stepfun.hist {ConnMatTools} | R Documentation |
Create a probability density step function from a histogram object
Description
This function creates a step function from the bars in a histogram
object. By default, the step function will be normalized so that it
integrates to 1.
Usage
stepfun.hist(h, ..., normalize = TRUE)
Arguments
h |
an object of type |
... |
Additional arguments for the default |
normalize |
Boolean indicating whether or not to normalize the output
stepfun so that it integrates to 1. Defaults to |
Value
A function of class stepfun
. The height of the steps will be
divided by the distance between breaks and possibly the total count.
Author(s)
David M. Kaplan dmkaplan2000@gmail.com
See Also
See also d.rel.conn.dists.func
,
optim.rel.conn.dists
.
Examples
library(ConnMatTools)
data(damselfish.lods)
# Histograms of simulated LODs
l <- seq(-1,30,0.5)
h.in <- hist(damselfish.lods$in.group,breaks=l)
h.out <- hist(damselfish.lods$out.group,breaks=l)
# PDFs for marked and unmarked individuals based on simulations
d.marked <- stepfun.hist(h.in)
d.unmarked <- stepfun.hist(h.out)
# Fraction of adults genotyped at source site
p.adults <- 0.25
# prior.shape1=1 # Uniform prior
prior.shape1=0.5 # Jeffreys prior
# Fraction of eggs from one or more genotyped parents
p <- dual.mark.transmission(p.adults)$p
# PDF for relative connectivity
D <- d.rel.conn.dists.func(damselfish.lods$real.children,
d.unmarked,d.marked,p,
prior.shape1=prior.shape1)
# Estimate most probable value for relative connectivity
phi.mx <- optim.rel.conn.dists(damselfish.lods$real.children,
d.unmarked,d.marked,p)$phi
# Estimate 95% confidence interval for relative connectivity
Q <- q.rel.conn.dists.func(damselfish.lods$real.children,
d.unmarked,d.marked,p,
prior.shape1=prior.shape1)
# Plot it up
phi <- seq(0,1,0.001)
plot(phi,D(phi),type="l",
xlim=c(0,0.1),
main="PDF for relative connectivity",
xlab=expression(phi),
ylab="Probability density")
abline(v=phi.mx,col="green",lty="dashed")
abline(v=Q(c(0.025,0.975)),col="red",lty="dashed")
[Package ConnMatTools version 0.3.5 Index]