pairwise: Pairwise analyses

In samc: Spatial Absorbing Markov Chains

Pairwise analyses

Description

Analysis for pairwise combinations locations

Usage

pairwise(fun, samc, origin, dest)

## S4 method for signature ''function',samc,location,location'
pairwise(fun, samc, origin, dest)

## S4 method for signature ''function',samc,location,missing'
pairwise(fun, samc, origin)

Arguments

fun	A samc analytical function with signature fun(samc, origin, dest)
samc	A samc-class object
origin	A vector of locations
dest	A vector of locations. Can be excluded to reuse the origin parameter

Details

When providing vector inputs for the 'origin' and 'dest' parameters to analytical functions, the package assumes that users are providing pairs of 'origin' and 'dest'. That is, 'origin[1]' is paired with 'dest[1]', 'origin[2]' is paired 'dest[2]', etc. Another way to think about it is that these two vector inputs can be treated as columns in the same dataframe. The result of the analytical function then is a vector of the same length as the input. This behavior works for any situation, so it is the default for the package.

However, some users may wish to run an analytical function for all the pairwise combinations of the values in the input vectors. That is, 'origin[1]' is paired with 'dest[1]','dest[2]', 'dest[3]', etc, before moving on to the next elements in 'origin'. This approach has the advantage of potentially reducing the amount of code needed for an analysis, and the results can be represented as a pairwise matrix, but it is not suitable for all situations. To enable this second approach more easily, the 'pairwise()' function runs all the combinations of the 'origin' and 'dest' parameters for an analytical function and returns the results in a 'long' format data.frame. This data.frame can then be reshaped into a pairwise matrix or 'wide' format data.frame using tools like the reshape2 or tidyr packages.

This function is not intended to be used with other inputs such as 'init' or 'time'

Value

A 'long' format data.frame

Examples

library(samc)

# Load example data
res_data <- samc::example_split_corridor$res
abs_data <- samc::example_split_corridor$abs


# Create samc-class object
samc_obj <- samc(res_data, abs_data,
                 model = list(fun = function(x) 1/mean(x), dir = 8, sym = TRUE))

# pairwise() example
pw <- pairwise(cond_passage, samc_obj, origin = 1:4, dest = 5)
print(pw)

# pairwise() example without dest
pw <- pairwise(dispersal, samc_obj, origin = c(2, 7))
print(pw)

samc documentation built on May 31, 2023, 5:23 p.m.