divparam {adiv} | R Documentation |

The function `divparam`

calculates parametric diversity indices. The parameter controls the relative importance given to rare versus abundant species in a community.
The function `plot.divparam`

plots the results of function `divparam`

.

divparam(comm, method = c("hill", "tsallis", "renyi"), q = 2, tol = 1e-08) ## S3 method for class 'divparam' plot(x, legend = TRUE, legendposi = "topright", axisLABEL = "Diversity", type = "b", col = if (is.numeric(x)) NULL else sample(colors(distinct = TRUE), nrow(x$div)), lty = if (is.numeric(x)) NULL else rep(1, nrow(x$div)), pch = if (is.numeric(x)) NULL else rep(19, nrow(x$div)), ...)

`comm` |
a data frame or a matrix typically with communities as rows, species as columns and abundance as entry. |

`method` |
a string: either "hill" for the Hill numbers (Hill 1973), "tsallis" for the Tsallis or HCDT entropy (Harvda and Charvat 1967; Daroczy 1970; Tsallis 1988), or "renyi" for Renyi's entropy (Renyi 1960). |

`q` |
a positive numeric or a vector of positive numerics that gives values for the |

`tol` |
numeric tolerance threshold: values between -tol and tol are considered equal to zero. |

`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 community. |

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

`axisLABEL` |
a string to display on the main axis of the plot to designate what we are measuring. The default is |

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

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

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

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

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

If only a single value of `q`

is given, function `divparam`

returns a vector with the diversities of the communities. If more than one value of `q`

is given, a list of two objects is returned:

`q` |
the vector of values for |

`div` |
a data frame with the diversities of the communities calculated for all values of |

The function `plot.divparam`

returns a graphic.

Sandrine Pavoine sandrine.pavoine@mnhn.fr

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. *Kybernatica*, **3**, 30–35.

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

Renyi, A. (1960) On measures of entropy and information. *Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability*, **1**, 547–561.

Tsallis, C. (1988) Possible generalization of Boltzmann-Gibbs statistics. *Journal of Statistical Physics*, **52**, 480–487.

data(batcomm) ab <- batcomm$ab plot(divparam(ab)) plot(divparam(ab, q=0:4))

[Package *adiv* version 2.1.1 Index]