Species position in motif_census_triplets

[david-beauchesne]

There seems to be an issue with the species positions identified with motif_census_triplets(). When I run the analysis, the position numbers are not as identified in the function documentation for the food chains, omnivory, apparent and competitive exploitation. The positions are:
1 2 3 4 5 9 10 11 12 13

> uid <- table64$name_uni %in% unique(table64$name_uni)[-1]
> sort(unique(c(table64$pos_i[uid], table64$pos_j[uid], table64$pos_k[uid])))
  [1]  1  2  3  4  5  9 10 11 12 13

Are those position results normal and should the documentation be adjusted?

[david-beauchesne]

Here is the current classification:

1: exploitative competition bottom
2: exploitative competition top
3: linear chains bottom
4: linear chains middle
5: linear chains top
9: apparent competition bottom
10: apparent competition top
11: omnivory bottom
12: omnivory middle
13: omnivory top

[KevCaz]

Yes, there is a missing piece in the documentation.... So far we actually have 2 different sets of ids: the one you've mentioned and the one for networks with bidirectional interactions that includes 64 possibilities and 30 unique positions. I used the latter nomenclature. And currently there is no conversion table that would identify the 13 unidirectional positions among the 30 bidirectional ones. This needs to be done.