plotPerm: Plot for comparison of actual model fitness vs...

In MUVR2: Multivariate Methods with Unbiased Variable Selection

Plot for comparison of actual model fitness vs permutation/resampling

Description

Plots histogram of null hypothesis (permutation/resampling) distribution, actual model fitness and cumulative p-value. Plot defaults to "greater than" or "smaller than" tests and cumulative probability in Student's t-distribution.

Usage

plotPerm(
  actual,
  distribution,
  xlab = NULL,
  side = c("greater", "smaller"),
  type = "t",
  ylab = NULL,
  xlim,
  ylim = NULL,
  breaks = "Sturges",
  pos,
  main = NULL,
  permutation_visual = "none",
  curve = TRUE,
  extend = 0.1,
  multiple_p_shown = NULL,
  show_actual_value = TRUE,
  show_p = TRUE,
  round_number = 4
)

Arguments

actual	Actual model fitness (e.g. Q2, AUROC or number of misclassifications)
distribution	Null hypothesis (permutation) distribution of similar metric as 'actual'
xlab	Label for x-axis (e.g. 'Q2 using real value',"Q2 using distributions","BER" 'AUROC', or 'Misclassifications')
side	Cumulative p either "greater" or "smaller" than H0 distribution (defaults to side of median(H0))
type	c('t','non',"smooth","rank","ecdf")
ylab	label for y-axis
xlim	Choice of user-specified x-limits (if default is not adequate)
ylim	Choice of user-specified y-limits (if default is not adequate)
breaks	Choice of user-specified histogram breaks (if default is not adequate)
pos	Choice of position of p-value label (if default is not adequate)
main	Choice of user-specified plot title
permutation_visual	choice of showing median or mean or none
curve	if add curve or not base on the mid
extend	how many percenrtage of the orignical range do we start
multiple_p_shown	show many p values
show_actual_value	show the actual value on the vertical line or not
show_p	if p value is added to the figure
round_number	How many digits does it keep

Value

Plot

Examples

data("freelive2")
actual <- sample(YR2, 1)
distribution <- YR2
plotPerm (actual, distribution)

MUVR2 documentation built on Sept. 16, 2024, 9:06 a.m.