[R] script development for Unconditional Density and Probability estimation

[jim holtman]

First start by putting it in a function so you can specify the
parameters you want to change.

On Mon, Jun 14, 2010 at 11:54 AM,  <Steve_Friedman at nps.gov> wrote:
>
> Hello,
>
> I'd like to automate this script a bit more and cycle several
> parameters(both the species and the metric).  For example where AnnualDepth
> occurs, I need to process about 12 metrics so instead of writing this
> entire script 12 times once for each metric  I'd like to be able to
> automatically get another metric.
>
> Any suggestion will be greatly appreciated.
>
> Currently running Windows XP, R 2.11.1
>
> ###############################################################################
>
> Marsh <- cbind(SoilVegHydro, vegcode)
> AnnualDepth <- Marsh[,'meanAnnualDepthAve']
>
> cattail_0 <- Marsh[,'cattail'] == '0'  # no           need to run for 8
> species, automate if possible
>  cattail_1 <- Marsh[,'cattail'] == '1' # yes         need to run for 8
> species
>
> spbase.rate.d1 <- sum(cattail_1)/(sum(cattail_1) + sum(cattail_0) )
> annualDepth.density <- density(AnnualDepth)    # this line needs either
> interactively defined or automatically cycle thru a number of metrics
>
> cattail.d0.density <- density(AnnualDepth[cattail_0])
> cattail.d1.density <- density(AnnualDepth[cattail_1])
>
> approxfun (cattail.d0.density$x, cattail.d0.density$y) -> cattail.d0.f
> approxfun (cattail.d1.density$x, cattail.d1.density$y) -> cattail.d1.f
>
> p.d.given.AnnualDepth <- function(AnnualDepth, spbase.rate.d1)
>     {
>        p1 <- cattail.d1.f(AnnualDepth) * spbase.rate.d1
>        p0 <- cattail.d0.f(AnnualDepth) * (1 - spbase.rate.d1)
>       p1/(cattail_0+cattail_1)
>    }
>
> x <- 1:1292
> y <- p.d.given.AnnualDepth(x, spbase.rate.d1)
> plot (x, y, type='l', col='red', xlab='Mean Annual Depth',
> main=c("Cattail"), ylab='estimated\nProbability(cattail|AnnualDepth)')
>
> plot (cattail.d0.density, col ='red', lty= 1, main = "")
>  lines(cattail.d1.density, col = 'blue', lty=1)
>  lines(annualDepth.density , col='black', lty = 1)
>  legend(2000, 0.0023, c("No Cattail", "Cattail", "Mean Annual Depth"),
>      col=c("red", "blue", "black"),lty=c(1))
>
>
>
>
> #####################################################################################################
>
> Steve Friedman Ph. D.
> Spatial Statistical Analyst
> Everglades and Dry Tortugas National Park
> 950 N Krome Ave (3rd Floor)
> Homestead, Florida 33034
>
> Steve_Friedman at nps.gov
> Office (305) 224 - 4282
> Fax     (305) 224 - 4147
>
> ______________________________________________
> 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.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?