iNEXT: ggiNEXT – R documentation

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ggiNEXT

ggplot2 extension for an iNEXT object

Description

ggiNEXT: the ggplot extension for iNEXT 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 'iNEXT'
ggiNEXT(x, type = 1, se = TRUE, facet.var = "none",
  color.var = "site", grey = FALSE)

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

Arguments

`x`	an `iNEXT` object computed by `iNEXT`.
`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

data(spider)
# single-assemblage abundance data
out1 <- iNEXT(spider$Girdled, q=0, datatype="abundance")
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
data(ant)
size <- round(seq(10, 500, length.out=20))
y <- iNEXT(ant$h500m, q=c(0,1,2), datatype="incidence_freq", size=size, se=FALSE)
ggiNEXT(y, se=FALSE, color.var="order")

# multiple-assemblage abundance data with three orders q
z <- iNEXT(spider, q=c(0,1,2), datatype="abundance")
ggiNEXT(z, facet.var="site", color.var="order")
ggiNEXT(z, facet.var="both", color.var="both")

## End(Not run)

iNEXT

Interpolation and Extrapolation for Species Diversity

v2.0.20

GPL (>= 3)

Authors

T. C. Hsieh, K. H. Ma and Anne Chao

Initial release