| Version: | 0.60-35 |
| Date: | 2016-02-29 |
| Title: | Jack-Knife Support for Evolutionary Distinctiveness Indices I and W |
| Author: | Daniel R. Miranda-Esquivel |
| Maintainer: | Daniel R. Miranda-Esquivel <dmiranda@uis.edu.co> |
| Depends: | ape |
| Description: | These functions calculate the taxonomic measures presented in Miranda-Esquivel (2016). The package introduces Jack-knife resampling in evolutionary distinctiveness prioritization analysis, as a way to evaluate the support of the ranking in area prioritization, and the persistence of a given area in a conservation analysis. The algorithm is described in: Miranda-Esquivel, D (2016) <doi:10.1007/978-3-319-22461-9_11>. |
| License: | GPL-3 |
| URL: | https://github.com/Dmirandae/jrich |
| BugReports: | https://github.com/Dmirandae/jrich/issues |
| LazyData: | false |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2016-03-06 04:22:27 UTC; rafael |
| Repository: | CRAN |
| Date/Publication: | 2016-03-06 17:50:38 |
Jack-knife indices in a single topology m times and evaluates a success rule.
Description
The function jack-knifes the terminals and calculates the indices value m (=replicates) times.
Usage
Best.Index(tree = tree, distribution = distribution, jtip = jtip,
replicates = replicates, success = c(success))
Arguments
tree |
is a single tree with n terminals, an ape phylo object. |
distribution |
species distributions in n areas, a data.frame |
jtip |
is the proportion of terminals to delete, real (range 0-1). |
replicates |
is the number of replicates, an integer. |
success |
the measure of the success, a vector. |
Value
The function returns the success that correspond to obtain the same ranking for X,Y positions, established as the vector success (by default success)).
The function returns the success that corresponds to obtain the same ranking for X,Y positions, established as the vector success (by default success))
Author(s)
Miranda-Esquivel Daniel R.
Examples
library(jrich)
data(tree)
data(distribution)
Best.Index(tree = tree, distribution = distribution, jtip =0.5, replicates =10, success=1)
Indices values and Jack-knife indices for a single topology.
Description
The funtion calculates standard and terminal jack-knifed indices I and W [see Miranda-Esquivel 2016], along with Posadas et al. 2001 modifications.
Usage
Calculate.Index(tree = tree, distribution = distribution, jtip = 0,
verbose = TRUE, standard = "distribution")
Arguments
tree |
is a single tree with n terminals, an ape phylo object. |
distribution |
species distributions in n areas, a data.frame |
jtip |
is the proportion of terminals to delete, real (range 0-1). |
verbose |
Boolean. If TRUE, the output reports the number of deleted terminals/topologies. |
standard |
"distribution" or "tree" to standarize by the by the sum of indices in the distribution or the sum of indices in the tree |
Author(s)
Miranda-Esquivel Daniel R.
Examples
library(jrich)
data(tree)
data(distribution)
## Standarized by the sum of indices in the distribution
Calculate.Index(tree=tree, distribution = distribution, verbose=TRUE, standard = "distribution")
## Standarized by the sum of indices in the tree (as figure 1 in Miranda-Esquivel 2016)
Calculate.Index(tree=tree, distribution = distribution, verbose=TRUE, standard = "tree")
Children of a node.
Description
Get the children of a node in a tree.
Usage
Children(tree = tree, node = node)
Arguments
tree |
is a single tree with n terminals, an ape phylo object. |
node |
representing the node in APE notation,is an integer. |
Value
The children nodes of the internal node; in most cases, two integers.
Author(s)
Miranda-Esquivel Daniel R.
Examples
library(jrich)
data(tree)
Children(tree,7)
I index value for a single topology.
Description
This function assigns the same weight to sister clades (see Van-Wright et al., 1981). The input tree is reordered in post order.
Usage
IndexI(tree = tree)
Arguments
tree |
is a single tree with n terminals, an ape phylo object. |
Value
Returns a vector with weights.
Author(s)
Miranda-Esquivel Daniel R.
Examples
library(jrich)
data(tree)
plot(tree)
indexi <- IndexI(tree)
newTree <- tree
newTree$tip.label <- indexi
plot(newTree)
W index value for a single topology.
Description
This function assigns the weight according to the ramification patterns (see Van-Wright et al., 1981). The input tree is reordered in post order. Returns a vector with weights.
Usage
IndexW(tree = tree)
Arguments
tree |
is a single tree with n terminals, an ape phylo object. |
Author(s)
Miranda-Esquivel Daniel R.
Examples
library(jrich)
data(tree)
plot(tree)
indexw <- IndexW(tree)
newTree <- tree
newTree$tip.label <- indexw
plot(newTree)
Jack-knife indices in n topologies one time.
Description
The function calculates the indices values for a MultiData list one time.
Usage
Multi.Index.Calc(MultiData = MultiData, jtip = 0, jtopol = 0)
Arguments
MultiData |
is the list of Trees and distributions to evaluate, a list object. |
jtip |
is the proportion of terminals to delete, real (range 0-1). |
jtopol |
is the proportion of topologies to delete, real (range 0-1). |
Value
Returns the indices values.
Author(s)
Miranda-Esquivel Daniel R.
Examples
## get the library
library(jrich)
## load the data
data(Multitaxon1)
Multi.Index.Calc(Multitaxon1, jtip = 0, jtopol = 0)
Jack-knife indices in n topologies m times.
Description
The function calculates the indices values for a MultiData list m (=replicates) times
Usage
Multi.Jack(MultiData = MultiData, times = 100, jtip = 0, jtopol = 0)
Arguments
MultiData |
is the list of Trees and distributions to evaluate, a list object. |
times |
in the number of times to repeat the process, an integer. |
jtip |
is the proportion of terminals to delete, real (range 0-1). |
jtopol |
is the proportion of topologies to delete, real (range 0-1). |
Author(s)
Miranda-Esquivel Daniel R.
Examples
## get the library
library(jrich)
## load the data
data(Multitaxon1)
Multi.Jack(Multitaxon1, jtip=0.25)
Multitaxon example.
Description
A multitaxon example with two hypothetical taxa / distributions
Usage
Multitaxon1
Format
A list with two objects, each with an APE object, class phylo and the distribution of the terminals.
Author(s)
Miranda-Esquivel Daniel R.
Rank indices.
Description
Renk indices according to the areas' absolute position. If the index value is empty, the function assigns a dummy position "X0X"
Usage
Rank.Indices(index.Value = index.Value)
Arguments
index.Value |
a table with indices values. |
Value
a table with the decreasing order of the areas It presents the ties alphabetically
Author(s)
Miranda-Esquivel Daniel R.
Examples
## get the library
library(jrich)
## load the data
data(tree)
data(distribution)
Rank.Indices(Calculate.Index(tree=tree, distrib = distribution, verbose=FALSE))
Read distributions.
Description
Read distributions as a csv with two columns species and area
Usage
Read.Data(data.File)
Arguments
data.File |
a csv file to read |
Value
a data.frame object with the distribution by species
Author(s)
Miranda-Esquivel Daniel R.
Sums two tables with indices values.
Description
You input two tables with indices and it function returns a single table with the sum.
Usage
Sum.Indices.2.Topologies(indices1 = indices1, indices2 = indices2)
Arguments
indices1 |
a table of indices values. |
indices2 |
a table of indices values. |
Value
a single table with the sum of the two indices.
Author(s)
Miranda-Esquivel Daniel R.
Examples
## get the library
library(jrich)
## load the data
data(Multitaxon1)
## calculate indices for two trees and their distributions
temp.Index.Value1 <- Calculate.Index(tree = Multitaxon1[[1]][[1]],
distribution = Multitaxon1[[1]][[2]],0)
temp.Index.Value2 <- Calculate.Index(tree = Multitaxon1[[2]][[1]],
distribution = Multitaxon1[[2]][[2]],0)
## sum the indices values
Sum.Indices.2.Topologies(temp.Index.Value1, temp.Index.Value2)
Distribution of five taxa.
Description
A data frame with five species distributions in eight areas, following Miranda-Esquivel (2016).
Usage
distribution
Format
A data.frame object with eight areas (columns) and five species (rows)
Author(s)
Miranda-Esquivel Daniel R.
A tree and the distribution of the taxa.
Description
A list with two objects: Taxon[[1]]: A tree as an APE object with five terminals and Taxon[[2]]: A data frame with five species distributions in eight areas, following Miranda-Esquivel (2016).
Usage
taxon1
Format
A list with two objects
Author(s)
Miranda-Esquivel Daniel R.
A tree with five terminals.
Description
A tree as an APE object with five terminals, following Miranda-Esquivel (2016).
Usage
tree
Format
An APE object, class phylo. A tree dataset with five terminals.
Author(s)
Miranda-Esquivel Daniel R.