dot-smooth_LOESS: LOESS smoothing function

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

LOESS smoothing function

Description

Prefer the use of the wrapper function smooth_incidence(..., smoothing_method = "LOESS") instead of .smooth_LOESS.

Usage

.smooth_LOESS(
  incidence_input,
  data_points_incl = 21,
  degree = 1,
  initial_Re_estimate_window = 5
)

Arguments

incidence_input	Module input object. List with two elements: A numeric vector named values: the incidence recorded on consecutive time steps. An integer named index_offset: the offset, counted in number of time steps, by which the first value in values is shifted compared to a reference time step This parameter allows one to keep track of the date of the first value in values without needing to carry a date column around. A positive offset means values are delayed in the future compared to the reference values. A negative offset means the opposite.
data_points_incl	integer. Size of the window used in the LOESS algorithm. The span parameter passed to loess is computed as the ratio of data_points_incl and the number of time steps in the input data.
degree	integer. LOESS degree. Must be 0, 1 or 2.
initial_Re_estimate_window	integer. In order to help with the smoothing, the function extends the data back in time, padding with values obtained by assuming a constant Re. This parameter represents the number of timesteps in the beginning of incidence_input to take into account when computing the average initial Re.

Details

This function implements the LOESS method for smoothing noisy data. It relies on loess. See the help section for loess for details on LOESS.

Value

A list with two elements:

1. A numeric vector named values: the result of the computations on the input data.

2. An integer named index_offset: the offset, counted in number of time steps, by which the result is shifted compared to an index_offset of 0. This parameter allows one to keep track of the date of the first value in values without needing to carry a date column around. A positive offset means values are delayed in the future compared to the reference values. A negative offset means the opposite. Note that the index_offset of the output of the function call accounts for the (optional) index_offset of the input.

If index_offset is 0 and simplify_output = TRUE, the index_offset is dropped and the values element is returned as a numeric vector.

covid-19-Re/estimateR documentation built on Sept. 14, 2024, 5:49 a.m.