ggiNEXT: ggplot2 extension for an iNextPD object

In iNextPD: Interpolation and Extrapolation for Phylogenetic Diversity

Description

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

Usage

ggiNEXT(x, type = 1, se = TRUE, facet.var = "none", color.var = "site",
  grey = FALSE)

## S3 method for class 'iNextPD'
ggiNEXT(x, type = 1, se = TRUE, facet.var = "none",
  color.var = "site", grey = FALSE)

## Default S3 method:
ggiNEXT(x, ...)

Arguments

x	an iNextPD object computed by iNextPD.
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"); a separate plot for each site (facet.var="site"); a separate plot for each combination of order x site (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"); use different colors for sites (color.var="site"); use different colors for combinations of order x site (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

# single-assemblage abundance data
data(bird)
bird.phy <- ade4::newick2phylog(bird$tre)
bird.lab <- rownames(bird$abun)
out1 <- iNextPD(bird$abun$North.site, bird.lab, bird.phy, 
        q=1, datatype="abundance", endpoint=400, se=TRUE)
ggiNEXT(x=out1, type=1)
ggiNEXT(x=out1, type=2)
ggiNEXT(x=out1, type=3)

## Not run: 
# single-assemblage incidence data with three orders q
out2 <- iNextPD(bird$inci$North.site, bird.lab, bird.phy, 
        q=c(0,1,2), datatype="incidence_raw", endpoint=25)
ggiNEXT(out2, se=FALSE, color.var="order")

# multiple-assemblage abundance data with three orders q
out3 <-  iNextPD(bird$abun, bird.lab, bird.phy, 
        q=c(0,1,2), datatype="abundance", endpoint=400)
ggiNEXT(out3, facet.var="site", color.var="order")
ggiNEXT(out3, facet.var="both", color.var="both")

## End(Not run)

iNextPD documentation built on May 2, 2019, 3:31 a.m.