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 `histogram` `...` Additional arguments for the default `stepfun` function. `normalize` Boolean indicating whether or not to normalize the output stepfun so that it integrates to 1. Defaults to `TRUE`. If `FALSE`, then the function will integrate to `sum(h\$counts)`

### 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 `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

# prior.shape1=1 # Uniform prior
prior.shape1=0.5 # Jeffreys prior

# Fraction of eggs from one or more genotyped parents

# 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]