distsPerClade: Summarising phylogenetic distances for each clade in a rooted...
In wanyuac/handyR: Handy functions for R programming.
View source: R/phylo__distsPerClade.R
distsPerClade R Documentation
Summarising phylogenetic distances for each clade in a rooted bifurcating phylogenetic tree
Description
This function extracts clades from a rooted bifurcating phylogenetic tree and reports
the minimum, median, and the maximum of phylogenetic distances of each clade. Phylogenetic distances
may be SNP counts (neighbour-joining tree), number of substitutions per site (maximum-likelihood tree),
and so forth. The input tree will be midpoint rooted if it is unrooted.
Usage
distsPerClade(tr, m = NULL, dec = 8, boots = NULL)
Arguments
tr
An input bifurcating phylogenetic tree
m
(Optional) A distance matrix with row and column names matching to tip labels of the input tree
dec
(Optional) Number of decimals kept for distance summaries (default: 8 digits)
boots
(Optional) A data frame of bootstrap values. Format: Node (integer/character values), Bootstrap (floating-point numbers)
Value
A data frame summarising phylogenetic distances for each clade
wanyuac/handyR documentation built on June 10, 2024, 1:24 a.m.
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View source: R/phylo__distsPerClade.R
| distsPerClade | R Documentation |
Summarising phylogenetic distances for each clade in a rooted bifurcating phylogenetic tree
Description
This function extracts clades from a rooted bifurcating phylogenetic tree and reports the minimum, median, and the maximum of phylogenetic distances of each clade. Phylogenetic distances may be SNP counts (neighbour-joining tree), number of substitutions per site (maximum-likelihood tree), and so forth. The input tree will be midpoint rooted if it is unrooted.
Usage
distsPerClade(tr, m = NULL, dec = 8, boots = NULL)
Arguments
tr |
An input bifurcating phylogenetic tree |
m |
(Optional) A distance matrix with row and column names matching to tip labels of the input tree |
dec |
(Optional) Number of decimals kept for distance summaries (default: 8 digits) |
boots |
(Optional) A data frame of bootstrap values. Format: Node (integer/character values), Bootstrap (floating-point numbers) |
Value
A data frame summarising phylogenetic distances for each clade
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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