ggiNEXT.link: ggplot2 extension for outcome from 'iNEXT.link'

In Chunger-Lo/iNEXT.link: Network diversity iNterpolation/Extrapolation Estimation

Description

ggiNEXT.link: the ggplot extension for iNEXT.link Object to plot sample-size- and coverage-based rarefaction/extrapolation curves along with a bridging sample completeness curve

Usage

ggiNEXT.link(
  outcome,
  diversity = "TD",
  type = 1,
  se = TRUE,
  facet.var = "Order.q",
  color.var = "Assemblage",
  text.size = 12,
  stript.size = 12
)

Arguments

outcome	a list object computed by iNEXT.link.
type	three types of plots: sample-size-based rarefaction/extrapolation curve (type = 1); sample completeness curve (type = 2); coverage-based rarefaction/extrapolation curve (type = 3).
se	a logical variable to display confidence interval around the estimated sampling curve.
facet.var	create a separate plot for each value of a specified variable: no separation (facet.var="None"); a separate plot for each diversity order (facet.var="Order.q"); a separate plot for each assemblage (facet.var="Assemblage"); a separate plot for each combination of order x assemblage (facet.var="Both").
color.var	create curves in different colors for values of a specified variable: all curves are in the same color (color.var="None"); use different colors for diversity orders (color.var="Order.q"); use different colors for sites (color.var="Assemblage"); use different colors for combinations of order x assemblage (color.var="Both").
grey	a logical variable to display grey and white ggplot2 theme.
...	other arguments passed on to methods. Not currently used.

Value

a ggplot2 object

Examples

## Not run: 
data(Norfolk)
out1 <- iNEXT.link(Norfolk, diversity = 'TD',datatype = "abundance", nboot = 0)
ggiNEXT.link(outcome = out1, type = 1)
ggiNEXT.link(outcome = out1, type = 2)
ggiNEXT.link(outcome = out1, type = 3)

#' data(puerto.rico)
out2 <- iNEXT.link(puerto.rico$data, diversity = 'PD', datatype="abundance",
row.tree = puerto.rico$row.tree, col.tree = puerto.rico$col.tree)
ggiNEXT.link(outcome = out2, type = 1)
ggiNEXT.link(outcome = out2, type = 2)
ggiNEXT.link(outcome = out2, type = 3)

## End(Not run)

Chunger-Lo/iNEXT.link documentation built on Dec. 17, 2021, 2:05 p.m.