b0*ones+b1*elev+b2*(elev^2)+b3*forest)
lik<-rep(0,length(z))
### evaluate log of binomial pmf
tmp<-log(dbinom(z,1,probs))
### substitute 0 for missing values
lik[!is.na(z)] <- tmp[!is.na(z)]
lik<- -1*sum(lik)
return(lik)
}
out <- nlm(lik,c(0,0,0,0),hessian=TRUE)
return(out)
}
------------------------------------------------------------------------------------
Daniel J. Hocking
122 James Hall
Department of Natural Resources & the Environment
University of New Hampshire
Durham, NH 03824
dhock...@unh.edu
http://sites.google.com/site/danieljhocking/
www.hockingphotography.smugmug.com
"Without data, all you are is just another person with an opinion."
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______________________________________________
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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.
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.
