showTSSdata {poweRbal}

Functions for displaying TSS distributions and TSS power

Description

showTSSdata - This function plots histograms of TSS data.

showPower - This function displays the power of TSS under different alternative models.

showPower_param - This function displays the power of TSS under different representatives of a family of tree models which vary only in one parameter.

Usage

showTSSdata(
  tss_data,
  main = NULL,
  xlab = NULL,
  test_type = "two-tailed",
  sig_lvl = 0.05,
  ...
)

showPower(
  power_data,
  tss_names = NULL,
  tss_colors = NULL,
  model_names = NULL,
  sig_lvl = 0.05,
  ...
)

showPower_param(
  power_data,
  tss_names = NULL,
  tss_colors = NULL,
  tss_ltys = NULL,
  model_name = NULL,
  model_param,
  sig_lvl = 0.05,
  ...
)

Arguments

tss_data

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

main

Title (default = NULL). A generic title is created by default.

xlab

Label of x-axis (default = NULL). A generic label is created by default.

test_type

Determines the method. Available are:

• "two-tailed" (default)

sig_lvl

Level of significance (default=0.05, must be >0 and <1). NO horizontal line is depicted if set to NULL.

...

Add further specifications for plot().

power_data

Numeric matrix, one row per TSS and one column per alternative model.

tss_names

Vector of characters/expression of the TSS names (default = NULL). If none are provided, the row names of power_data are used as names for the TSS.

tss_colors

Vector of colors for the TSS (default = NULL).

model_names

Vector of characters/expression of the model names (default = NULL). If none are provided, the column names of power_data are used as names for the models.

tss_ltys

Vector of line types for the TSS (default = NULL).

model_name

Vector of characters/expressions of the name of the tree model family and of the parameter (default = NULL), e.g. c("Aldous\'", expression(beta)). If none are provided, the first column name of power_data is used.

model_param

Numeric vector containing the parameter values of the representatives of the tree model.

Value

showTSSdata No return value, called for side effects (plotting).

showPower No return value, called for side effects (plotting).

showPower_param No return value, called for side effects (plotting).

Author(s)

Sophie Kersting

Examples

showTSSdata(tss_data = getTSSdata_trees(tss = c("Colless", "Sackin"),
                treeList = lapply(1:20L, function(x) genYuleTree(10))),
                breaks=15)
# With error bars:
showPower(power_data = powerComp(tss = c("Sackin", "Colless", "B1I"),
                                     alt_models = list("pda", "etm"), n=10L,
                                     sample_size = 50L,
                                     with_CIradius = TRUE),
              tss_names = getTSSnames(c("Sackin", "Colless", "B1I")),
              tss_colors = getTSScolors(c("Sackin", "Colless", "B1I")),
              model_names = c("PDA", "ETM"),
              main = "Power (Yule as null model, n = 10, N=50)",
              ylim = c(0,1), ylab = "Power (null model rejected)")
# Without error bars:
showPower(power_data = powerComp(tss = c("Sackin", "Colless", "B1I"),
                                     alt_models = list("pda", "etm"), n=10L,
                                     sample_size = 50L),
              tss_names = getTSSnames(c("Sackin", "Colless", "B1I")),
              tss_colors = getTSScolors(c("Sackin", "Colless", "B1I")),
              model_names = c("PDA", "ETM"),
              main = "Power (Yule as null model, n = 10, N=50)",
              ylim = c(0,1), ylab = "Power (null model rejected)")
# With confidence bands:
showPower_param(power_data = powerComp(tss = c("Sackin", "Colless", "B1I"),
                                   alt_models = list(list("aldous", 0.5),
                                   list("aldous", 0),list("aldous", -0.5),
                                   list("aldous", -1),list("aldous", -1.5)),
                                   n=20L, sample_size = 50L,
                                   with_CIradius = TRUE),
              tss_names = getTSSnames(c("Sackin", "Colless", "B1I")),
              tss_colors = getTSScolors(c("Sackin", "Colless", "B1I")),
              model_name = c("Aldous-beta splitting model", "beta"),
              model_param = c(0.5,0,-0.5,-1,-1.5),
              ylim = c(0,1), ylab = "Power (null model rejected)")
# Without confidence bands:
showPower_param(power_data = powerComp(tss = c("Sackin", "Colless", "B1I"),
                                   alt_models = list(list("aldous", 0.5),
                                   list("aldous", 0),list("aldous", -0.5),
                                   list("aldous", -1),list("aldous", -1.5)),
                                   n=20L, sample_size = 50L),
              tss_names = getTSSnames(c("Sackin", "Colless", "B1I")),
              tss_colors = getTSScolors(c("Sackin", "Colless", "B1I")),
              model_name = c("Aldous-beta splitting model", "beta"),
              model_param = c(0.5,0,-0.5,-1,-1.5),
              ylim = c(0,1), ylab = "Power (null model rejected)")