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Omission of taxa that have a poor occurrence record

Source: R/diversityDynamics.r
omit.Rd

Function to quickly omit single-collection and single-reference taxa.

Usage

omit(
  x,
  om = "ref",
  tax = "genus",
  bin = "bin",
  coll = NULL,
  ref = NULL,
  filterNA = FALSE
)

Arguments

x

(data.frame) Occurrence dataset, with bin, tax and coll as column names.

om

(character) The type of omission. "coll" omits occurrences of taxa that occurr only in one collection. "ref" omits occurrences of taxa that were described only in one reference. "binref" will omit the set of single reference taxa that were described by more than one references, but appear in only one reference in a time bin.

tax

(character) The name of the taxon variable.

bin

(character) The name of the bin variable (has to be numeric for the function to run). For time series, this is the time slice variable.

coll

(character) The variable name of the collection identifiers.

ref

(character) The variable name of the reference identifiers (optional).

filterNA

(logical) Additional entries can be added to influence the dataset that might not have reference or collection information (NA entries). These occurrences are treated as single-collection or single-reference taxa if the na.rm argument is set to FALSE (default). Setting this argument to TRUE will keep these entries. (see example)

Value

A logical vector.

Details

The function returns a logical vector, with a value for each row. TRUE values indicate rows to be omitted, FALSE values indicate rows to be kept. The function is embedded in the divDyn function, but can be called independently.

Examples

# omit single-reference taxa
  data(corals)
  data(stages)
  toOmit <- omit(corals, bin="stg", tax="genus", om="ref", ref="reference_no")
  x <- corals[!toOmit,]

# within divDyn
  # plotting
  tsplot(stages, shading="series", boxes="sys", xlim=c(260,0), 
    ylab="range-through diversity (genera)", ylim=c(0,230))
  # multiple ref/slice required
  ddNoSing <- divDyn(corals, tax="genus", bin="stg", om="binref", ref="reference_no")
  lines(stages$mid, ddNoSing$divRT, lwd=2, col="red")

  # with the recent included (NA reference value)
  ddNoSingRec <- divDyn(corals, tax="genus", bin="stg",
    om="binref", filterNA=TRUE,ref="reference_no")
  lines(stages$mid, ddNoSingRec$divRT, lwd=2, col="blue")
  
  # legend
  legend("topleft", legend=c("no single-ref. taxa", 
    "no single-ref. taxa,\n with recent"), 
    col=c("red", "blue"), lwd=c(2,2))