Classes
struct	renewal_state

Functions
void	check_convolve_len (int n, int D, int len)

Eigen::VectorXd	convolve_forward (const Eigen::VectorXd &x, const Eigen::VectorXd &y, int len)

void	convolve_reverse (const Eigen::VectorXd &x, const Eigen::VectorXd &y, const Eigen::VectorXd &zbar, Eigen::VectorXd xbar, Eigen::VectorXd ybar)

void	R_to_r_sums (double r, const Eigen::VectorXd &g, double &s0, double &s1, Eigen::VectorXd *e=nullptr)

double	R_to_r_newton (double R, const Eigen::VectorXd &g, double abs_tol)

bool	renewal_depletes (int use_pop, int s, int nht)

template<typename State >
void	renewal_forward (const Eigen::VectorXd &seed, const Eigen::VectorXd &R, const Eigen::VectorXd &g, double pop, int use_pop, double pop_floor, int nht, State &st)

template<typename State >
void	renewal_reverse (const State &st, const Eigen::VectorXd &R, const Eigen::VectorXd &g, int use_pop, const Eigen::VectorXd &Ibar_in, Eigen::VectorXd &seedbar, Eigen::VectorXd &Rbar, Eigen::VectorXd &gbar, double &popbar)

Variables
constexpr int	R_to_r_max_steps = 100

Function Documentation

◆ check_convolve_len()

void epinow2::internal::check_convolve_len	(	int	n,
		int	D,
		int	len )

inline

Check that len is a valid output length for the convolution.

Parameters

n	Length of x.
D	Length of y.
len	Requested output length.

Exceptions

std::domain_error if len < n or len > n + D - 1.

Definition at line 51 of file convolve_with_rev_pmf.hpp.

Referenced by epinow2::convolve_with_rev_pmf().

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◆ convolve_forward()

Eigen::VectorXd epinow2::internal::convolve_forward	(	const Eigen::VectorXd &	x,
		const Eigen::VectorXd &	y,
		int	len )

inline

Forward pass of the convolution on doubles.

Computes z_{d+1:d+m} += w_d x_{1:m} for each lag d, with w_d = y_{D - d}.

Parameters

x	Input vector of length n.
y	Reversed PMF of length D.
len	Output length, n <= len <= n + D - 1.

Returns: Vector z of length len.

Definition at line 71 of file convolve_with_rev_pmf.hpp.

Referenced by epinow2::convolve_with_rev_pmf().

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◆ convolve_reverse()

void epinow2::internal::convolve_reverse	(	const Eigen::VectorXd &	x,
		const Eigen::VectorXd &	y,
		const Eigen::VectorXd &	zbar,
		Eigen::VectorXd *	xbar,
		Eigen::VectorXd *	ybar )

inline

Reverse pass of the convolution on doubles.

Accumulates xbar_{1:m} += w_d zbar_{d+1:d+m} and wbar_d += zbar_{d+1:d+m}^T x_{1:m}, writing wbar_d to ybar_{D - d}.

Parameters

x	Input vector of length n.
y	Reversed PMF of length D.
zbar	Adjoint of the output, of length len.
xbar	Adjoint of x, of length n, accumulated into. May be null.
ybar	Adjoint of y, of length D, accumulated into. May be null.

Definition at line 98 of file convolve_with_rev_pmf.hpp.

Referenced by epinow2::convolve_with_rev_pmf().

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◆ R_to_r_newton()

double epinow2::internal::R_to_r_newton	(	double	R,
		const Eigen::VectorXd &	g,
		double	abs_tol )

inline

Solve for the growth rate by Newton's method on doubles.

Parameters

R	Reproduction number.
g	Reversed generation time PMF.
abs_tol	Stop once a step is no larger than this in absolute value.

Returns: The growth rate after the last step.

Definition at line 88 of file R_to_r.hpp.

References R_to_r_max_steps, and R_to_r_sums().

Referenced by epinow2::R_to_r().

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◆ R_to_r_sums()

void epinow2::internal::R_to_r_sums	(	double	r,
		const Eigen::VectorXd &	g,
		double &	s0,
		double &	s1,
		Eigen::VectorXd *	e = nullptr )

inline

Sums used by the Newton step and the gradient.

Computes S0 = sum_k p_k exp(-r k) and S1 = sum_k k p_k exp(-r k), with p_k = g[G - 1 - k].

Parameters

r	Growth rate.
g	Reversed generation time PMF.
s0	Set to S0.
s1	Set to S1.
e	If not null, set to exp(-r k) in e[G - 1 - k].

Definition at line 61 of file R_to_r.hpp.

Referenced by epinow2::R_to_r(), and R_to_r_newton().

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◆ renewal_depletes()

bool epinow2::internal::renewal_depletes	(	int	use_pop,
		int	s,
		int	nht )

inline

Whether susceptible depletion applies at a time step.

Parameters

use_pop	Population adjustment (0 none, 1 after nht, 2 all).
s	Zero-based time step after the seeds.
nht	Number of time steps before the adjustment starts when use_pop = 1.

Returns: True if depletion applies.

Definition at line 87 of file renewal_infections.hpp.

Referenced by renewal_forward().

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◆ renewal_forward()

template<typename State >

void epinow2::internal::renewal_forward	(	const Eigen::VectorXd &	seed,
		const Eigen::VectorXd &	R,
		const Eigen::VectorXd &	g,
		double	pop,
		int	use_pop,
		double	pop_floor,
		int	nht,
		State &	st )

inline

Forward pass of the renewal equation on doubles.

Fills st with the infections and the values needed by renewal_reverse().

Parameters

seed	Seeding infections.
R	Reproduction numbers.
g	Reversed generation time PMF.
pop	Initial susceptible population.
use_pop	Population adjustment (0 none, 1 after nht, 2 all).
pop_floor	Minimum susceptible population.
nht	Number of time steps before the adjustment starts when use_pop = 1.
st	State to fill.

Definition at line 107 of file renewal_infections.hpp.

References renewal_depletes().

Referenced by epinow2::renewal_infections().

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◆ renewal_reverse()

template<typename State >

void epinow2::internal::renewal_reverse	(	const State &	st,
		const Eigen::VectorXd &	R,
		const Eigen::VectorXd &	g,
		int	use_pop,
		const Eigen::VectorXd &	Ibar_in,
		Eigen::VectorXd &	seedbar,
		Eigen::VectorXd &	Rbar,
		Eigen::VectorXd &	gbar,
		double &	popbar )

inline

Reverse pass of the renewal equation on doubles.

Parameters

st	State filled by renewal_forward().
R	Reproduction numbers.
g	Reversed generation time PMF.
use_pop	Population adjustment (0 none, 1 after nht, 2 all).
Ibar_in	Adjoint of the infections, seeds included.
seedbar	Set to the adjoint of the seeds.
Rbar	Adjoint of R, accumulated into.
gbar	Adjoint of g, accumulated into.
popbar	Adjoint of pop, accumulated into.

Definition at line 167 of file renewal_infections.hpp.

Referenced by epinow2::renewal_infections().

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Variable Documentation

◆ R_to_r_max_steps

int epinow2::internal::R_to_r_max_steps = 100

constexpr

Maximum number of Newton steps taken by R_to_r_newton().

Definition at line 78 of file R_to_r.hpp.

Referenced by R_to_r_newton().

Classes

Functions

Variables

Function Documentation

◆ check_convolve_len()

◆ convolve_forward()

◆ convolve_reverse()

◆ R_to_r_newton()

◆ R_to_r_sums()

◆ renewal_depletes()

◆ renewal_forward()

◆ renewal_reverse()

Variable Documentation

◆ R_to_r_max_steps