# DivProfile: Diversity Profile of a metacommunity In entropart: Entropy Partitioning to Measure Diversity

## Description

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

## Usage

 ``` 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, ...) ```

## Arguments

 `q.seq` A numeric vector. `MC` A `MetaCommunity` object. `Biased` Logical; if `FALSE`, a bias correction is appplied. `Correction` A string containing one of the possible corrections. The correction must be accepted by `AlphaEntropy`, `BetaEntropy` and `GammaEntropy`. `"Best"` is the default value. `Tree` An object of class `hclust`, `phylo`, `phylog` or `PPtree`. The tree must be ultrametric. `Normalize` If `TRUE` (default), diversity is not affected by the height of the tree. If `FALSE`, diversity is proportional to the height of the tree. `Z` A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1. `NumberOfSimulations` The number of simulations to run, 0 by default. `Alpha` The risk level, 5% by default. `CheckArguments` Logical; if `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere. `x` An object to be tested or plotted. `main` The main title of the plot. Ignored if `Which = "All"`. `xlab` The x axis label of the plots. `ylab` The y axis label of the plot. Ignored if `Which = "All"`. `Which` May be `"Communities"`, `"Alpha"`, `"Beta"` or `"Gamma"` to respectively plot the alpha diversity of communities or the metacommunity's alpha, beta or gamma diversity. If `"All"` (default), all four plots are shown. `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 `MCdiversity` object to be summarized. `...` Additional arguments to be passed to the generic methods.

## Details

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.

## Value

A `DivProfile` object. It is a list:

 `MetaCommunity` The name of the `MetaCommunity` object containing inventory data. `Order` A vector containing the values of `q`. `Biased` Logical. If `FALSE`, bias corrected values of diversity have been computed. `Correction` The estimation bias correction used to calculate diversity. Usually a string, but it may be a list if different corrections have been used in the estimation of phylodiversity. `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 `GammaEntropyLow`

`DivProfile` objects can be summarized and plotted.

## Author(s)

Eric Marcon <[email protected]> and Bruno Herault <[email protected]>

## References

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.

`DivPart`

## Examples

 ```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) ```

### Example output

```Diversity profile of MetaCommunity Paracou618.MC
with correction: Best
Diversity against its order:
Order Alpha Diversity Beta Diversity Gamma Diversity
ChaoWangJost   0.0       238.36351       1.321238       314.93484
ChaoWangJost   0.1       221.29193       1.321166       292.36347
ChaoWangJost   0.2       204.17972       1.323271       270.18504
ChaoWangJost   0.3       187.24324       1.327987       248.65650
ChaoWangJost   0.4       170.72117       1.335708       228.03372
ChaoWangJost   0.5       154.85926       1.346729       208.55339
ChaoWangJost   0.6       139.89024       1.361171       190.41457
ChaoWangJost   0.7       126.01236       1.378937       173.76304
ChaoWangJost   0.8       113.37058       1.399674       158.68180
ChaoWangJost   0.9       102.04503       1.422796       145.18921
ChaoWangJost   1.0        92.04908       1.447498       133.24089
ChaoWangJost   1.1        83.33700       1.473077       122.76180
ChaoWangJost   1.2        75.81819       1.498587       113.62013
ChaoWangJost   1.3        69.37405       1.523374       105.68260
ChaoWangJost   1.4        63.87372       1.546905        98.80658
ChaoWangJost   1.5        59.18644       1.568829        92.85340
ChaoWangJost   1.6        55.18979       1.588960        87.69438
ChaoWangJost   1.7        51.77425       1.607247        83.21401
ChaoWangJost   1.8        48.84485       1.623736        79.31112
ChaoWangJost   1.9        46.32106       1.638533        75.89860
ChaoWangJost   2.0        44.13559       1.651781        72.90234
```

entropart documentation built on Feb. 6, 2018, 1:04 a.m.