bgpart: Biogeographic partitioning of occurrence data.

In adamkocsis/obigeo: Occurrence-based biogeography

Biogeographic partitioning of occurrence data.

Description

This function will produce bioregion/cell membership tables based on a variety of partitioning algorithms.

Usage

bgpart(
  dat,
  tax,
  cell,
  bin = NULL,
  ocq = 0,
  base = "network",
  feedback = FALSE,
  slq = 50,
  tracing = FALSE,
  coll = NULL,
  cols = TRUE,
  omitted = TRUE,
  ...
)

Arguments

dat	(data.frame) Occurrence table.
tax	(character) Variable name of the occurring taxa (variable type: factor or character - such as "genus"
cell	(character) The variable name of the cell, site or sample entries.
bin	(character) Variable name of the time bin numbers of the occurrences. This variable should be numeric.
ocq	numeric The minimum occurrence/cell quota. Cells with a lower number of occurrences will be omitted from the analysis.
base	(character) The basic type of the partitiong method. Currently only "network" or "distance"-based methods are provided, which are implemented in the groupNet and groupDist functions, respectively.
feedback	(logical) Should the functions output information about progress?
slq	numeric Only used if bin is not NULL. The minimum occurrence/time slice quota. Time slices with a lower number of occurrences will be omitted from the analysis.
coll	Used only for the 'network' approaches implemented in groupNet, and when bipartite is FALSE. The column name of the collection/sample identifiers. Setting this value to a valid column name will enforce a collection-based correction (Rojas et al., 2016), and will make 'sampcorr' argument irrelevant.
cols	logical Should colors be automatically assigned to each group?
...	Arguments passed to the groupNet or groupDist functions.

Details

A lot stuff should come here!

Examples

# load example dataset
data(ceno6)
# single-slice partitioning (using infomap)
oneC6 <- bgpart(ceno6,bin=NULL, tax="trinomen", cell="icos", ocq=10, base="network", method="infomap")

# iteration of sing slice partitiongs for every stg, separately (using infomap)
slicewiseC6 <- bgpart(ceno6,bin="stg", tax="trinomen", cell="icos", ocq=10, base="network", method="infomap")

# tracing method, coarser resolution (using infomap)
tracing <- bgpart(ceno6,bin="stg", tax="trinomen", cell="icos", ocq=10, base="network", method="infomap", tracing=TRUE)

# SEE THE bgplot() function for plotting!	

adamkocsis/obigeo documentation built on Oct. 14, 2024, 8:46 a.m.