In mdlincoln/pathway: Find Point Pathways Through a Matrix

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

pathway

pathway finds a pathway of observations between two points in a matrix.

Installation

You can install pathway from GitHub with:

# install.packages("devtools")
devtools::install_github("mdlincoln/pathway")

Example

library(pathway)

set.seed(34)
m <- matrix(rnorm(1000), nrow = 500, ncol = 2)
p1 <- 2L
p2 <- 11L
p <- pathway(m, p1, p2, n = 5)
# Returns both the ideal points between p1 and p2
p$line
# as well as the indices of the nearest neighbors
p$i

plot_pathway(m, p)

It is also possible to place conditional restraints on the solution that pathway finds by using navigate_ functions. For example, navigate_unique will not revisit the same point along a path, and navigate_ordered will only look at points that occurr in later rows in the matrix.

p_ordered <- pathway(m, 5, 380, n = 5, navigator = navigate_ordered)
p_ordered$i
plot_pathway(m, p_ordered)

To use your own predicate function, define a function that returns a vector of indices to search and call it with navigator = navigate(f)

obs_types <- sample(c("setosa", "versicolor", "virginica"), 500, replace = TRUE)

# A custom predicate function must take the original matrix, the list of
# previously-selected pathway points, along with p1 and p2.
different_species <- function(x, pi, p1, p2, obs_types) {
  if (is.null(pi)) {
    search_space <- 1:nrow(x)
  } else {
    # Only search observations that do not have the same species as the immediately previous one.
    prev_type <- obs_types[tail(pi, 1)]
    search_space <- which(obs_types != prev_type)
  }

  # Don't forget to exclude p1 and p2
  setdiff(search_space, c(p1, p2))
}

p_species <- pathway(m, p1, p2, n = 8, navigator = navigate(different_species, obs_types))
obs_types[p_species$i]