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Draw pseudo-absences from a pool of background units

Source: R/pseudo_absences.R
pseudo_absences.Rd

Presence-only records give a response of ones. A model needs units where the response is zero, and these are drawn from pool, a table of background units that carry the same columns as the targets (an identifier, the static predictors, the coords, and a record in series for each). The strategies are bm_PseudoAbsences()'s:

Usage

pseudo_absences(
  pool,
  presences,
  n,
  strategy = c("random", "sre", "disk"),
  id = NULL,
  env = NULL,
  quantile = 0.025,
  coords = NULL,
  dist_min = 0,
  dist_max = Inf,
  lonlat = FALSE,
  repeats = 1L,
  seed = 1L
)

Arguments

pool

A data frame of background units.

presences

A data frame of the presences, with the columns the strategy reads.

n

Number of pseudo-absences in each draw.

strategy

"random", "sre" or "disk".

id

The column naming a unit in both tables, or NULL where no unit of the pool is a presence.

env

For "sre", the numeric columns the envelope is drawn on.

quantile

For "sre", the share of the presences left outside at each end of a column, in [0, 0.5].

coords

For "disk", the two columns holding the coordinates.

dist_min, dist_max

For "disk", the least and greatest distance from the nearest presence.

lonlat

For "disk", whether coords are longitude and latitude in degrees.

repeats

Number of independent draws, each with its own seed.

seed

Random seed of the first draw; draw r uses seed + r - 1.

Value

The drawn rows of pool, with the columns set (the draw) and pseudo (TRUE), of class timesift_pseudo_absences.

Details

  • "random": any unit of the pool that is not a presence.

  • "sre": a unit outside the envelope of the presences, the band between the quantile and 1 - quantile quantiles of each of the env columns over the presences, as envelope() draws it. A unit is outside where it leaves the band in at least one column.

  • "disk": a unit whose distance to the nearest presence lies between dist_min and dist_max, both included, on coords. The distance is planar in the units of the coordinates, or in metres from longitude and latitude in degrees where lonlat is TRUE, on a sphere of radius 6371008.8 m.

A presence is never its own absence: a unit of the pool whose id is one of the presences' is not a candidate. The units a strategy admits are the same in both languages; which n of them are drawn depends on the language's generator, as the folds of fold_map() do. To fix the units, draw once and keep the table. A set of one's own is the rows of pool it names, and needs no strategy.

The drawn units are not flagged in a fit: bind them to the presences with a response of zero and fit as one table. Their pseudo column says which they are, and set which draw.

Examples

pool <- data.frame(cell = 1:200, x = rep(1:20, 10), y = rep(1:10, each = 20),
                   temp = rnorm(200))
presences <- pool[c(5, 25, 45), ]
pseudo_absences(pool, presences, n = 10, strategy = "disk", id = "cell",
                coords = c("x", "y"), dist_min = 3, dist_max = 8)