Robinson-Foulds {TreeDist} | R Documentation |
Robinson–Foulds distances, with adjustments for phylogenetic information content
Description
Calculate the Robinson–Foulds distance
(Robinson and Foulds 1981), or
the equivalent similarity measure, with options to
(i) annotate matched splits;
(ii) weight splits according to their phylogenetic information content
(Smith 2020).
Whilst slower to calculate, information theoretic modifications of the
Robinson–Foulds distance (see TreeDistance()
)
are better suited to most use cases
(Smith 2020, 2022).
Usage
InfoRobinsonFoulds(
tree1,
tree2 = NULL,
similarity = FALSE,
normalize = FALSE,
reportMatching = FALSE
)
InfoRobinsonFouldsSplits(
splits1,
splits2,
nTip = attr(splits1, "nTip"),
reportMatching = FALSE
)
RobinsonFoulds(
tree1,
tree2 = NULL,
similarity = FALSE,
normalize = FALSE,
reportMatching = FALSE
)
RobinsonFouldsMatching(
tree1,
tree2,
similarity = FALSE,
normalize = FALSE,
...
)
RobinsonFouldsSplits(
splits1,
splits2,
nTip = attr(splits1, "nTip"),
reportMatching = FALSE
)
Arguments
tree1 , tree2 |
Trees of class |
similarity |
Logical specifying whether to report the result as a tree similarity, rather than a difference. |
normalize |
If a numeric value is provided, this will be used as a
maximum value against which to rescale results.
If |
reportMatching |
Logical specifying whether to return the clade matchings as an attribute of the score. |
splits1 , splits2 |
Logical matrices where each row corresponds to a leaf,
either listed in the same order or bearing identical names (in any sequence),
and each column corresponds to a split, such that each leaf is identified as
a member of the ingroup ( |
nTip |
(Optional) Integer specifying the number of leaves in each split. |
... |
Not used. |
Details
Note that if reportMatching = TRUE
, the pairScores
attribute returns
a logical matrix specifying whether each pair of splits is identical.
InfoRobinsonFoulds()
calculates the tree similarity or distance by summing
the phylogenetic information content of all splits that are (or are not)
identical in both trees. Consequently, splits that are more likely
to be identical by chance alone make a smaller contribution to overall
tree distance, because their similarity is less remarkable.
Rapid comparison between multiple pairs of trees employs the Day (1985) linear-time algorithm.
Value
RobinsonFoulds()
and InfoRobinsonFoulds()
return an array of numerics providing the
distances between each pair of trees in tree1
and tree2
,
or splits1
and splits2
.
Functions
-
RobinsonFouldsMatching()
: Matched splits, intended for use withVisualizeMatching()
.
Normalization
-
RobinsonFoulds()
is normalized against the total number of splits that are present. -
InfoRobinsonFoulds()
is normalized against the sum of the phylogenetic information of all splits in both trees, treated independently.
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
References
Day WHE (1985).
“Optimal algorithms for comparing trees with labeled leaves.”
Journal of Classification, 2(1), 7–28.
doi:10.1007/BF01908061.
Robinson DF, Foulds LR (1981).
“Comparison of phylogenetic trees.”
Mathematical Biosciences, 53(1-2), 131–147.
doi:10.1016/0025-5564(81)90043-2.
Smith MR (2020).
“Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees.”
Bioinformatics, 36(20), 5007–5013.
doi:10.1093/bioinformatics/btaa614.
Smith MR (2022).
“Robust analysis of phylogenetic tree space.”
Systematic Biology, 71(5), 1255–1270.
doi:10.1093/sysbio/syab100.
See Also
Display paired splits: VisualizeMatching()
Other tree distances:
JaccardRobinsonFoulds()
,
KendallColijn()
,
MASTSize()
,
MatchingSplitDistance()
,
NNIDist()
,
NyeSimilarity()
,
PathDist()
,
SPRDist()
,
TreeDistance()
Examples
# For BalancedTree, PectinateTree, as.phylo:
library("TreeTools", quietly = TRUE)
balanced7 <- BalancedTree(7)
pectinate7 <- PectinateTree(7)
RobinsonFoulds(balanced7, pectinate7)
RobinsonFoulds(balanced7, pectinate7, normalize = TRUE)
VisualizeMatching(RobinsonFouldsMatching, balanced7, pectinate7)
InfoRobinsonFoulds(balanced7, pectinate7)
VisualizeMatching(InfoRobinsonFoulds, balanced7, pectinate7)