ggplot2 extension for an iNEXT object

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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

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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

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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)