Script 01_Taxonomic scope?

[CecSve]

Should we carry out analysis for Class = Insecta only or should we include Arachnids and some other arthropod classes as well, or just stick to flying invertebrates (which may be difficult to pin point)? We should at least remove the weird ones:

• Phylum = Cnidaria (e.g. jelly fish)
• Phylum = Nemertea (worms, unsure whether some species could be associated with insects?)
• Class = Pycnogonida (sea spiders)
• Class = Polychaeta (we have one marine species in the taxonomy list)
• Class = Turbellaria (again a marine species)
• Kingdom = Protista
• Phylum = Onychophora (velvet worm, would be super cool if we found one, but they all live in the southern hemisphere and are extinct in the north)
• Phylum = Rotifera
• Phylum = Chordata (we have wild boar, cows, human and wolf/dog)
• Order = Isopoda
• Order = Decapoda
• Class = Malacostraca (would take care of Decapoda and Isopoda)

[bowlerbear]

ooh exciting! I would do insects + spiders. Spiders at least balloon, so reasonable to catch them in the air.

[CecSve]

I will only include Arachnida and Insecta. Here's a list of all the unique IDs by class level.

unique(taxonomy_cleaned$class) [1] "Arachnida" "Insecta" NA "Florideophyceae" [5] "Chromadorea" "Gastropoda" "Mammalia" "Oomycota"
[9] "Malacostraca" "Hydrozoa" "Monogononta" "Enoplea"
[13] "Demospongiae" "Scyphozoa" "Collembola" "Diplopoda"
[17] "Haptoglossa" "Bdelloidea" "Crinoidea" "Clitellata"
[21] "Eutardigrada" "Aves" "Anthozoa" "Bangiophyceae"
[25] "Branchiopoda" "Polychaeta" "Hoplonemertea" "Onychophorida"
[29] "Pycnogonida" "Protura" "Turbellaria" "Amphibia"
[33] "Actinopterygii" "Palaeonemertea" "Myzocytiopsis" "Cubozoa"
[37] "Cestoda"

[CecSve]

script_01 is now ready for your taxize magic @bowlerbear - you can add it from line 186! We need to make sure the # of obs is the same between the asv table and the taxonomy table prior to analysis, but I can make that minor change once you have included the taxize step.

[CecSve]

We analyse on insects and spiders