Calculate the diversity profiles (alpha, beta, gamma) of a metacommunity.

1 2 3 4 5 6 7 8 9 10 | ```
DivProfile(q.seq = seq(0, 2, 0.1), MC, Biased = TRUE, Correction = "Best",
Tree = NULL, Normalize = TRUE, Z = NULL,
NumberOfSimulations = 0, Alpha = 0.05, CheckArguments = TRUE)
is.DivProfile(x)
## S3 method for class 'DivProfile'
plot(x, ..., main = NULL, xlab = "Order of Diversity",
ylab = NULL, Which = "All",
LineWidth = 2, ShadeColor = "grey75", BorderColor = "red")
## S3 method for class 'DivProfile'
summary(object, ...)
``` |

`q.seq` |
A numeric vector. |

`MC` |
A |

`Biased` |
Logical; if |

`Correction` |
A string containing one of the possible corrections. The correction must be accepted by |

`Tree` |
An object of class |

`Normalize` |
If |

`Z` |
A relatedness matrix, |

`NumberOfSimulations` |
The number of simulations to run, 0 by default. |

`Alpha` |
The risk level, 5% by default. |

`CheckArguments` |
Logical; if |

`x` |
An object to be tested or plotted. |

`main` |
The main title of the plot. Ignored if |

`xlab` |
The x axis label of the plots. |

`ylab` |
The y axis label of the plot. Ignored if |

`Which` |
May be |

`LineWidth` |
The width of the line that represents the actual profile. |

`ShadeColor` |
The color of the shaded confidence envelope. |

`BorderColor` |
The color of the bounds of the confidence envelope. |

`object` |
A |

`...` |
Additional arguments to be passed to the generic methods. |

If `Tree`

is provided, the phylogenetic diversity is calculated.

`DivPart`

partitions the diversity of the metacommunity into alpha and beta components. It supports estimation-bias correction.

If `Tree`

is provided, the phylogenetic diversity is calculated else if `Z`

is not `NULL`

, then similarity-based entropy is calculated.

Beta diversity/entropy is calculated from Gamma and Alpha when bias correction is required, so community values are not available.

If `NumberOfSimulations`

is greater than 0, a bootstrap confidence interval is produced by simulating communities from a multinomial distribution following the observed frequencies (Marcon et al, 2012; 2014) and calculating their profiles.

A `DivProfile`

object. It is a list:

`MetaCommunity` |
The name of the |

`Order` |
A vector containing the values of |

`Biased` |
Logical. If |

`Correction` |
The estimation bias correction used to calculate diversity. |

`Method` |
The method used to calculate entropy ("HCDT", "Similarity-based"). |

`Tree` |
The phylogenetic or functional tree used to calculate phylodiversity. |

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

`Z` |
The matrix used to calculate similarity-based entropy. |

`CommunityAlphaDiversities` |
A matrix containing the alpha diversity of each community. |

`TotalAlphaDiversity` |
A vector containing the alpha diversity of communities for each order. |

`BetaDiversity` |
A vector containing the beta diversity of communities for each order. |

`GammaDiversity` |
A vector containing the gamma diversity of the metacommunity for each order. |

`CommunityAlphaEntropies` |
A matrix containing the alpha entropy of each community. |

`TotalAlphaEntropy` |
A vector containing the alpha entropy of communities for each order. |

`BetaEntropy` |
A vector containing the beta entropy of communities for each order. |

`GammaEntropy` |
A vector containing the gamma entropy of the metacommunity for each order. |

`confidence envelopes` |
Total Alpha, Beta and Gamma Entropy and Diversity may come with a confidence envelope whose value is stored in twelve more vectors named suffixed Low or High, such as |

`DivProfile`

objects can be summarized and plotted.

Eric Marcon <Eric.Marcon@ecofog.gf> and Bruno Herault <Bruno.Herault@ecofog.gf>

Marcon, E., Herault, B., Baraloto, C. and Lang, G. (2012). The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity. *Oikos* 121(4): 516-522.

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. *PLOS One* 9(3): e90289.

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

1 2 3 4 5 6 | ```
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest)
data(Paracou618)
# Estimate diversity.
Profile <- DivProfile(q.seq = seq(0, 2, 0.1), Paracou618.MC, Biased = FALSE)
plot(Profile)
summary(Profile)
``` |

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