Return.ispline: Computing splines coordinates from I-spline-based multi-site...

In zetadiv: Functions to Compute Compositional Turnover Using Zeta Diversity

Computing splines coordinates from I-spline-based multi-site generalised dissimilarity modelling

Description

Stores the coordinates of the I-splines resulting from Zeta.msgdm for plotting.

Usage

Return.ispline(msgdm, data.env, distance = FALSE, biotic = 0)

Arguments

msgdm	Output of function Zeta.msgdm computed with reg.type = ispline.
data.env	Site-by-variable data frame used for the computation of msgdm, with sites as rows and environmental variables as columns.
distance	Boolean, indicates is distance was used in the computation of msgdm.
biotic	Integer, indicates the number of other groups of taxa for which zeta diversity was computed and used in the computation of msgdm.

Details

Return.ispline allows to store the same number of coordinates for all I-splines, to average replicates and obtain confidence intervals.

Value

Return.ispline returns a list containing the following components used to plot the I-splines:

env	A data frame containing the rescaled environmental (numeric and factor), distance and biotic x-values.
Ispline	A data frame containing the I-spline values corresponding to the rescaled environmental (numeric and factor), distance and biotic x-values.

See Also

Zeta.msgdm, Ispline

Examples

utils::data(Marion.species)
xy.marion <- Marion.species[1:2]
data.spec.marion <- Marion.species[3:33]

utils::data(Marion.env)
data.env.marion <- Marion.env[3]

zeta.ispline <- Zeta.msgdm(data.spec.marion, data.env.marion, xy.marion, sam = 100,
    order = 3, normalize = "Jaccard", reg.type = "ispline")
zeta.ispline
zeta.ispline.r <- Return.ispline(zeta.ispline, data.env.marion, distance = TRUE)
zeta.ispline.r

dev.new()
Plot.ispline(isplines = zeta.ispline.r, distance = TRUE)

dev.new()
Plot.ispline(msgdm = zeta.ispline, data.env = data.env.marion, distance = TRUE)

zetadiv documentation built on June 11, 2022, 1:12 a.m.