getAccRegion {poweRbal}

Functions for computing the region of acceptance

Description

getAccRegion - Computes the region of acceptance based on quantiles for a specified level of significance and method. The critical region is everything strictly outside this interval, i.e., the interval limits still belong to the acceptance region.

getAccRegion_data - Computes the region of acceptance for the given TSS values based on quantiles for a specified level of significance and method. The critical region is everything strictly outside this interval, i.e., the interval limits still belong to the acceptance region.

Usage

getAccRegion(
  tss,
  null_model = "yule",
  n,
  distribs = "sampled",
  sample_size = 1000L,
  test_type = "two-tailed",
  sig_lvl = 0.05
)

getAccRegion_data(tss_data, test_type = "two-tailed", sig_lvl = 0.05)

Arguments

tss

Vector containing the names (as character) of the tree shape statistics that should be compared. You may either use the short names provided in tssInfo to use the already included TSS, or use the name of a list object containing similar information as the entries in tssInfo. Example:
Use "new_tss" as the name for the list object new_tss containing at least the function new_tss$func = function(tree){...}, and optionally also the information new_tss$short, new_tss$simple, new_tss$name, new_tss$type, new_tss$only_binary, and new_tss$safe_n.

null_model

The null model that is to be used to determine the power of the tree shape statistics. In general, it must be a function that produces rooted binary trees in phylo format.
If the respective model is included in this package, then specify the model and its parameters by using a character or list. Available are all options listed under parameter tm in the documentation of function genTrees (type ?genTrees).
If you want to include your own tree model, then use the name of a list object containing the function (with the two input parameters n and Ntrees). Example:
Use "new_tm" for the list object new_tm <- list(func = function(n, Ntrees){...}).

n

Integer value that specifies the desired number of leaves, i.e., vertices with in-degree 1 and out-degree 0.

distribs

Determines how the distributions and quantiles are computed. Available are:

• "sampled" (default): sample_size many trees are sample under the respective models to determine the quantiles for the null model and how many trees under the alternative models lie outside.

sample_size

Sample size (integer >=10) if distributions are sampled (default= 1000L).

test_type

Determines the method. Available are:

• "two-tailed" (default)

sig_lvl

Level of significance (default=0.05, must be >0 and <1).

tss_data

Numeric matrix of TSS values (one row per TSS). The row names are used as names for the TSS.

Value

getAccRegion Numeric matrix (one row per TSS) with two columns for the interval limits of the acceptance region.

getAccRegion_data Numeric matrix (one row per TSS) with two columns for the interval limits of the acceptance region.

Author(s)

Sophie Kersting

Examples

getAccRegion(tss = c("Sackin", "Colless", "B1I"), n = 8L, sample_size = 100L)
getAccRegion_data(getTSSdata(tss = c("Colless", "Sackin"), n = 8L,
                             Ntrees = 20L, tm = "yule"))