#### fix bug of layoutEqualAngle

xiangpin authored on 06/07/2022 13:33:17
Showing 1 changed files
 ... ... @@ -21,12 +21,14 @@ tree as data.frame with equal angle layout. 21 21  } 22 22  \references{ 23 23  The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm" 24 -in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children 24 +in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein. 25 + 26 +\if{html}{\out{
}}\preformatted{Leafs are subtrees with no children 25 27  Initialise tree using equal angle algorithm 26 28  tree_df = equal_angle(tree) 27 29   28 30  nodes = get list of nodes in tree_df breadth-first 29 31  nodes = remove tip nodes. 30 32   31 -} 33 +}\if{html}{\out{
}} 32 34  }

#### roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
Showing 1 changed files
 ... ... @@ -21,15 +21,12 @@ tree as data.frame with equal angle layout. 21 21  } 22 22  \references{ 23 23  The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm" 24 -in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein. 25 - 26 - 27 -Leafs are subtrees with no children 24 +in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children 28 25  Initialise tree using equal angle algorithm 29 26  tree_df = equal_angle(tree) 30 27   31 28  nodes = get list of nodes in tree_df breadth-first 32 29  nodes = remove tip nodes. 33 30   34 - 31 +} 35 32  }

#### update doc

Guangchuang Yu authored on 02/12/2018 14:13:05
Showing 1 changed files
 ... ... @@ -4,12 +4,14 @@ 4 4  \alias{layoutDaylight} 5 5  \title{Equal daylight layout method for unrooted trees.} 6 6  \usage{ 7 -layoutDaylight(model, branch.length) 7 +layoutDaylight(model, branch.length, MAX_COUNT = 5) 8 8  } 9 9  \arguments{ 10 10  \item{model}{tree object, e.g. phylo or treedata} 11 11   12 12  \item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.} 13 + 14 +\item{MAX_COUNT}{the maximum number of iterations to run (default 5)} 13 15  } 14 16  \value{ 15 17  tree as data.frame with equal angle layout.

#### update docs

Guangchuang Yu authored on 11/10/2018 02:44:13
Showing 1 changed files
 ... ... @@ -4,10 +4,10 @@ 4 4  \alias{layoutDaylight} 5 5  \title{Equal daylight layout method for unrooted trees.} 6 6  \usage{ 7 -layoutDaylight(tree, branch.length) 7 +layoutDaylight(model, branch.length) 8 8  } 9 9  \arguments{ 10 -\item{tree}{phylo object} 10 +\item{model}{tree object, e.g. phylo or treedata} 11 11   12 12  \item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.} 13 13  }

#### clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
 ... ... @@ -1,5 +1,5 @@ 1 1  % Generated by roxygen2: do not edit by hand 2 -% Please edit documentation in R/tidytree.R 2 +% Please edit documentation in R/tree-utilities.R 3 3  \name{layoutDaylight} 4 4  \alias{layoutDaylight} 5 5  \title{Equal daylight layout method for unrooted trees.}

#### geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
 ... ... @@ -31,4 +31,3 @@ nodes = remove tip nodes. 31 31   32 32   33 33  } 34 -

#### update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
 ... ... @@ -31,3 +31,4 @@ nodes = remove tip nodes. 31 31   32 32   33 33  } 34 +

 ... ... @@ -31,4 +31,3 @@ nodes = remove tip nodes. 31 31   32 32   33 33  } 34 -
 1 1 new file mode 100644 ... ... @@ -0,0 +1,34 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/tidytree.R 3 +\name{layoutDaylight} 4 +\alias{layoutDaylight} 5 +\title{Equal daylight layout method for unrooted trees.} 6 +\usage{ 7 +layoutDaylight(tree, branch.length) 8 +} 9 +\arguments{ 10 +\item{tree}{phylo object} 11 + 12 +\item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.} 13 +} 14 +\value{ 15 +tree as data.frame with equal angle layout. 16 +} 17 +\description{ 18 +#' @title 19 +} 20 +\references{ 21 +The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm" 22 +in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein. 23 + 24 + 25 +Leafs are subtrees with no children 26 +Initialise tree using equal angle algorithm 27 +tree_df = equal_angle(tree) 28 + 29 +nodes = get list of nodes in tree_df breadth-first 30 +nodes = remove tip nodes. 31 + 32 + 33 +} 34 +`