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change AbstractTrees compat #28

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Nov 7, 2022
Merged

change AbstractTrees compat #28

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11670bb
add usage for lca and DataAPI
banhbio Nov 7, 2022
5d0b835
format
banhbio Nov 7, 2022
73b1a48
change AbstractTrees compat (stop abusing type)
banhbio Nov 7, 2022
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2 changes: 1 addition & 1 deletion Project.toml
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Expand Up @@ -10,7 +10,7 @@ InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"

[compat]
AbstractTrees = "0.4.2"
AbstractTrees = "0.4.3"
DataAPI = "1.6"
OrderedCollections = "1"
julia = "1.5"
Expand Down
34 changes: 33 additions & 1 deletion docs/src/man/usage.md
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Expand Up @@ -121,9 +121,11 @@ julia> human = Taxon(9606); gorilla = Taxon(9592); orangutan = Taxon(9600);
juliia> lca(human, gorilla)
207598 [subfamily] Homininae

# lca is a "varargs" function
julia> lca(human, gorilla, orangutan)
9604 [family] Hominidaes

# Vector input is also available
julia> lca([human, gorilla, orangutan])
9604 [family] Hominidae
```
Expand Down Expand Up @@ -224,6 +226,37 @@ julia> lineage[:species]
```

`Between`, `From`, `Until`, `Cols` and `All` selectors are available in more complex rank selection scenarios.
```julia
julia> lineage[Between(:order, :family)]
6-element Lineage{Taxon}:
9443 [order] Primates
376913 [suborder] Haplorrhini
314293 [infraorder] Simiiformes
9526 [parvorder] Catarrhini
314295 [superfamily] Hominoidea
9604 [family] Hominidae

julia> lineage[From(:family)]
4-element Lineage{Taxon}:
9604 [family] Hominidae
207598 [subfamily] Homininae
9605 [genus] Homo
9606 [species] Homo sapiens

julia> lineage[Until(:kingdom)]
5-element Lineage{Taxon}:
1 [no Rank] root
131567 [no rank] cellular organisms
2759 [superkingdom] Eukaryota
33154 [clade] Opisthokonta
33208 [kingdom] Metazoa

julia> lineage[Cols(:superkingdom, :genus, :species)]
3-element Lineage{Taxon}:
2759 [superkingdom] Eukaryota
9605 [genus] Homo
9606 [species] Homo sapiens
```

## Reformat `Lineage`
Reformation of `Linage` to your ranks can be performed by using `reformat()`.
Expand Down Expand Up @@ -328,4 +361,3 @@ julia> taxa .|> Lineage .|> (x -> reformat(x, seven_rank)) .|> (x -> namedtuple
3 │ 2759 [superkingdom] Eukaryota 7711 [phylum] Chordata 40674 [class] Mammalia 9443 [order] Primates 9604 [family] Hominidae 9592 [genus] Gorilla 9593 [species] Gorilla gorilla
4 │ 2157 [superkingdom] Archaea 1655434 [phylum] Candidatus Loki… missing missing missing missing 2053489 [species] Candidatus Lok…
```