ggObsAsy3D {iNEXT.3D}

ggplot2 extension for plotting q-profile, time-profile, and tau-profile

Description

ggObsAsy3D is a ggplot2 extension for an ObsAsy3D object to plot 3D q-profile (which depicts the observed diversity and asymptotic diversity estimate with respect to order q) for q between 0 and 2 (in increments of 0.2).

It also plots time-profile (which depicts the observed and asymptotic estimate of PD or mean PD with respect to reference times when diversity = "PD" specified in the ObsAsy3D function), and tau-profile (which depicts the observed and asymptotic estimate of FD with respect to threshold level tau when diversity = "FD" and FDtype = "tau_values" specified in the ObsAsy3D function) based on the output of ObsAsy3D.

In the plot of profiles, only confidence intervals of the asymptotic diversity will be shown when both the observed and asymptotic diversity estimates are computed.

Usage

ggObsAsy3D(output, profile = "q")

Arguments

output

the output of the function ObsAsy3D.

profile

a selection of profile. User can choose 'q', 'time', and 'tau'. Default is 'q' profile.

Value

a q-profile, time-profile, or tau-profile based on the observed diversity and the asymptotic diversity estimate.

Examples

# Plot q-profile of taxonomic diversity for abundance data
# with order q between 0 and 2 (in increments of 0.2 by default).
data(Brazil_rainforest_abun_data)
output_ObsAsy_TD_abun <- ObsAsy3D(Brazil_rainforest_abun_data, diversity = 'TD', 
                                  datatype = "abundance")
ggObsAsy3D(output_ObsAsy_TD_abun)


# Plot time-profile of phylogenetic diversity for abundance data
# with order q = 0, 1, 2 under reference times from 0.01 to 400 (tree height).
data(Brazil_rainforest_abun_data)
data(Brazil_rainforest_phylo_tree)
data <- Brazil_rainforest_abun_data
tree <- Brazil_rainforest_phylo_tree
output_ObsAsy_PD_abun <- ObsAsy3D(data, diversity = 'PD', q = c(0, 1, 2), 
                                  PDreftime = seq(0.01, 400, length.out = 20),
                                  datatype = "abundance", nboot = 20, PDtree = tree)
ggObsAsy3D(output_ObsAsy_PD_abun, profile = "time")


# Plot tau-profile of functional diversity for abundance data
# with order q = 0, 1, 2 under tau values from 0 to 1.
data(Brazil_rainforest_abun_data)
data(Brazil_rainforest_distance_matrix)
data <- Brazil_rainforest_abun_data
distM <- Brazil_rainforest_distance_matrix
output_ObsAsy_FD_abun_tau <- ObsAsy3D(data, diversity = 'FD', q = c(0, 1, 2), 
                                      datatype = "abundance", nboot = 10, FDdistM = distM, 
                                      FDtype = 'tau_values', FDtau = seq(0, 1, 0.05))
ggObsAsy3D(output_ObsAsy_FD_abun_tau, profile = "tau")


# Plot q-profile of functional diversity for abundance data
# with order q between 0 and 2 (in increments of 0.5).
data(Brazil_rainforest_abun_data)
data(Brazil_rainforest_distance_matrix)
data <- Brazil_rainforest_abun_data
distM <- Brazil_rainforest_distance_matrix
output_ObsAsy_FD_abun <- ObsAsy3D(data, diversity = 'FD', q = seq(0, 2, 0.5), 
                                  datatype = "abundance", nboot = 10, 
                                  FDdistM = distM, FDtype = 'AUC')
ggObsAsy3D(output_ObsAsy_FD_abun, profile = "q")


# Plot q-profile of taxonomic diversity for incidence data
# with order q between 0 and 2 (in increments of 0.2 by default)
data(Fish_incidence_data)
output_ObsAsy_TD_inci <- ObsAsy3D(Fish_incidence_data, diversity = 'TD', 
                                  datatype = "incidence_raw")
ggObsAsy3D(output_ObsAsy_TD_inci)


# Plot q-profile of phylogenetic diversity for incidence data 
# with order q between 0 and 2 (in increments of 0.2 by default), 
# for the default reference time = 0.977 (the tree depth).
data(Fish_incidence_data)
data(Fish_phylo_tree)
data <- Fish_incidence_data
tree <- Fish_phylo_tree
output_ObsAsy_PD_inci <- ObsAsy3D(data, diversity = 'PD', q = seq(0, 2, 0.2), 
                                  datatype = "incidence_raw", nboot = 20, PDtree = tree, 
                                  PDreftime = NULL)
ggObsAsy3D(output_ObsAsy_PD_inci, profile = "q")


# Plot q-profile of functional diversity for incidence data
# with order q between 0 and 2 (in increments of 0.2 by default)
data(Fish_incidence_data)
data(Fish_distance_matrix)
data <- Fish_incidence_data
distM <- Fish_distance_matrix
output_ObsAsy_FD_inci <- ObsAsy3D(data, diversity = 'FD', datatype = "incidence_raw", 
                                  nboot = 20, FDdistM = distM, FDtype = 'AUC')
ggObsAsy3D(output_ObsAsy_FD_inci, profile = "q")