Constructor of Weibull decay functions

The weibullDecay() constructor either creates a decay function or returns a ggplot object for visualizing the decay model. It is a utility function used internally by circularProjection and polarProjection.

Usage

weibullDecay(
  decay = 0.001,
  pdist = 0.15,
  shape = 1.05,
  plot = FALSE,
  demo.signal = 1
)

Arguments

decay: A decay factor (in [0,1]). This term indicates how much a signal decreases as a function of distance in pathway space. For example, at a specific distance defined by the pdist parameter, the signal intensity will be the initial signal multiplied by decay.
pdist: A distance normalization term (in (0, 1]) at which the signal reaches signal * decay. This parameter is used to anchor the decay to a meaningful distance (see details). Also, when pdist = 1, it will represent the diameter of the inscribed circle within the coordinate space of a PathwaySpace object.
shape: A parameter (>=1) of a Weibull function. When shape=1 the Weibull decay follows an exponential decay. When shape>1 the function is first convex, then concave with an inflection point.
plot: A logical value indicating whether to return a ggplot object.
demo.signal: A numeric value in [-Inf, Inf], only passed when plot = TRUE to visualize the decay curve with a specific signal intensity. The value is ignored by the function constructor, as the decay function itself is returned without using an initial signal.

Value

Returns either a function of the form function(x, signal) { ... } or, if plot = TRUE, a ggplot object illustrating the decay model.

Details

The weibullDecay() constructor creates a decay model based on the Weibull distribution. It describes how a signal decreases as a function of distance, controlled by both a decay rate and a shape parameter.

The decay function is defined as:

$$y = signal \times decay^{\left(\frac{x}{pdist}\right)^{shape}}$$

where $signal$ represents the initial intensity, $decay$ controls the rate of attenuation, $x$ is a vector of normalized distances, and $shape$ adjusts the curvature of the decay. When $shape = 1$, the function follows an exponential decay. For $shape > 1$, the curve transitions from convex to concave, exhibiting an inflection point. The $pdist$ parameter anchors the model such that:

$y = signal$ when $x = 0$
$y = signal \times decay$ when $x = pdist$

Author

Sysbiolab Team

Examples

# Return a decay function
decay_fun <- weibullDecay(decay = 0.5, pdist = 0.4, shape = 2)

# Plot decay model parameters
# weibullDecay(decay = 0.5, pdist = 0.4, shape = 2, plot = TRUE)