iNEXT.beta3D (version 1.0.2)

ggiNEXTbeta3D: ggplot2 extension for the iNEXTbeta3D object

Description

ggiNEXTbeta3D is an ggplot2 extension for the iNEXTbeta3D object to plot sample-size- and coverage-based rarefaction/extrapolation curves.

Usage

ggiNEXTbeta3D(output, type = "B")

Value

a figure for gamma, alpha, and beta diversity, or a figure for four dissimilarity indices for base = "coverage"; or a figure for gamma and alpha diversity when base = "size".

Arguments

output

output from the function iNEXTbeta3D.

type

(argument only for base = "coverage"),
type = 'B' for plotting the rarefaction and extrapolation sampling curves for gamma, alpha, and beta diversity;
type = 'D' for plotting the rarefaction and extrapolation sampling curves for four dissimilarity indices.
Skip the argument for plotting size-based rarefaction and extrapolation sampling curves for gamma and alpha diversity.

Examples

# \donttest{
## (Graphic Display) Taxonomic diversity for abundance data
# Coverage-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
output_TDc_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'TD', 
                              datatype = 'abundance', base = "coverage", nboot = 10)

ggiNEXTbeta3D(output_TDc_abun, type = 'B')
ggiNEXTbeta3D(output_TDc_abun, type = 'D')
# }

# Size-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
output_TDs_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'TD', 
                              datatype = 'abundance', base = "size", nboot = 10)

ggiNEXTbeta3D(output_TDs_abun)

# \donttest{
## (Graphic Display) Taxonomic diversity for incidence data
# Coverage-based rarefaction and extrapolation sampling curves 
data(Second_growth_forests)
output_TDc_inci = iNEXTbeta3D(data = Second_growth_forests, diversity = 'TD', 
                              datatype = 'incidence_raw', base = "coverage", nboot = 10)

ggiNEXTbeta3D(output_TDc_inci, type = 'B')
ggiNEXTbeta3D(output_TDc_inci, type = 'D')
# }

# Size-based rarefaction and extrapolation sampling curves 
data(Second_growth_forests)
output_TDs_inci = iNEXTbeta3D(data = Second_growth_forests, diversity = 'TD', 
                              datatype = 'incidence_raw', base = "size", nboot = 10)

ggiNEXTbeta3D(output_TDs_inci)

# \donttest{
## (Graphic Display) Phylogenetic diversity for abundance data
# Coverage-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
data(Brazil_tree)
output_PDc_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'PD', 
                              datatype = 'abundance', base = "coverage", nboot = 10, 
                              PDtree = Brazil_tree, PDreftime = NULL, PDtype = 'meanPD')

ggiNEXTbeta3D(output_PDc_abun, type = 'B')
ggiNEXTbeta3D(output_PDc_abun, type = 'D')


# Size-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
data(Brazil_tree)
output_PDs_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'PD', 
                              datatype = 'abundance', base = "size", nboot = 10, 
                              PDtree = Brazil_tree, PDreftime = NULL, PDtype = 'meanPD')

ggiNEXTbeta3D(output_PDs_abun)


## (Graphic Display) Functional diversity for abundance data when all threshold levels 
## from 0 to 1 are considered
# Coverage-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
data(Brazil_distM)
output_FDc_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'FD', 
                              datatype = 'abundance', base = "coverage", nboot = 10, 
                              FDdistM = Brazil_distM, FDtype = 'AUC', FDcut_number = 30)

ggiNEXTbeta3D(output_FDc_abun, type = 'B')
ggiNEXTbeta3D(output_FDc_abun, type = 'D')


# Size-based rarefaction and extrapolation sampling curves 
data(Brazil_rainforests)
data(Brazil_distM)
output_FDs_abun = iNEXTbeta3D(data = Brazil_rainforests, diversity = 'FD', 
                              datatype = 'abundance', base = "size", nboot = 10, 
                              FDdistM = Brazil_distM, FDtype = 'AUC', FDcut_number = 30)

ggiNEXTbeta3D(output_FDs_abun)
# }