Convolution Functions

Functions for convolving time series. More...

Collaboration diagram for Convolution Functions:

Functions
array[] int	calc_conv_indices_xlen (int s, int xlen, int ylen)
array[] int	calc_conv_indices_len (int s, int xlen, int ylen)
vector	convolve_with_rev_pmf (vector x, vector y, int len)
vector	convolve_to_report (vector infections, vector delay_rev_pmf, int seeding_time)

Description

Functions for convolving time series.

Functions from convolve.stan for implementing convolutions between infections and delay distributions.

Function Documentation

calc_conv_indices_len()

array[] int calc_conv_indices_len	(	int	s,
		int	xlen,
		int	ylen )

Calculate convolution indices for the case where s > xlen

Parameters

s	Current position in the output vector
xlen	Length of the x vector
ylen	Length of the y vector

Returns

An array of integers: {start_x, end_x, start_y, end_y}

Definition at line 39 of file convolve.stan.

Referenced by convolve_with_rev_pmf().

Here is the caller graph for this function:

calc_conv_indices_xlen()

array[] int calc_conv_indices_xlen	(	int	s,
		int	xlen,
		int	ylen )

convolution_functions Functions

This file contains functions for performing discrete convolutions, which are used throughout the model to combine time series with delay distributions. Calculate convolution indices for the case where s <= xlen

Parameters

s	Current position in the output vector
xlen	Length of the x vector
ylen	Length of the y vector

Returns

An array of integers: {start_x, end_x, start_y, end_y}

Definition at line 20 of file convolve.stan.

Referenced by convolve_with_rev_pmf().

Here is the caller graph for this function:

convolve_to_report()

vector convolve_to_report	(	vector	infections,
		vector	delay_rev_pmf,
		int	seeding_time )

Convolve infections to reported cases.

This function convolves a vector of infections with a reversed delay distribution to produce a vector of reported cases.

Parameters

infections	A vector of infection counts.
delay_rev_pmf	A vector representing the reversed probability mass function of the delay distribution.
seeding_time	The number of initial time steps to exclude from the output.

Returns

A vector of reported cases, starting from seeding_time + 1.

Definition at line 105 of file convolve.stan.

References convolve_with_rev_pmf().

Here is the call graph for this function:

convolve_with_rev_pmf()

vector convolve_with_rev_pmf	(	vector	x,
		vector	y,
		int	len )

Convolve a vector with a reversed probability mass function.

This function performs a discrete convolution of two vectors, where the second vector is assumed to be an already reversed probability mass function.

Parameters

x	The input vector to be convolved.
y	The already reversed probability mass function vector.
len	The desired length of the output vector.

Returns

A vector of length len containing the convolution result.

Exceptions

If	len is not of equal length to the sum of the lengths of x and y.

Definition at line 62 of file convolve.stan.

References calc_conv_indices_len(), and calc_conv_indices_xlen().

Referenced by convolve_to_report(), and get_delay_rev_pmf().

Here is the call graph for this function:

Here is the caller graph for this function: