# C.score: Calculates the (normalised) mean number of checkerboard... In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

## Description

Calculates the C-score for all higher-level species; the C-score represents the average number of checkerboard units for each unique species pair.

## Usage

 `1` ```C.score(web, normalise = TRUE, FUN = mean, ...) ```

## Arguments

 `web` A matrix with pollinators as columns and plants as rows. Alternatively, when used on e.g. species occurrences across islands, rows are islands. `normalise` Logical; if `TRUE` (default), the C-score is ranged between 0 (no checkerboards) and 1 (only checkerboards). For `FALSE` the standard value of mean number of checkerboard pairs is returned. This is somewhat awkward for comparing different data sets, that's what the normalisation is for. `FUN` Function to use when summarising the C-scores for each pairwise comparison. Defaults to `mean`, but other useful functions could be `median` (because C-scores are rather skewed) or `hist` (for a nice graph). `...` Options to be passed on to FUN, e.g. na.rm=T for matrices with many zeros and normalise=TRUE.

## Details

As a first step, any quantitative matrix is converted to a binary matrix of presences and absences.

Then, the formula given in Stone and Roberts (1990) is calculated for all species combinations, by calling `designdist` from the package vegan. See code for details.

## Value

Returns whatever the FUN produces as output. Default would be a single value, i.e. the mean C-score of the web.

## Note

The normalisation, since Jan. 2015, is by brute force: the 1s and 0s are distributed for each pairwise comparison for maximum checkerboardness. (The previously used approach was incorrect!) As a consequence, large matrices will take some time to compute.

The minimum is set to 0.

## Author(s)

Carsten F. Dormann

## References

Gotelli, N.J. and Rohde, K. (2002) Co-occurrence of ectoparasites of marine fishes: a null model analysis. Ecology Letters 5, 86–94

Stone, L. and Roberts, A. (1990) The checkerboard score and species distributions. Oecologia 85, 74–79

## Examples

 ```1 2 3 4``` ```m <- matrix(c(1,0,0, 1,1,0, 1,1,0, 0,1,1, 0,0,1), 5,3,TRUE) C.score(m) C.score(m, normalise=FALSE) C.score(m, normalise=FALSE, FUN=print) ```

bipartite documentation built on May 30, 2017, 1:25 a.m.