iNEXT3D | 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, 2data(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, 2data(Brazil_rainforest_abun_data)data(Brazil_rainforest_phylo_tree)data <- Brazil_rainforest_abun_datatree <- Brazil_rainforest_phylo_treeoutput_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 datadata(Brazil_rainforest_abun_data)data(Brazil_rainforest_distance_matrix)data <- Brazil_rainforest_abun_datadistM <- Brazil_rainforest_distance_matrixoutput_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, 2data(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, 2data(Fish_incidence_data)data(Fish_phylo_tree)data <- Fish_incidence_datatree <- Fish_phylo_treeoutput_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 datadata(Fish_incidence_data)data(Fish_distance_matrix)data <- Fish_incidence_datadistM <- Fish_distance_matrixoutput_FD_inci <- iNEXT3D(data, diversity = 'FD', datatype = "incidence_raw", nboot = 20, FDdistM = distM, FDtype = 'AUC')output_FD_inci