mobr (version 3.0.0)

make_mob_in: 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
)

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.

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.

Author

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'))