Calculate Contrasts of Arrays in Different Methods

Provides five methods to baseline an array and calculate contrast.

Usage

baseline_array(x, along_dim, unit_dims = seq_along(dim(x))[-along_dim], ...)

# S3 method for class 'array'
baseline_array(
  x,
  along_dim,
  unit_dims = seq_along(dim(x))[-along_dim],
  method = c("percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore",
    "subtract_mean"),
  baseline_indexpoints = NULL,
  baseline_subarray = NULL,
  ...
)

Arguments

x: array (tensor) to calculate contrast
along_dim: integer range from 1 to the maximum dimension of x. baseline along this dimension, this is usually the time dimension.
unit_dims: integer vector, baseline unit: see Details.
...: passed to other methods
method: character, baseline method options are: "percentage", "sqrt_percentage", "decibel", "zscore", and "sqrt_zscore"
baseline_indexpoints: integer vector, which index points are counted into baseline window? Each index ranges from 1 to dim(x)[[along_dim]]. See Details.
baseline_subarray: sub-arrays that should be used to calculate baseline; default is NULL (automatically determined by baseline_indexpoints).

Value

Contrast array with the same dimension as x.

Details

Consider a scenario where we want to baseline a bunch of signals recorded from different locations. For each location, we record n sessions. For each session, the signal is further decomposed into frequency-time domain. In this case, we have the input x in the following form: $$session x frequency x time x location$$ Now we want to calibrate signals for each session, frequency and location using the first 100 time points as baseline points, then the code will be $$baseline_array(x, along_dim=3, baseline_window=1:100, unit_dims=c(1,2,4))$$ along_dim=3 is dimension of time, in this case, it's the third dimension of x. baseline_indexpoints=1:100, meaning the first 100 time points are used to calculate baseline. unit_dims defines the unit signal. Its value c(1,2,4) means the unit signal is per session (first dimension), per frequency (second) and per location (fourth).

In some other cases, we might want to calculate baseline across frequencies then the unit signal is $frequency x time$, i.e. signals that share the same session and location also share the same baseline. In this case, we assign unit_dims=c(1,4).

There are five baseline methods. They fit for different types of data. Denote $z$ is an unit signal, $z_0$ is its baseline slice. Then these baseline methods are:

"percentage": $$ \frac{z - \bar{z_{0}}}{\bar{z_{0}}} \times 100\% $$
"sqrt_percentage": $$ \frac{\sqrt{z} - \bar{\sqrt{z_{0}}}}{\bar{\sqrt{z_{0}}}} \times 100\% $$
"decibel": $$ 10 \times ( \log_{10}(z) - \bar{\log_{10}(z_{0})} ) $$
"zscore": $$ \frac{z-\bar{z_{0}}}{sd(z_{0})} $$
"sqrt_zscore": $$ \frac{\sqrt{z}-\bar{\sqrt{z_{0}}}}{sd(\sqrt{z_{0}})} $$

Examples


# Set ncores = 2 to comply to CRAN policy. Please don't run this line
ravetools_threads(n_threads = 2L)


library(ravetools)
set.seed(1)

# Generate sample data
dims = c(10,20,30,2)
x = array(rnorm(prod(dims))^2, dims)

# Set baseline window to be arbitrary 10 timepoints
baseline_window = sample(30, 10)

# ----- baseline percentage change ------

# Using base functions
re1 <- aperm(apply(x, c(1,2,4), function(y){
  m <- mean(y[baseline_window])
  (y/m - 1) * 100
}), c(2,3,1,4))

# Using ravetools
re2 <- baseline_array(x, 3, c(1,2,4),
                      baseline_indexpoints = baseline_window,
                      method = 'percentage')

# Check different, should be very tiny (double precisions)
range(re2 - re1)
#> [1] -5.684342e-13  1.818989e-12

# \donttest{
# Check speed for large dataset, might take a while to profile

ravetools_threads(n_threads = -1)

dims <- c(200,20,300,2)
x <- array(rnorm(prod(dims))^2, dims)
# Set baseline window to be arbitrary 10 timepoints
baseline_window <- seq_len(100)
f1 <- function(){
  aperm(apply(x, c(1,2,4), function(y){
    m <- mean(y[baseline_window])
    (y/m - 1) * 100
  }), c(2,3,1,4))
}
f2 <- function(){
  # equivalent as bl = x[,,baseline_window, ]
  #
  baseline_array(x, along_dim = 3,
                 baseline_indexpoints = baseline_window,
                 unit_dims = c(1,2,4), method = 'percentage')
}
range(f1() - f2())
#> [1] -1.818989e-12  2.273737e-12
microbenchmark::microbenchmark(f1(), f2(), times = 10L)
#> Unit: milliseconds
#>  expr       min         lq      mean    median        uq       max neval
#>  f1() 103.20007 107.214137 132.60957 110.69598 187.32534 193.17856    10
#>  f2()   8.27162   9.633646  11.10498  10.44148  12.65416  15.11332    10

# }