Diversity index

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Question

How to calculate diversity indices?

Answer

Use the function diversity to calculate the most common indices. These parameters are used:

  • amount: the number (or proportion) of individuals of a species in a transect.
  • species: an identifier for a species
  • transect: an identifier for a transect
  • q: exponent for the diversity calculation


Amount, species, and transect are vectors (i.e. ordered sets of values). The parameters can be given to the function in several different ways. This is hopefully practical for the user.

  • Amount, species, and transect must be of same length.
  • If parameter names are not used (e.g. diversity(param1, param2, param3)), it is assumed that they are given in this order: amount, species, transect, q.
  • If individual data is given using species identifiers, it the parameter name must be given: diversity(species = param1).
  • The following default values are used for parameters:
    • Amount: 1 for each species, i.e. each species is equally abundant.
    • Species: 1, 2, 3, ... n, where n = number of rows in data, i.e. each row is a different species.
    • Transect: 1, i.e. there is only one transect.
    • q: q.wiki. You MUST define an object q.wiki before using diversity, otherwise alpha diversities will be calculated wrong. q.wiki can be a single number or a vector of numbers.


There are several ways to upload your data so that you can use the diversity function.

  • Upload your data to Opasnet Base and call for the data using op_baseGetData function.
  • Upload a CSV file to Opasnet using Special:Upload and call for the data using opasnet.data function.
  • Use Example 1 code below to enter your data. The data must be in format c(4,6,2,5,7,4,3,9) where the values are either
    • identifiers of the species 1,2,3... in which the individuals belong (one entry per individual), or
    • abundancies of species, i.e. proportions or amounts of individuals belonging to each species among the whole population (one entry per species).

Rationale

Actual function diversity

Initiate functions

+ Show code

The function diversity produces a list where the first, second, and third element are the gamma, the alpha, and transect-specific gamma diversities, respectively.

Function diversity.table produces a data.frame of several diversity indices.

Examples

Example 1 to use function

Give your data in R format or leave empty for example data:

Is your data individual data or group abundancies?:

+ Show code

Example 2

Select your data:

Which q values you want to calculate.:
0
0.5
1
2
3
6

+ Show code

The data should be given in R format as a list of values in parenthesis, beginning with c:

c(3,5,3,5,2,1,3,3,4,2) or equivalently c(0.1,0.2,0.4,0.1,0.2)

where the values are either

  • identifiers of the species 1,2,3... in which the individuals belong (one entry per individual), or
  • abundancies of species, i.e. proportions of individuals belonging to each species among the whole population (one entry per species).

Calculations


Diversity indices are thoroughly described in Wikipedia.

See also

References


Related files

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