PhyloApply {entropart} | R Documentation |

## Apply a Function over a Phylogenetic Tree

### Description

Cuts the tree into slices separated by nodes, applies the function to each slice and returns the weighted (by slice lengths) sum of the results.

### Usage

```
PhyloApply(Tree, FUN, NorP, Normalize = TRUE, dfArgs = NULL,
..., CheckArguments = TRUE)
```

### Arguments

`Tree` |
An object of class |

`FUN` |
The function to be applied to each interval of the tree. |

`NorP` |
A numeric vector or a two-column matrix. Contains either abundances or probabilities. Two-column matrices should contain the observed abundances (or probabilities) in the first column and the expected ones in the second column, to allow using beta diversity functions. |

`Normalize` |
If |

`dfArgs` |
A dataframe. Columns are arguments for |

`...` |
Further arguments to pass to |

`CheckArguments` |
Logical; if |

### Details

This funtion is generally not used directly. It is a tool to calculate `PhyloEntropy`

and `PhyloDiversity`

.

Intervals (slices) separate two cuts (nodes) in a tree: no node is found at heights contained in an interval.

Objects of class **PPtree** are returned by `Preprocess.Tree`

.

... allow passing arguments to the function but they can't change along the tree. If necessary, `dfArgs`

allow passing a different value for each slice of the tree.

### Value

An object of class `PhyloValue`

. It is a list:

`Distribution` |
The distribution used to calculate the value |

`Function` |
The function used to calculate the value |

`Tree` |
The functional or phylogenetic tree used to calculate the value |

`Normalized` |
Logical. Indicates whether phylovalue is normalized or proportional to the height of the tree. |

`Cuts` |
A named vector containing values along the tree. Names are cut ends, |

`Corrections` |
A named vector containing the correction used by FUN to obtain each value of |

`Total` |
The total value, multiplied by the tree height if |

### References

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. *Methods in Ecology and Evolution* 6(3): 333-339.

### See Also

### Examples

```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
# and their taxonomy)
data(Paracou618)
# Plot the taxonomy
plot(Paracou618.Taxonomy, type="fan", show.tip.label=FALSE)
# Calculate the mean number of trees (individuals) per species
# (Cuts are 1=species, 2=genus, 3=family)
summary(PhyloApply(Paracou618.Taxonomy, mean, Paracou618.MC$Ns, TRUE))
```

*entropart*version 1.6-13 Index]