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Calculate ranges with the minimum spanning tree length method

Source: R/mstlength.R
mstlength.Rd

This family of metrics rely on constructing a minimum spanning tree from the distances between the points, and use its length to describe spreading.

Usage

mstlength(x, s, ...)

# S4 method for class 'matrix,missing'
mstlength(
  x,
  dm = NULL,
  long = NULL,
  lat = NULL,
  duplicates = FALSE,
  plot = FALSE,
  plot.args = NULL,
  full = FALSE,
  q = 1
)

# S4 method for class 'data.frame,missing'
mstlength(
  x,
  long = "long",
  lat = "lat",
  tax = NULL,
  dm = NULL,
  duplicates = FALSE,
  q = 1,
  plot = FALSE,
  plot.args = NULL,
  full = FALSE
)

Arguments

x

Either a 2D numeric matrix with two columns: longitudes and latitudes, a data.frame with the same information.

s

Structure to replace the points, either missing (coordinate pairs) or a trigrid (icosahedral grid from the package icosa).

...

Additional arguments passed to class-specific methods.

dm

If there is a pre-made distance matrix, it can be plugged in here. If this is provided, the default coordinates will not be used.

long

character, column name of the longitudes.

lat

character, column name of the latitudes.

duplicates

logical, should identical coordinates be included in the calculation (default is FALSE)

plot

Logical, should the result be plotted? Will plot over active plot (as in add=TRUE).

plot.args

List arguments passed to the plotting function: sf::plot.

full

logical, should only the estimate (FALSE) be returned, or additional data as well?(TRUE).

q

numeric, a value between 0 and 1, the quantile.

tax

character, used only in the data.frame method. Column name of groups (e.g. taxa) that allows the iteration of the method for multiple groups.

Value

A list with an estimate an two indices the rows of the input matrix that represent the length of the tree (or one of them).

Details

This metrics includes maximum great circle distance and similar methods.

Examples

# 1. Records
data(pinna)
# Subset to Pinna nobilis
nobilis <- pinna[pinna$species=="Pinna nobilis", ]
plot(nobilis[c("decimalLongitude", "decimalLatitude")], pch=16, col="#00BBAA66")

# 2. calculate and visualize
mst <- mstlength(nobilis, long="decimalLongitude", lat="decimalLatitude", plot=TRUE, full=TRUE)

mst$estimate
#> [1] 11163.76