[R] nls & optimize

[Muhammad Rahiz]

That works - Thanks Ravi.

Muhammad Rahiz

On Tue, 19 Oct 2010, Ravi Varadhan wrote:

> You can do this.
>
> dsm = c(800,600,NA,525,NA,450,400,NA,NA,NA,0)
> s3 = seq(0.05,1.05,0.1)
>
> plot(s3,dsm,col="blue",las=1,xlab="fraction",ylab="distance (km)")
>
> fc <- function(x,a,b){a*exp(-b*x)}
> fm <- nls(dsm~fc(s3,a,b),start=c(a=800,b=0))
> co <- coef(fm)
> curve(fc(x,a=co[1],b=co[2]),add=TRUE,col="black",lwd=1)
>
> r <- range(s3,na.rm=TRUE)  # range should be changed
> n.dsm <- fc(1/2.71, co[1], co[2])  # calculate a different intersection
> val <- optimize(f=function(x) abs(fc(x,a=co[1],b=co[2])-n.dsm),c(r[1],r[2]))
>
> abline(h=n.dsm,lty=2,col="blue",lwd=1)
> abline(v=n,lty=2,col="red",lwd=1)
> text(0.1, 500, paste(round(n.dsm,2),"km",sep=" ")) # text should be placed
> at different location
>
> However, note that you do not need `optimize'.  The answer that you are
> seeking is `n.dsm', which is obtained directly from the nls fit.
>
> Ravi.
>
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
> Behalf Of Muhammad Rahiz
> Sent: Tuesday, October 19, 2010 5:45 AM
> To: x.r-help
> Subject: [R] nls & optimize
>
> Hi all,
>
> I'm plotting to get the intersection value of three curves. Defining
> the x-axis as dsm, the following code works;
>
> dsm = c(800,600,NA,525,NA,450,400,NA,NA,NA,0)
> s3 = seq(0.05,1.05,0.1)
>
> plot(dsm,s3,col="blue",las=1,ylab="fraction",xlab="distance (km)")
>
> fc <- function(x,a,b){a*exp(-b*x)}
> fm <- nls(s3~fc(dsm,a,b),start=c(a=1,b=0))
> co <- coef(fm)
> curve(fc(x,a=co[1],b=co[2]),add=TRUE,col="black",lwd=1)
>
> r <- range(dsm,na.rm=TRUE)
> n <- 1/2.71
> val <- optimize(f=function(x) abs(fc(x,a=co[1],b=co[2])-n),c(r[1],r[2]))
>
> abline(v=val$minimum,lty=2,col="blue",lwd=1)
> abline(h=n,lty=2,col="red",lwd=1)
> text(100,0.1,paste(round(val$minimum,2),"km",sep=" "))
>
> When I flip the axes, i.e. x-axis = s3, and change the nls start up value
> to a=800, the three curves does not intersect.
>
> dsm = c(800,600,NA,525,NA,450,400,NA,NA,NA,0)
> s3 = seq(0.05,1.05,0.1)
>
> plot(s3,dsm,col="blue",las=1,xlab="fraction",ylab="distance (km)")
>
> fc <- function(x,a,b){a*exp(-b*x)}
> fm <- nls(dsm~fc(s3,a,b),start=c(a=800,b=0))
> co <- coef(fm)
> curve(fc(x,a=co[1],b=co[2]),add=TRUE,col="black",lwd=1)
>
> r <- range(dsm,na.rm=TRUE)
> n <- 1/2.71
> val <- optimize(f=function(x) abs(fc(x,a=co[1],b=co[2])-n),c(r[1],r[2]))
>
> abline(h=val$minimum,lty=2,col="blue",lwd=1)
> abline(v=n,lty=2,col="red",lwd=1)
> text(100,0.1,paste(round(val$minimum,2),"km",sep=" "))
>
> It's merely reversing the axes - the code should work, shouldn't it?
> Any suggestions why this happens and how I can correct it?
>
> Thanks.
>
> Muhammad
>
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