SpatialPointsBreeding: Converts a 'data.frame' to an object of class...

In mpio-be/expp: Spatial Analysis of Extra-Pair Paternity

Description

Converts a data.frame to a SpatialPointsBreeding object. The SpatialPointsBreeding class extends SpatialPointsDataFrame with three extra slots defining the id (i.e. nest or breeding box) and the pair identity (i.e. male and female), respectively.

Usage

SpatialPointsBreeding(
  data,
  proj4string,
  coords = ~x + y,
  breeding = ~male + female,
  id
)

## S4 method for signature 'SpatialPointsBreeding,missing'
plot(
  x,
  pch = 20,
  axes = FALSE,
  add = FALSE,
  xlim = NULL,
  ylim = NULL,
  ...,
  cex = 1,
  col = "grey",
  lwd = 1,
  bg = "grey90"
)

## S4 method for signature 'SpatialPointsBreeding,eppMatrix'
plot(
  x,
  y,
  pch = 20,
  axes = FALSE,
  add = FALSE,
  xlim = NULL,
  ylim = NULL,
  ...,
  cex = 1,
  col = "grey",
  col.epp = "red",
  lwd = 1,
  lty = 2,
  bg = "grey90"
)

Arguments

data	a data.frame containing the coordinates (e.g. "x","y"), the location id, and the pair identity (e.g. "male", "female") together with any other optional variables (e.g. individuals or nest traits).
proj4string	A CRS object containing a valid proj4 string. See CRS proj4string for details.
coords	Formula specifying which columns in object are the spatial coordinates. Argument passed to coordinates
breeding	One side formula defining the male and female ID in that order (e.g. ~ male + female)
id	Integer specifying the location id (e.g. nest box number, den ID).
x	a SpatialPointsBreeding object
pch	see plot.default
axes	see plot.default
add	see plot.default
xlim	see plot.default
ylim	see plot.default
...	further arguments to pass to plot(as(x, "Spatial")
cex	see plot.default
col	see plot.default
lwd	see plot.default
bg	see plot.default
y	an eppMatrix object
col.epp	extra-pair partners color
lty	see plot.default

See Also

epp

Examples

d = data.frame(
  x = c(4, 17, 16, 41, 41, 43, 86, 62, 71, 92, 95,53, 34, 27, 53), 
  y = c(3, 18, 36, 6, 18, 50, 3, 21, 40, 43, 57, 62, 62, 45, 37), 
  id = 1:15,male = paste0('m', 1:15), female = paste0('f', 1:15), 
    stringsAsFactors = FALSE)

b = SpatialPointsBreeding(d, id = 'id', breeding = ~ male+female)    

plot(b)

mpio-be/expp documentation built on June 23, 2021, 1:08 p.m.