Description Usage Arguments Details Value Author(s) References Examples

Sample units without any species result in "NaN" values in the distance matrix for some of the methods of `vegdist`

(vegan). The function replaces "NA" by "0" if both sample units do not contain any species and "NA" by "1" if only one sample unit does not have any species.

1 | ```
dist.zeroes(comm,dist)
``` |

`comm` |
Community data frame with sites as rows, species as columns and species abundance as cell values. |

`dist` |
Distance matrix as calculated with function |

This functions changes a distance matrix by replacing "NaN" values by "0" if both sample units do not contain any species and by "1" if only one sample unit does not contain any species.

Please note that there is a valid reason (deliberate removal of zero abundance values from calculations) that the original distance matrix contains "NaN", so you may not wish to do this transformation and remove sample units with zero abundances from further analysis.

The function provides a new distance matrix where "NaN" values have been replaced by "0" or "1".

Roeland Kindt (World Agroforestry Centre)

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

1 2 3 4 5 6 7 8 |

```
Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
BiodiversityR 2.11-1: Use command BiodiversityRGUI() to launch the Graphical User Interface;
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)
Warning message:
no DISPLAY variable so Tk is not available
Warning messages:
1: In vegdist(matrix, method = "kulc") :
you have empty rows: their dissimilarities may be meaningless in method "kulczynski"
2: In vegdist(matrix, method = "kulc") : missing values in results
1 2 3 4
2 NaN
3 NaN NaN
4 NaN NaN NaN
5 NaN NaN NaN 0.4166667
1 2 3 4
2 0.0000000
3 0.0000000 0.0000000
4 1.0000000 1.0000000 1.0000000
5 1.0000000 1.0000000 1.0000000 0.4166667
```

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