Description Usage Format Details Methods tested Source References Examples
Distances between each possible pairing of the 945 unrooted seven-leaf trees (equivalent to rooted 6-leaf trees). Following Kendall and Colijn (2016).
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An object of class list
of length 21.
Each list entry is named with the abbreviation of the corresponding tree distance method (see 'Methods tested' below).
Each item in the list contains a 945×945 matrix reporting the distance between each pair of seven-leaf trees. The first 630 trees are pectinate (tree shape 0), the final 315 are balanced (tree shape 1).
pid
: Phylogenetic Information Distance (Smith 2020), normalized
against the phylogenetic information content of the splits in the trees
being compared.
msid
: Matching Split Information Distance (Smith 2020), normalized
against the phylogenetic information content of the splits in the trees
being compared.
cid
: Clustering Information Distance (Smith 2020), normalized
against the entropy of the splits in the trees being compared.
qd
: Quartet divergence (Smith 2019), normalized against its maximum
possible value for n-leaf trees.
nye
: Nye et al. tree distance (Nye et al. 2006), normalized against
the total number of splits in the trees being compared.
jnc2
, jnc4
: Jaccard-Robinson-Foulds distances with k = 2, 4,
conflicting pairings prohibited ('no-conflict'), normalized against
the total number of splits in the trees being compared.
jco2
, jco4
: Jaccard-Robinson-Foulds distances with k = 2, 4,
conflicting pairings permitted ('conflict-ok'), normalized against
the total number of splits in the trees being compared.
ms
: Matching Split Distance (Bogdanowicz & Giaro 2012), unnormalized.
mast
: Size of Maximum Agreement Subtree (Valiente 2009), unnormalized.
masti
: Information content of Maximum Agreement Subtree, unnormalized.
nni_l
, nni_L
, nni_t
, nni_U
, nni_u
:
Lower, best lower, tight upper, best upper, and
upper bounds for nearest-neighbour interchange distance (Li et al. 1996),
unnormalized.
'Best' lower bounds jump sharply when mismatched regions of a tree become
large enough that a tight upper bound cannot be exactly calculated, so
are discontinuous and cannot readily be compared between trees.
spr
: Approximate subtree prune and regraft SPR distance,
unnormalized.
tbr_l
, tbr_u
: Lower and upper bound for tree bisection and reconnection
(TBR) distance, calculated using
TBRDist; unnormalized.
rf
: Robinson-Foulds distance (Robinson & Foulds 1981), unnormalized.
icrf
: Robinson-Foulds distance, splits weighted by phylogenetic
information content (Smith 2020), unnormalized.
path
: Path distance (Steel & Penny 1993), unnormalized.
Scripts used to generate data objects are housed in the
data-raw
directory.
Bogdanowicz2012TreeDist
\insertRefLi1996TreeDist
\insertRefKendall2016TreeDistData
\insertRefNye2006TreeDist
\insertRefRobinson1981TreeDist
\insertRefSmith2019TreeDist
\insertRefSmithDistTreeDist
\insertRefSteel1993TreeDist
\insertRefValiente2009TreeDist
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