ggiNEXTPD: Plots the outcome of 'iNEXTPD' using the 'ggplot2' package.

In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description

Function ggiNEXTPD plots the outcome of iNEXTPD using the ggplot2 package.

Usage

ggiNEXTPD(outcome, plot.type = 1:3)

Arguments

outcome	the outcome of the function iNEXTPD
plot.type	a positive integer or sequence specifying types of curves. There are three types of plots: sample-size-based rarefaction and extrapolation curve ($RE.plot.size, plot.type = 1); sample coverage curve as a function of sample size ($RE.plot.sizeC, plot.type = 2); coverage-based rarefaction and extrapolation curve ($RE.plot.C, plot.type = 3). Default is c(1,2,3).

Value

Returns different plots of the estimated diversity curves based on the ggplot2 package. Three choices of plot.type:

• $RE.plot.size: size-based rarefaction and extrapolation curve (plot.type = 1), sampling curve depicting phylogenetic diversity estimates as a function of sample size.
  

• $RE.plot.sizeC: sample completeness curve (plot.type = 2), the curve of sample coverage as a function of sample size.
  

• $RE.plot.C: coverage-based rarefaction and extrapolation curve (plot.type = 3), sampling curve depicting phylogenetic diversity estimates as a function of sample coverage.

Examples

# Datatype: abundance data
data(data.abu)
data <- data.abu$data
tree <- data.abu$tree
out <- iNEXTPD(data = data, tree = tree, datatype = "abundance", q = c(0, 1, 2), nboot = 30)
ggiNEXTPD(out)

# Datatype: incidence_raw data
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
out <- iNEXTPD(data = data, nT = nT, datatype = "incidence_raw", tree = tree, 
q = c(0, 1, 2), nboot = 30)
ggiNEXTPD(out)

YanHanChen/iNEXTPD2 documentation built on Aug. 24, 2020, 4:15 a.m.