iNEXT3D {iNEXT.3D} | R Documentation |
iNterpolation and EXTrapolation with three dimensions of biodiversity
Description
iNEXT3D
mainly computes standardized 3D estimates with a common sample size or sample coverage for orders q = 0, 1 and 2. It also computes relevant information/statistics.
For diversity = "TD"
, relevant data information is summarized in the output $TDInfo
. Diversity estimates for rarefied and extrapolated samples are provided in the output $TDiNextEst
, which includes two data frames ("$size_based"
and "$coverage_based"
) based on two different standardizations; in the size-based standardization, all samples are standardized to a common target sample size, whereas the in the latter standardization, all samples are standardized to a common target level of sample coverage. The asymptotic diversity estimates for q = 0, 1 and 2 are provided in the list $TDAsyEst
.
For diversity = "PD"
, the corresponding three lists are $PDInfo
, $PDiNextEst
and $PDAsyEst
.
For diversity = "FD"
, the corresponding three lists are $FDInfo
, $FDiNextEst
and $FDAsyEst
.
Usage
iNEXT3D(
data,
diversity = "TD",
q = c(0, 1, 2),
datatype = "abundance",
size = NULL,
endpoint = NULL,
knots = 40,
nboot = 50,
conf = 0.95,
nT = NULL,
PDtree = NULL,
PDreftime = NULL,
PDtype = "meanPD",
FDdistM,
FDtype = "AUC",
FDtau = NULL,
FDcut_number = 50
)
Arguments
data |
(a) For |
diversity |
selection of diversity type: |
q |
a numerical vector specifying the diversity orders. Default is |
datatype |
data type of input data: individual-based abundance data ( |
size |
an integer vector of sample sizes (number of individuals or sampling units) for which diversity estimates will be computed.
If |
endpoint |
an integer specifying the sample size that is the |
knots |
an integer specifying the number of equally-spaced |
nboot |
a positive integer specifying the number of bootstrap replications when assessing sampling uncertainty and constructing confidence intervals. Enter 0 to skip the bootstrap procedures. Default is 50. |
conf |
a positive number < 1 specifying the level of confidence interval. Default is 0.95. |
nT |
(required only when |
PDtree |
(required argument for |
PDreftime |
(argument only for |
PDtype |
(argument only for |
FDdistM |
(required argument for |
FDtype |
(argument only for |
FDtau |
(argument only for |
FDcut_number |
(argument only for |
Value
a list of three objects:
(1) $TDInfo
($PDInfo
, or $FDInfo
) for summarizing data information for q = 0, 1 and 2. Refer to the output of DataInfo3D
for details.
(2) $TDiNextEst
($PDiNextEst
, or $FDiNextEst
) for showing diversity estimates for rarefied and extrapolated samples along with related statistics. There are two data frames: "$size_based"
and "$coverage_based"
.
In "$size_based"
, the output includes:
Assemblage |
the name of assemblage. |
Order.q |
the diversity order of q. |
m , mT |
the target sample size (or number of sampling units for incidence data). |
Method |
Rarefaction, Observed, or Extrapolation, depending on whether the target sample size is less than, equal to, or greater than the size of the reference sample. |
qTD , qPD , qFD |
the estimated diversity estimate. |
qTD.LCL , qPD.LCL , qFD.LCL and qTD.UCL , qPD.UCL , qFD.UCL |
the bootstrap lower and upper confidence limits for the diversity of order q at the specified level (with a default value of 0.95). |
SC |
the standardized coverage value. |
SC.LCL , SC.UCL |
the bootstrap lower and upper confidence limits for coverage at the specified level (with a default value of 0.95). |
Reftime |
the reference times for PD. |
Type |
|
Tau |
the threshold of functional distinctiveness between any two species for FD (under |
Similar output is obtained for "$coverage_based"
.
(3) $TDAsyEst
($PDAsyEst
, or $FDAsyEst
) for showing asymptotic diversity estimates along with related statistics:
Assemblage |
the name of assemblage. |
qTD , qPD , qFD |
the diversity order of q. |
TD_obs , PD_obs , FD_obs |
the observed diversity. |
TD_asy , PD_asy , FD_asy |
the asymptotic diversity estimate. |
s.e. |
standard error of asymptotic diversity. |
qTD.LCL , qPD.LCL , qFD.LCL and qTD.UCL , qPD.UCL , qFD.UCL |
the bootstrap lower and upper confidence limits for asymptotic diversity at the specified level (with a default value of 0.95). |
Reftime |
the reference times for PD. |
Type |
|
Tau |
the threshold of functional distinctiveness between any two species for FD (under |
Examples
# Compute standardized estimates of taxonomic diversity 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")
output_TD_abun
# Compute standardized estimates 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)
output_PD_abun
# Compute standardized estimates 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')
output_FD_abun
# Compute standardized estimates 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")
output_TD_inci
# Compute standardized estimates of phylogenetic diversity 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)
output_PD_inci
# Compute estimates 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')
output_FD_inci