Package 'BET' reference manual

Title:	Binary Expansion Testing
Description:	Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Wan Zhang, Zhigen Zhao, Wen Zhou. (2023). BEAUTY Powered BEAST, <doi:10.48550/arXiv.2103.00674> and Wan Zhang, Zhigen Zhao, Michael Baiocchi, Yao Li, Kai Zhang. (2023) SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables, Techinical report.
Authors:	Wan Zhang [aut, cre], Zhigen Zhao [aut], Michael Baiocchi [aut], Kai Zhang [aut]
Maintainer:	Wan Zhang <[email protected]>
License:	GPL
Version:	0.5.4
Built:	2024-11-09 03:21:06 UTC
Source:	https://github.com/cran/BET

Binary Expansion Adaptive Symmetry Test

Description

BEAST (Binary Expansion Adaptive Symmetry Test) is used for nonparametric detection of nonuniformity or dependence.

Usage

BEAST(
  X,
  dep,
  subsample.percent = 1/2,
  B = 100,
  unif.margin = FALSE,
  lambda = NULL,
  index = list(c(1:ncol(X))),
  method = "p",
  num = NULL
)
BEAST(
  X,
  dep,
  subsample.percent = 1/2,
  B = 100,
  unif.margin = FALSE,
  lambda = NULL,
  index = list(c(1:ncol(X))),
  method = "p",
  num = NULL
)

Arguments

`X`	a matrix to be tested.
`dep`	depth of the binary expansion for the `BEAST`.
`subsample.percent`	sample size for subsampling.
`B`	times of subsampling.
`unif.margin`	logicals. If `TRUE` the marginal distribution is known to be Uniform[0,1]. Default is `FALSE`, and empirical cdf transformation will be applied to each marginal distribution.
`lambda`	tuning parameter for soft-thresholding, default to be $\sqrt{\log(2^{p \cdot dep}) / (8n)}.$
`index`	a list of indices. If provided, test the independence among two or more groups of variables. For example, `index = list(c(1,2), c(3)))` refers to test the independence between $(X_1, X_2)$ and $X_3$ . Default to be `list(c(1:p))` to test if the data follow the multivariate uniform distribution over $[0,1]^p$ , where `p = ncol(X)`.
`method`	If `"p"`, then compute null distribution with permutations. If `"s"`, then compute null distribution with simulations. If `"stat"`, only return interaction and BEAST Statistic. The `method = "s"` option is only available for testing uniformity and bivariate independence.
`num`	number of permutations if method == "p" (default to be 100), or simulations if method == "s" (default to be 1000).

Value

`Interaction`	the most frequent interaction among all subsamples.
`BEAST.Statistic`	BEAST statistic.
`Null.Distribution`	simulated null distribution.
`p.value`	simulated p-value.

Examples

## Elapsed times 7.32 secs
## Measured in R 4.0.2, 32 bit, on a processor 3.3 GHz 6-Core Intel Core i5 under MacOS, 2024/9/6
## Not run: 
  x1 = runif(128)
  x2 = runif(128)
  y = sin(4*pi*(x1 + x2)) + 0.8*rnorm(128)
  ##test independence between (x1, x2) and y
  BEAST(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))
  ##test mutual independence among x1, x2 and y
  BEAST(cbind(x1, x2, y), 3, index = list(1, 2, 3))
  
  ##test bivariate uniformity
  x1 = rbeta(128, 2, 4)
  x2 = rbeta(128, 2, 4)
  BEAST(cbind(x1, x2), 3)
  ##test multivariate uniformity
  x1 = rbeta(128, 2, 4)
  x2 = rbeta(128, 2, 4)
  x3 = rbeta(128, 2, 4)
  BEAST(cbind(x1, x2, x3), 3)

## End(Not run)
## Elapsed times 7.32 secs
## Measured in R 4.0.2, 32 bit, on a processor 3.3 GHz 6-Core Intel Core i5 under MacOS, 2024/9/6
## Not run: 
  x1 = runif(128)
  x2 = runif(128)
  y = sin(4*pi*(x1 + x2)) + 0.8*rnorm(128)
  ##test independence between (x1, x2) and y
  BEAST(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))
  ##test mutual independence among x1, x2 and y
  BEAST(cbind(x1, x2, y), 3, index = list(1, 2, 3))
  
  ##test bivariate uniformity
  x1 = rbeta(128, 2, 4)
  x2 = rbeta(128, 2, 4)
  BEAST(cbind(x1, x2), 3)
  ##test multivariate uniformity
  x1 = rbeta(128, 2, 4)
  x2 = rbeta(128, 2, 4)
  x3 = rbeta(128, 2, 4)
  BEAST(cbind(x1, x2, x3), 3)

## End(Not run)

Binary Expansion Testing

Description

The BET package provides functions for nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET).

BET functions

MaxBET symm get.signs cell.counts bet.plot MaxBETs BEAST

Reference(s)

Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, doi:10.1080/01621459.2018.1537921, Kai Zhang, Zhigen Zhao, and Wen Zhou (2021). BEAUTY Powered BEAST, <arXiv:2103.00674> and Wan Zhang, Zhigen Zhao, Michael Baiocchi, Yao Li, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables. Techinical report, 2023.

Plotting Binary Expansion Testing (2-dimensions)

Description

bet.plot shows the cross interaction of the strongest asymmetry, which the BET returns with the rejection of independence null. This function only works for the test on two variables, that is, X can only have two columns. There are $2^{2dep} - 1$ nontrivial binary variables in the $\sigma$ -field and $(2^dep - 1)^2$ of them are cross interactions, whose positive regions are in plotted in white and whose negative regions are plotted in blue. plot.bet shows the cross interaction where the difference of number of observations in the positive and negative region is largest.

Usage

## S3 method for class 'plot'
bet(X, dep, unif.margin = FALSE, cex=0.5, index = list(c(1:ncol(X))), ...)
## S3 method for class 'plot'
bet(X, dep, unif.margin = FALSE, cex=0.5, index = list(c(1:ncol(X))), ...)

Arguments

`X`	a matrix with two columns.
`dep`	depth of BET.
`unif.margin`	logicals. If `TRUE` the marginal distribution is known to be Uniform[0,1]. Default is `FALSE`, and empirical cdf transformation will be applied to each marginal distribution.
`cex`	number indicating the amount by which plotting text and symbols should be scaled relative to the default.
`index`	a list of indices. If provided, test the independence among two or more groups of variables. For example, `index = list(c(1,2))` refers to test data uniformity, `index = list(1, 2)` refers to test independence between $X_1$ and $X_2$ . Default to be `list(c(1:p))`, where `p = ncol(X)`, then test data uniformity.
`...`	graphical parameters to plot

Examples

v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
bet.plot(cbind(X1, X2), 3, index = list(1,2))
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
bet.plot(cbind(X1, X2), 3, index = list(1,2))

Counts the amount of points in each cell after binary expansion.

Description

cell.counts returns the amount of data points in each cell getting from binary expansion.

Usage

cell.counts(X, dep, unif.margin = FALSE)
cell.counts(X, dep, unif.margin = FALSE)

Arguments

`X`	a matrix to be tested.
`dep`	depth of the marginal binary expansions.
`unif.margin`	logicals. If `TRUE` the data has been uniformed based on empirical cumulative distribution function. Default to be `FALSE` and the function uniforms the data.

Value

The result is a dataframe with 2 rows and $2^(p*dep)$ columns, where $p$ is the number of columns of X. The first column is the binary index, the second column is the amount of data points.

Examples

v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
cell.counts(cbind(X1, X2), 3)
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
cell.counts(cbind(X1, X2), 3)

Signs of Colors of all Points for all Interactions

Description

get.signs returns all the signs of colors for each point under all interactions up to depth d in marginal binary expansions for the tests BET and BETs.

Usage

get.signs(X, dep, unif.margin = FALSE)
get.signs(X, dep, unif.margin = FALSE)

Arguments

`X`	a matrix to be tested.
`dep`	depth of the marginal binary expansions.
`unif.margin`	logicals. If `TRUE` the data has been uniformed based on empirical cumulative distribution function. Default to be `FALSE` and the function uniforms the data.

Value

The result is a dataframe with $n$ rows and $2^(p*dep)$ columns, where $p$ is the number of columns of X and $n$ is the number of rows of X. The values of $1$ or $-1$ stand for the sign of color, while the marginal interactions return $0$ .

Examples

v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
get.signs(cbind(X1, X2), 3)
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
get.signs(cbind(X1, X2), 3)

Binary Expansion Testing at a Certain Depth

Description

MaxBET stands for Binary Expansion Testing. It is used for nonparametric detection of nonuniformity or dependence. It can be used to test whether a column vector is [0, 1]-uniformly distributed. It can also be used to detect dependence between columns of a matrix X, if X has more than one column.

Usage

MaxBET(
  X,
  dep,
  unif.margin = FALSE,
  asymptotic = TRUE,
  plot = FALSE,
  index = list(c(1:ncol(X)))
)
MaxBET(
  X,
  dep,
  unif.margin = FALSE,
  asymptotic = TRUE,
  plot = FALSE,
  index = list(c(1:ncol(X)))
)

Arguments

`X`	a matrix to be tested. When `X` has only one column, `BET` will test whether `X` is [0, 1]-uniformly distributed (an error will be given if data is out of range [0, 1]). When `X` has two or more columns, `BET` tests the independence among those column vectors.
`dep`	depth of the binary expansion for the `BET`.
`unif.margin`	logicals. If `TRUE` the marginal distribution is known to be Uniform[0,1]. Default is `FALSE`, and empirical cdf transformation will be applied to each marginal distribution.
`asymptotic`	logicals. If `TRUE` the p-value is computed by asymptotic distribution. Default to be `TRUE`. Ignored if `X` has three or more columns.
`plot`	logicals. If `TRUE`, make the plot of cross interaction of the strongest asymmetry. Default to be `FALSE`. This option only works for X with two columns.
`index`	a list of indices. If provided, test the independence among two or more groups of variables. For example, `index = list(c(1,2), c(3)))` refers to test the independence between $(X_1, X_2)$ and $X_3$ . Default to be `list(c(1:p))`, where `p = ncol(X)`, then test data uniformity.

Details

MaxBET tests the independence or uniformity by considering the maximal magnitude of the symmetry statistics in the $sigma$ -field generated from marginal binary expansions at the depth d.

Value

`Interaction`	a dataframe with $p$ columns, where $p$ is the number of columns of `X`. It displays the interactions where the extreme symmetry statistics happens. For each column in `X`, we use a binary index to indicate binary variables involved in the extreme symmetry statistic.
`Extreme.Asymmetry`	the extreme asymmetry statistics.
`p.value.bonf`	p-value of the test with Bonferroni adjustment.
`z.statistic`	normal approximation of the test statistic.

Examples

##test mutual independence
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
MaxBET(cbind(X1, X2), 3, asymptotic = FALSE, index = list(1,2))

##test independence between (x1, x2) and y
x1 = runif(128)
x2 = runif(128)
y = sin(4*pi*(x1 + x2)) + 0.4*rnorm(128)
MaxBET(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))

##test uniformity
x1 = rbeta(128, 2, 4)
x2 = rbeta(128, 2, 4)
x3 = rbeta(128, 2, 4)
MaxBET(cbind(x1, x2, x3), 3)
##test mutual independence
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
MaxBET(cbind(X1, X2), 3, asymptotic = FALSE, index = list(1,2))

##test independence between (x1, x2) and y
x1 = runif(128)
x2 = runif(128)
y = sin(4*pi*(x1 + x2)) + 0.4*rnorm(128)
MaxBET(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))

##test uniformity
x1 = rbeta(128, 2, 4)
x2 = rbeta(128, 2, 4)
x3 = rbeta(128, 2, 4)
MaxBET(cbind(x1, x2, x3), 3)

Binary Expansion Testing up to a Certain Depth

Description

MaxBETs is used for nonparametric dependence detection. Extended from BET, for a chosen maximal depth d.max, MaxBETs does a sequential test up to d.max and avoids overlapping symmetry statistics in different depths, for all $2 \le d \le d.max$ . The adjustment is done by multiplying the number of interactions which are in the $\sigma$ -field generated by marginal binary expansions at depth $d$ but not in that at depth $d-1$ .

Usage

MaxBETs(
  X,
  d.max = 4,
  unif.margin = FALSE,
  asymptotic = TRUE,
  plot = FALSE,
  index = list(c(1:ncol(X)))
)
MaxBETs(
  X,
  d.max = 4,
  unif.margin = FALSE,
  asymptotic = TRUE,
  plot = FALSE,
  index = list(c(1:ncol(X)))
)

Arguments

`X`	a matrix to be tested. When `X` has only one column, `BETs` will test whether `X` is [0, 1]-uniformly distributed (an error will be given if data is out of range [0, 1]). When `X` has two or more columns, `BETs` tests the independence among those column vectors.
`d.max`	the maximal depth of the binary expansion for `BETs`.
`unif.margin`	logicals. If `TRUE` the marginal distribution is known to be Uniform[0,1]. Default is `FALSE`, and empirical cdf transformation will be applied to each marginal distribution.
`asymptotic`	logicals. If `TRUE` the p-value is computed by asymptotic distribution. Default to be `TRUE`. Ignored if `X` has three or more columns.
`plot`	logicals. If `TRUE`, make the plot of cross interaction of the strongest asymmetry. Default to be `FALSE`. This option only works for X with two columns.
`index`	a list of indices. If provided, test the independence among two or more groups of variables, for example, $(X_1, X_2)$ and $X_3$ .

Value

`bet.s.pvalue.bonf`	the overall p-value on the test.
`bet.s.index`	the interaction that the p-value is minimal.
`bet.s.zstatistic`	normal approximation of the test statistic.

Examples

##test mutual independence
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
MaxBETs(cbind(X1, X2), 3, asymptotic = FALSE, index = list(1,2))

##test independence between (x1, x2) and y
x1 = runif(128)
x2 = runif(128)
y = sin(4*pi*(x1 + x2)) + 0.4*rnorm(128)
MaxBETs(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))

##test uniformity
x1 = rbeta(128, 2, 4)
x2 = rbeta(128, 2, 4)
x3 = rbeta(128, 2, 4)
MaxBETs(cbind(x1, x2, x3), 3)
##test mutual independence
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
MaxBETs(cbind(X1, X2), 3, asymptotic = FALSE, index = list(1,2))

##test independence between (x1, x2) and y
x1 = runif(128)
x2 = runif(128)
y = sin(4*pi*(x1 + x2)) + 0.4*rnorm(128)
MaxBETs(cbind(x1, x2, y), 3, index = list(c(1,2), c(3)))

##test uniformity
x1 = rbeta(128, 2, 4)
x2 = rbeta(128, 2, 4)
x3 = rbeta(128, 2, 4)
MaxBETs(cbind(x1, x2, x3), 3)

Coordinates of Brightest Stars in the Night Sky

Description

This data set collects the galactic coordinates of the 256 brightest stars in the night sky (Perryman et al. 1997). We consider the longitude (x) and sine latitude (y) here.

Usage

data(star)
data(star)

Format

An object of class data.frame with 256 rows and 2 columns.

Examples

data(star)
MaxBETs(cbind(star$x.raw, star$y.raw), asymptotic = FALSE, plot = TRUE, index = list(1,2))
data(star)
MaxBETs(cbind(star$x.raw, star$y.raw), asymptotic = FALSE, plot = TRUE, index = list(1,2))

Symmetry Statistics for all Interactions

Description

symm returns all the symmetry statistics up to depth d in marginal binary expansions for the tests BET and BETs.

Usage

symm(
  X,
  dep,
  unif.margin = FALSE,
  print.sample.size = TRUE
)
symm(
  X,
  dep,
  unif.margin = FALSE,
  print.sample.size = TRUE
)

Arguments

`X`	a matrix to be tested.
`dep`	depth of the marginal binary expansions.
`unif.margin`	logicals. If `TRUE` the data has been uniformed based on empirical cumulative distribution function. Default to be `FALSE` and the function uniforms the data.
`print.sample.size`	logicals. If `TRUE` print the sample size. Default to be `TRUE`.

Value

The result is a dataframe with $(p+2)$ columns, where $p$ is the number of columns of X. The first column gives the binary index for all variables, the next $p$ columns displays all the interactions of respective variables, the last column of Statistics gives the respective symmetry statistic.

Examples

v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
symm(cbind(X1, X2), 3)
v <- runif(128, -pi, pi)
X1 <- cos(v) + 2.5 * rnorm(128, 0, 1/20)
X2 <- sin(v) + 2.5 * rnorm(128, 0, 1/20)
symm(cbind(X1, X2), 3)

Package 'BET'

Help Index

Binary Expansion Adaptive Symmetry Test

Description

Usage

Arguments

Value

Examples

Binary Expansion Testing

Description

BET functions

Reference(s)

Plotting Binary Expansion Testing (2-dimensions)

Description

Usage

Arguments

Examples

Counts the amount of points in each cell after binary expansion.

Description

Usage

Arguments

Value

Examples

Signs of Colors of all Points for all Interactions

Description

Usage

Arguments

Value

Examples

Binary Expansion Testing at a Certain Depth

Description

Usage

Arguments

Details

Value

Examples

Binary Expansion Testing up to a Certain Depth

Description

Usage

Arguments

Value

Examples

Coordinates of Brightest Stars in the Night Sky

Description

Usage

Format

Examples

Symmetry Statistics for all Interactions

Description

Usage

Arguments

Value

Examples