On 06/11/15 04:33, Rob Sargent wrote:
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!
You're actually going 'DOWN' the tree, in terms of how trees are used in
computer science & graph theory!
See http://www.mathcove.net/petersen/lessons/get-lesson?les=32
Cheers,
Gavin
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