make_mob_in: Create the 'mob_in' object.

In MoBiodiv/mobr: Measurement of Biodiversity

Create the 'mob_in' object.

Description

The 'mob_in' object will be passed on for analyses of biodiversity across scales.

Usage

make_mob_in(
  comm,
  plot_attr,
  coord_names = NULL,
  binary = FALSE,
  latlong = FALSE
)

Arguments

comm	community matrix in which rows are samples (e.g., plots) and columns are species.
plot_attr	matrix which includes the environmental attributes and spatial coordinates of the plots. Environmental attributes are mandatory, while spatial coordinates are optional.
coord_names	character vector with the names of the columns of plot_attr that specify the coordinates of the samples. Defaults to NULL (no coordinates). When providing coordinate names, the order the names are provided matters when working with latitude-longitude coordinates (i.e., argument latlong = TRUE, and it is expected that the column specifying the x-coordinate or the longitude is provided first, y-coordinate or latitude provided second. To provide coordinate names use the following syntax: coord_names = c('longitude_col_name','latitude_col_name')
binary	Boolean, defaults to FALSE. Whether the plot by species matrix "comm" is in abundances or presence/absence.
latlong	Boolean, defaults to FALSE. Whether the coordinates are latitude-longitudes. If TRUE, distance calculations by downstream functions are based upon great circle distances rather than Euclidean distances. Note latitude-longitudes should be in decimal degree.

Value

a "mob_in" object with four attributes. "comm" is the plot by species matrix. "env" is the environmental attribute matrix, without the spatial coordinates. "spat" contains the spatial coordinates (1-D or 2-D). "tests" specifies whether each of the three tests in the biodiversity analyses is allowed by data.

Author(s)

Dan McGlinn and Xiao Xiao

Examples

 data(inv_comm)
 data(inv_plot_attr)
 inv_mob_in = make_mob_in(inv_comm, inv_plot_attr, coord_names = c('x', 'y'))

MoBiodiv/mobr documentation built on Jan. 31, 2024, 6:15 p.m.