R help - Jun 2010 - script development for Unconditional Density and Probability estimation

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

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?