R: Example for pmgram

z.no {ecodist} | R Documentation

## Example for pmgram

### Description

An object of class mgram for use in the example for `pmgram`. Many of the functions in `ecodist` take a long time to run, so prepared examples have been included.

### Usage

    data(z.no)

### Format

See `pmgram` for current format specification.

### Author(s)

Sarah Goslee

### See Also

`pmgram`, `z.z1`,

### Examples

    #### Partial pmgram example

    # generate a simple surface
    # with complex nonlinear spatial pattern

    x <- matrix(1:25, nrow=25, ncol=25, byrow=FALSE)
    y <- matrix(1:25, nrow=25, ncol=25, byrow=TRUE)

    # create z1 and z2 as functions of x, y
    # and scale them to [0, 1]
    z1 <- x + 3*y
    z2 <- y - cos(x)

    z1 <- (z1 - min(z1)) / (max(z1) - min(z1))
    z2 <- (z2 - min(z2)) / (max(z2) - min(z2))

    z12 <- (z1 + z2*2)/3

    # look at patterns

    layout(matrix(c(
    1, 1, 2, 2,
    1, 1, 2, 2,
    3, 3, 4, 4,
    3, 3, 5, 5), nrow=4, byrow=TRUE))

    image(z1, col=gray(seq(0, 1, length=20)), zlim=c(0,1))
    image(z2, col=gray(seq(0, 1, length=20)), zlim=c(0,1))
    image(z12, col=gray(seq(0, 1, length=20)), zlim=c(0,1))

    # analyze the pattern of z across space
    z1 <- as.vector(z1)
    z2 <- as.vector(z2)
    z12 <- as.vector(z12)
    z1.d <- dist(z1)
    z2.d <- dist(z2)
    z12.d <- dist(z12)

    space <- cbind(as.vector(x), as.vector(y))
    space.d <- dist(space)

    # take partial correlogram without effects of z1
    ### pgram() is time-consuming, so this was generated
    ### in advance and saved.
    ### set.seed(1234)
    ### z.no <- pmgram(z12.d, space.d, nperm=1000, resids=FALSE)
    ### save(z.no, file="ecodist/data/z.no.rda")
    plot(z.no)

    # take partial correlogram of z12 given z1
    ### pgram() is time-consuming, so this was generated
    ### in advance and saved.
    ### set.seed(1234)
    ### z.z1 <- pmgram(z12.d, space.d, z2.d, nperm=1000, resids=FALSE)
    ### save(z.z1, file="ecodist/data/z.z1.rda")
    plot(z.z1)

[Package ecodist version 2.0.7 Index]