ggiNEXT3D {iNEXT.3D}

ggplot2 extension for an iNEXT3D object

Description

ggiNEXT3D is a ggplot extension for an iNEXT3D object to plot sample-size- and coverage-based rarefaction/extrapolation sampling curves along with a bridging sample completeness curve.

Usage

ggiNEXT3D(output, type = 1:3, facet.var = "Assemblage", color.var = "Order.q")

Arguments

output

an iNEXT3D object computed by iNEXT3D.

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).

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.q"); a separate plot for each assemblage (facet.var = "Assemblage"); a separate plot for each combination of diversity order and assemblage (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.q"); use different colors for assemblages/sites (color.var = "Assemblage"); use different colors for combinations of diversity order and assemblage (color.var = "Both").

Value

a ggplot2 object for sample-size-based rarefaction/extrapolation curve (type = 1), sample completeness curve (type = 2), and coverage-based rarefaction/extrapolation curve (type = 3).

Examples

# Plot three types of curves of taxonomic diversity with facet.var = "Assemblage"
# for abundance data with order q = 0, 1, 2
data(Brazil_rainforest_abun_data)
output_TD_abun <- iNEXT3D(Brazil_rainforest_abun_data, diversity = 'TD', q = c(0, 1, 2), 
                          datatype = "abundance")
ggiNEXT3D(output_TD_abun, facet.var = "Assemblage")


# Plot two types (1 and 3) of curves of phylogenetic diversity 
# for abundance data with order q = 0, 1, 2
data(Brazil_rainforest_abun_data)
data(Brazil_rainforest_phylo_tree)
data <- Brazil_rainforest_abun_data
tree <- Brazil_rainforest_phylo_tree
output_PD_abun <- iNEXT3D(data, diversity = 'PD', q = c(0, 1, 2), datatype = "abundance", 
                          nboot = 20, PDtree = tree)
ggiNEXT3D(output_PD_abun, type = c(1, 3))


# Plot three types of curves of functional diversity for abundance data
data(Brazil_rainforest_abun_data)
data(Brazil_rainforest_distance_matrix)
data <- Brazil_rainforest_abun_data
distM <- Brazil_rainforest_distance_matrix
output_FD_abun <- iNEXT3D(data, diversity = 'FD', datatype = "abundance", nboot = 0, 
                          FDdistM = distM, FDtype = 'AUC')
ggiNEXT3D(output_FD_abun)


# Plot three types of curves of taxonomic diversity for incidence data with order q = 0, 1, 2
data(Fish_incidence_data)
output_TD_inci <- iNEXT3D(Fish_incidence_data, diversity = 'TD', q = c(0, 1, 2), 
                          datatype = "incidence_raw")
ggiNEXT3D(output_TD_inci)


# Plot three types of curves of phylogenetic diversity with facet.var = "Order.q"
#  and color.var = "Assemblage" for incidence data with order q = 0, 1, 2
data(Fish_incidence_data)
data(Fish_phylo_tree)
data <- Fish_incidence_data
tree <- Fish_phylo_tree
output_PD_inci <- iNEXT3D(data, diversity = 'PD', q = c(0, 1, 2), datatype = "incidence_raw", 
                          nboot = 20, PDtree = tree)
ggiNEXT3D(output_PD_inci, facet.var = "Order.q", color.var = "Assemblage")


# Plot three types of curves of functional diversity for incidence data
data(Fish_incidence_data)
data(Fish_distance_matrix)
data <- Fish_incidence_data
distM <- Fish_distance_matrix
output_FD_inci <- iNEXT3D(data, diversity = 'FD', datatype = "incidence_raw", nboot = 20, 
                          FDdistM = distM, FDtype = 'AUC')
ggiNEXT3D(output_FD_inci)