tabinate {divDyn} | R Documentation

## Apply function to TAxon/BIN subset of occurrences and iterATE

### Description

The function takes another function and reruns it on every taxon- and/or bin-specific subsets of an occurrence dataset.

### Usage

    tabinate(x, bin = NULL, tax = NULL, FUN = NULL, ...)

### Arguments

`x` | `(data.frame)` Fossil occurrence table.
`bin` | `(character)` Variable name of the bin numbers of the occurrences. This variable should be `numeric`.
`tax` | `(character)` Variable name of the occurring taxa (variable type: `factor` or `character` - such as `"genus"`
`FUN` | (`function`) The function applied to the subset of occurrences. The subset of occurence data will be passed to this function as `x`.
`...` | arguments passed to `FUN`

### Details

The main `tabinate` function acts as a wrapper for any type of function that requires a subset of the occurrence dataset that represents either one `bin` or one `tax` entry or both. For example, the iterator can be used to calculate geographic ranges from occurrence coordinates (`georange`).

The output structure of FUN should be independent from the input subset, or the function will return an error. Setting both `bin` If `bin=NULL` and codetax=NULL, will run `FUN` on the entire dataset (no effect). Providing either `bin` or `tax` and keeping the other `NULL` will iterate `FUN` for every `bin` or `tax` entry (whichever is presented). The function returns a vector of values if the return value of `FUN` is a single value. In case it is a vector, the final output will be a matrix. When both `bin` and `tax` is presented, the function output will be a matrix (one output value for a taxon/bin subset) or an array (3d, when `FUN` returns a vector). Setting `FUN` to `NULL` will return the occurrence dataset as `list`s.

### Examples

     data(corals)

    # the number of different coordinate pairs in every time slice
      tabinate(corals, bin="stg", FUN=georange, lat="paleolat",
        lng="paleolng", method="co")
    # geographic range (site occupancy) of every taxon in every bin
      tabinate(corals, bin="stg", tax="genus", FUN=georange,
        lat="paleolat", lng="paleolng", method="co")

[Package divDyn version 0.8.0 Index]