ggAsy3D: ggplot for Asymptotic diversity

In KaiHsiangHu/iNEXT3D: Interpolation and Extrapolation for Species Diversity in three dimensions

Description

ggasy3D Plots q-profile, time-profile, and tau-profile based on the outcome of asy3D using the ggplot2 package.
It will only show the confidence interval of 'Estimated'.

Usage

ggasy3D(outcome, profile = "q")

Arguments

outcome

the outcome of the functions asy3D .

Value

a figure of asymptotic of empirical three-divrsity

Examples

## example for abundance-based data
# diversity = 'TD'
data(spider)
out1 <- rbind(asy3D(spider, diversity = 'TD', datatype = "abundance"), obs3D(spider, diversity = 'TD', datatype = "abundance"))
ggasy3D(out1)

# diversity = 'PD'
data(data.abu)
data <- data.abu$data
tree <- data.abu$tree
out2 <- asy3D(data, diversity = 'PD', q = seq(0, 2, by = 0.25), datatype = "abundance", nboot = 30, PDtree = tree, PDtype = "meanPD")
ggasy3D(out2, profile = "q")

# diversity = 'FD' & FDtype = 'tau_values'
data(FunDdata.abu)
data <- FunDdata.abu$data
distM <-  FunDdata.abu$dij
out3 <- asy3D(data, diversity = 'FD', q = c(0, 1, 2), datatype = "abundance", nboot = 0, FDtau = seq(0, 0.6, 0.1), FDdistM = distM, FDtype = 'tau_values')
ggasy3D(out3, profile = "tau")

# diversity = 'FD' & FDtype = 'AUC'
data(FunDdata.abu)
data <- FunDdata.abu$data
distM <-  FunDdata.abu$dij
out4 <- asy3D(data = data[,2], diversity = 'FD', q = seq(0, 2, 0.5), datatype = "abundance", nboot = 0, FDdistM = distM)
ggasy3D(out4)

## example for incidence-based data
# diversity = 'TD'
data(ant)
out5 <- rbind(asy3D(ant, diversity = 'TD', datatype = "incidence_freq"), obs3D(ant, diversity = 'TD', datatype = "incidence_freq"))
ggasy3D(out5)

# diversity = 'PD'
data(data.inc)
data <- data.inc$data
tree <- data.inc$tree
nT <- data.inc$nT
out6 <- asy3D(data, diversity = 'PD', q = c(0, 1, 2), datatype = "incidence_raw", nT = nT, PDtree = tree, PDreftime = seq(0.1, 82.8575, length.out = 40))
ggasy3D(out6, profile = "time")

# diversity = 'FD' & FDtype = 'tau_values'
data(FunDdata.inc)
data <- FunDdata.inc$data
distM <-  FunDdata.inc$dij
out7 <- asy3D(data, diversity = 'FD', datatype = "incidence_freq", FDdistM = distM, FDtype = 'tau_values')
ggasy3D(out7)

# diversity = 'FD' & FDtype = 'AUC'
data(FunDdata.inc)
data <- FunDdata.inc$data
distM <-  FunDdata.inc$dij
out8 <- asy3D(data, diversity = 'FD', datatype = "incidence_freq", nboot = 20, FDdistM = distM)
ggasy3D(out8)

KaiHsiangHu/iNEXT3D documentation built on July 18, 2021, 8:11 p.m.