dissimilarity: dissimilarity objects
In skiptoniam/bbgdm: Bayesian Bootstrap Generalised Dissimilarity Models.

Description Usage Arguments Value Examples

creates a dissim_table which is required by bbgdm

dissim_table(sp.dat, env.dat, dism_metric = "number_non_shared",
  spline_type = "ispline", spline_df = 1, spline_knots = 2,
  coord.names = c("X", "Y"), intercept = FALSE, geo = FALSE,
  geo.type = "euclidean")

is.dissim_table(x)

is.spline(object)

`sp.dat`	Presence absence matrix.
`env.dat`	Matrix of covariates for bbgdm; if using own data as covariates make sure to set sim_covar=FALSE, otherwise simulated covariates will be caluclated instead.
`dism_metric`	Dissimilarity to caluclate; If "bray_curtis" calculates Bray-Curtis dissimilarity, if "number_non_shared" returns number of shared species at site_ij which can be used in a binomial model for GDM.
`spline_type`	If "ispline" calculates ispline. If "bspline" calculates bc from spline package.
`spline_df`	degrees of freedom; one can specify df rather than knots. Default = 3.
`spline_knots`	The internal breakpoints that define the spline. Default = NULL for bs spline and 1 for ispline.
`coord.names`	c("X","Y") character.vector names of coordinates.
`intercept`	logical if TRUE it only returns the dissimilarities.
`geo`	logical If true geographic distance is calculated if
`geo.type`	type of geographic distance to estimate, can call 'euclidean','greater_circle' or 'least_cost'. If least_cost is called extra parameters are required (lc_data, minr and maxr).
`x`	dissim_table class
`object`	spline class object

dissim_table dissimilarity table; creates a table of dissimilarities, and difference of covariates between each sites_ij. If select dissim="number_non_shared", will return "nonsharedspp_ij","sumspp_ij", which can be used as response variables in a binomial bbgdm.

1
2
3

x <- matrix(rbinom(100,1,.5),10,10) #toy presence absence matrix
y <- simulate_covariates(x,4)
diff_table <- dissim_table(x,y,dism_metric="number_non_shared")