omit {divDyn} | R Documentation

## Omission of taxa that have a poor occurrence record

### Description

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)

### 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))

[Package divDyn version 0.8.0 Index]