abgevodivparam {adiv} | R Documentation |

Function `abgevodivparam`

calculates alpha, beta and gamma components of phylogenetic diversity using parametric indices derived from Tsallis (HCDT) and Hill compositional indices. Alpha is for within-community diversity, beta for between-community diversity and gamma for the diversity of all combined communities.

abgevodivparam(phyl, comm, w = c("evoab", "even", "speciesab"), method = c("hillCJC", "hillR", "tsallis"), q = 2, option = c("multiplicative", "additive", "proportional", "C", "U", "V", "S", "Renyi"), tol = 1e-08) ## S3 method for class 'abgevodivparam' plot(x, legend = TRUE, legendposi = "topright", type = "b", col = if (is.numeric(x)) NULL else 1:nrow(x$div), lty = if (is.numeric(x)) NULL else rep(1, nrow(x$div)), pch = if (is.numeric(x)) NULL else 1:nrow(x$div), ylim1 = range(x$div[c("Alpha", "Gamma"), ]), ylim2 = NULL, ...)

`phyl` |
an object inheriting the class |

`comm` |
a data frame or a matrix typically with communities as rows, species as columns and an index of abundance as entries. Species should be labeled as in the phylogenetic tree where they are the tips. |

`w` |
either a numeric vector giving weights for communities (same order as in comm), or a code: one of |

`method` |
a string with one of the following codes: |

`q` |
a vector with nonnegative value(s) for parameter |

`option` |
a string code: either |

`tol` |
numeric tolerance threshold: values between - |

`x` |
an object of class |

`legend` |
a logical. If TRUE a legend is given with the colour, the type of line (etc.) used to define the diversity curve of each diversity level (gamma, alpha, beta). |

`legendposi` |
a string that gives the position of the legend to be passed to function |

`type` |
a string to be passed to the graphic argument |

`col` |
vector of colours to be passed to the graphic argument |

`lty` |
vector of types of line (plain, broken etc.) to be passed to the graphic argument |

`pch` |
vector of types of point (open circle, close circle, square etc.) to be passed to the graphic argument |

`ylim1` |
a vector with two numerics indicating the range to be used to display alpha and gamma diversity. |

`ylim2` |
a vector with two numerics indicating the range to be used to display beta diversity. |

`...` |
other arguments can be added and passed to the functions |

Consider a phylogenetic tree *T*, *b_T* the set of branches in *T*, *k* a branch, *L_k* the length of branch *k*, *j* a community (*j*=1,...,*m*), *a_jk* the abundance associated with branch *k* in community *j* (sum of abundance of all species descending from the branch). *q* is the parameter that increases with the importance given to abundant species compared to rare species in diversity.

The methods available are:
`tsallis`

(decomposition of Tsallis or HCDT entropy (Harvda and Charvat 1967; Daroczy 1970; Tsallis 1988) into alpha, beta, gamma components adapted here to phylogenetic diversity):

*qγ_evoTsallis=[1-sum_k L_k (sum_j w_j a_jk/(sum_k L_k a_jk))^q]/(q-1)*

*qα_evoTsallis=sum_j w_j [1-sum_k L_k (a_jk/(sum_k L_k a_jk))^q]/(q-1)*

`hillR`

(Routledge decomposition of Hill diversity into alpha, beta, gamma components adapted hete to phylogenetic diversity):

*qγ_evoHill=[sum_k L_k (sum_j w_j a_jk/(sum_k L_k a_jk))^q]^(1/(1-q))*

*qα_evoHill-R=[sum_j w_j sum_k L_k (a_jk/(sum_k L_k a_jk))^q]^(1/(1-q))*

`hillCJC`

(Chiu et al. (2014) decomposition of phylogenetic diversity into alpha, beta, gamma components, see Supplementary material Appendix 2 in Pavoine (2016) for a justification of the formulas):

*qγ_evoHill=[sum_k L_k (sum_j w_j a_jk/(sum_k L_k a_jk))^q]^(1/(1-q))*

*qα_evoHill-CJC=(1/m)*[sum_k L_k sum_j (w_j)^q (a_jk/(sum_k L_k a_jk))^q]^(1/(1-q))*

Then option `"additive"`

calculates *β* diversity as *γ-α*.
Option `"proportional"`

calculates *β* as *(γ-α)/γ*.
Option `"multiplicative"`

calculates *β* diversity as *γ/α*.
Only for `method`

=`"hillCJC"`

, options `"C"`

, `"U"`

, `"V"`

, `"S"`

, use the multiplicative option and also calculate one of the transformations introduced by Chiu et al. (2014): indices *1-C_qm*, *1-U_qm*, *1-V_qm*, and *1-S_qm*, respectively. `"Renyi"`

is the *qevoD_Renyi* index introduced in Pavoine (2016), see also Supplementary material Appendix 1 in Pavoine (2016).

The weights of the sites (argument `w`

) can be `"even"`

(even weights), `"evoab"`

(proportional to the summed abundances of all evolutionary units), or `"speciesab"`

(proportional to the summed abundances of all species). Note that if the phylogenetic tree is ultrametric (the distance from any species to the root is constant), then options `"evoab"`

and `"speciesab"`

are equivalent.

If only one value of `q`

is given, abgevodivparam returns a vector with alpha, beta, and gamma diversities.
If more than one value of `q`

is given, it returns a list of two objects:

`q` |
the numeric vector of values for |

`div` |
a data frame with alpha, beta, gamma calculated for all values of |

Only if `method`

=`"hillCJC"`

and `option`

= `"C"`

, `"U"`

, `"V"`

, `"S"`

, or `"Renyi"`

, the index *1-C_qm* (for `"C"`

), *1-U_qm* (for `"U"`

), *1-V_qm* (for `"V"`

), *1-S_qm* (for `"S"`

) or the Renyi transformation (see above, for `"Renyi"`

is also provided in the `div`

data frame under the name "transformed.beta".

The function `plot.abgevodivparam`

returns a graphic.

Sandrine Pavoine sandrine.pavoine@mnhn.fr

The methodologies and scripts were presented in

Pavoine, S. (2016) A guide through a family of phylogenetic dissimilarity measures among sites. *Oikos*, **125**, 1719–1732.

using earlier work by

Daroczy, Z. (1970) Generalized information functions. *Information and Control*, **16**, 36–51.

Havrda, M., Charvat F. (1967) Quantification method of classification processes: concept of structural alpha-
entropy. *Kybernetik*, **3**, 30–35

Hill, M.O. (1973) Diversity and evenness: a unifying notation and its consequences. *Ecology*, **54**, 427–432.

Routledge, R.D. (1979) Diversity indices: which ones are admissible? *Journal of Theoretical Biology*, **76**, 503–515.

Rao, C.R. (1986) Rao's axiomatization of diversity measures. In: Kotz S, Johnson NL, editors. *Encyclopedia of Statistical Sciences*. New York: Wiley and Sons. pp. 614–617.

Chiu, C.-H., Jost, L., Chao, A. (2014) Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers. *Ecological Monographs*, **84**, 21–44.

`evodiss`

, `divparam`

, `evodivparam`

## Not run: if(require(ape)){ data(batcomm) phy <- read.tree(text=batcomm$tre) ab <- batcomm$ab[,phy$tip.label] abgevodivparam(phy, ab) plot(abgevodivparam(phy, ab)) abgevodivparam(phy, ab, q=0:4) plot(abgevodivparam(phy, ab, q=0:4)) } ## End(Not run)

[Package *adiv* version 2.1.1 Index]