R: Data objects for node-based analysis

distrib_data {nodiv}

R Documentation

Data objects for node-based analysis

Description

Functions to collect and display data with matching species distributions and phylogenies

Usage

distrib_data(commatrix, coords = NULL, proj4string_in = CRS(as.character(NA)), 
  type = c("auto", "grid", "points"), shape = NULL)
nodiv_data(phylo, commatrix, coords, proj4string_in = CRS(as.character(NA)), 
  type = c("auto", "grid", "points"), shape = NULL)
## S3 method for class 'distrib_data'
summary(object, ...)
## S3 method for class 'nodiv_data'
summary(object, ...)
## S3 method for class 'distrib_data'
plot(x, ...)
## S3 method for class 'nodiv_data'
plot(x,  ...)
## S3 method for class 'distrib_data'
identify(x,  ...)

Arguments

`phylo`	A phylogeny in ape's phylo format, with tip.labels that correspond to the species names in commatrix
`commatrix`	A community matrix or data.frame of species distributions, with species as columns, sites as rows, and 0/1 denoting the absence or presence of a species in a given site. Alternatively, the functions accept a `data.frame` in the phylocom format, i.e. with three columns containing plot id, abundance (ignored) and species id. The `nodiv_data` function also accepts an object of type `distrib_data`, in which case `coords` is ignored. The `nodiv_data` function matches the species in the matrix to the tips of `phylo`.
`coords`	The coordinates of all sites in the data. The input can be of a variety of different formats. Can be a `data.frame` or `matrix` with two columns. If more columns are present, the function will search for typical coordinate names such as X/Y or Lon/Lat. Alternatively, an object inheriting from `SpatialPoints` from package `sp` is accepted. The coordinates are transformed to `SpatialPoints` using the proj4string argument. Site names can be given as a third column of the data.frame, as rownames for the matrix or omitted. If site names are given, and `commatrix` has row.names, these are matched.
`proj4string_in`	Projection string as defined in package `sp`
`type`	A descriptor of whether the sites are point (community) sites, or the centres of regular grid cells. If omitted or set to `auto`, the function will guess the type from `coords`.
`shape`	An optional shapefile to overlay plots upon.
`object`	An object of type distrib_data or nodiv_data
`x`	An object of type distrib_data or nodiv_data
`...`	Further arguments to be passed to the plotting function

Details

When making an object of type 'grid', the coordinates will be stored as SpatialPixels from package sp. This may result in a warning if there are rows or columns in the grid without data. The function removes these. This may affect plotting, but can otherwise be ignored.

Value

The distrib_data function produces an object of type distrib_data, which has the following components:

`coords`	A `SpatialPointsDataFrame` or `SpatialPixelsDataFrame` (from `sp`) with spatial coordinates, and one column named `sites` containing the site names
`comm`	The community matrix
`type`	A character vector describing the type of data
`species`	A list of species names
`shape`	An optional slot detailing a shapefile object for plotting the data

The nodiv_data function produces an object of type nodiv_data, which contains the additional component:

phylo

A phylogeny of type phylo from package ape

Author(s)

Michael Krabbe Borregaard