On 11/05/2015 04:56 AM, Achilleas Mantzios wrote:
> On 04/11/2015 17:53, Rob Sargent wrote:
>> On 11/04/2015 03:03 AM, Achilleas Mantzios wrote:
>>> Sorry for being kind of late to the party (I was in 2015.PgConf.EU
>>> !!), and not having read
>>> most of the replies, what we have been successfully doing for this
>>> problem for our app
>>> is do it this way :
>>> parents int[] -- where parents stores the path from the node to the
>>> root of the tree
>>> and then have those indexes :
>>> btree (first(parents))
>>> btree (level(parents)) -- length
>>> btree (last(parents))
>>> gin (parents gin__int_ops) -- the most important
>>>
>>> This has been described as "genealogical tree" approach, and works
>>> very good, IMHO much better
>>> than nested sets.
>>>
>> Is there a more complete description of this approach available? By
>> the title one might assume could be applied to populations as opposed
>> to phylogeny (the OP's use case). Does it deal with consanguinity?
>> Does it perform well going "up" the tree (which is of course branched
>> at every level)?
>
> From here https://en.wikipedia.org/wiki/Phylogenetic_tree I assume
> that phylogenetic trees are normal
> trees, and I see no reason why not be modeled with the genealogical
> approach described. The earliest paper
> I based my work on was :
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CCUQFjABahUKEwiR6auUlvnIAhXGvhQKHVyDA-s&url=https%3A%2F%2Fdownload.samba.org%2Fpub%2Funpacked%2Fldb%2Fldb_sqlite3%2Ftrees.ps&usg=AFQjCNEktJsibP435MBki5cdGmO_CzKmwg&sig2=I9yC_tpyeWrEueDJTXbyAA&bvm=bv.106674449,d.d24&cad=rja
>
> Finding the root is O(1). Going "up" the tree or finding common
> ancestry is reduced to the problem
> of finding overlap/intersections/contains/contained between postgresql
> arrays.
>
> The indexes, functions and operators provided by contrib/intarray were
> a basic element for the success of this
> approach.
>
Going "up" a genealogy to me means getting two parents, four
grandparents, 8 great grandparents etc. On a good day, at least when
there are no loops. This isn't, to my understanding, how phylogeny
works (but my genetics degree was thirty year ago) so perhaps I'm still
confused by the titles used. And certainly not to say that your
approach isn't what the OP really needs!