Lancelot progression parameters — lancelot_parameters

Lancelot progression parameters. The s_ parameters are the scaling parameters for the Erlang distibution (a.k.a 'k'), while the gamma_ parameters are the gamma parameters of that distribution. These need to be aligned with Bob's severity outputs, and we will come up with a better way of coordinating the two.

lancelot_parameters_progression(
  dt,
  gamma_E = NULL,
  gamma_A = NULL,
  gamma_P = NULL,
  gamma_C_1 = NULL,
  gamma_C_2 = NULL,
  gamma_ICU_pre = NULL,
  gamma_ICU_D = NULL,
  gamma_ICU_W_D = NULL,
  gamma_ICU_W_R = NULL,
  gamma_H_D = NULL,
  gamma_H_R = NULL,
  gamma_W_D = NULL,
  gamma_W_R = NULL,
  gamma_G_D = NULL,
  gamma_U = NULL,
  gamma_PCR_pre = NULL,
  gamma_PCR_pos = NULL
)

Arguments

dt: The step size
gamma_E: Time-varying parameters for the Erlang rate parameter of the duration in the E (exposed) compartment. See Details.
gamma_A: Time-varying parameters for the Erlang rate parameter of the duration in the I_A (asymptomatic) compartment. See Details.
gamma_P: Time-varying parameters for the Erlang rate parameter of the duration in the I_P (presymptomatic) compartment. See Details.
gamma_C_1: Time-varying parameters for the Erlang rate parameter of the duration in the I_C_1 (first stage symptomatic) compartment. See Details.
gamma_C_2: Time-varying parameters for the Erlang rate parameter of the duration in the I_C_2 (second stage symptomatic) compartment. See Details.
gamma_ICU_pre: Time-varying parameters for the Erlang rate parameter of the duration in the ICU_pre (general beds stay before ICU) compartment. See Details.
gamma_ICU_D: Time-varying parameters for the Erlang rate parameter of the duration in the ICU_D (ICU stay for individuals who die in ICU) compartment. See Details.
gamma_ICU_W_D: Time-varying parameters for the Erlang rate parameter of the duration in the ICU_W_D (ICU stay for individuals who go on to die in stepdown) compartment. See Details.
gamma_ICU_W_R: Time-varying parameters for the Erlang rate parameter of the duration in the ICU_W_R (ICU stay for individuals who go on to recover in stepdown) compartment. See Details.
gamma_H_D: Time-varying parameters for the Erlang rate parameter of the duration in the H_D (general beds stay for individuals who die in general beds) compartment. See Details.
gamma_H_R: Time-varying parameters for the Erlang rate parameter of the duration in the H_R (general beds stay for individuals who recover in general beds) compartment. See Details.
gamma_W_D: Time-varying parameters for the Erlang rate parameter of the duration in the W_D (stepdown for individuals who die in stepdown) compartment. See Details.
gamma_W_R: Time-varying parameters for the Erlang rate parameter of the duration in the W_R (stepdown for individuals who recover in stepdown) compartment. See Details.
gamma_G_D: Time-varying parameters for the Erlang rate parameter of the duration in the G_D (delay to death in the community/care homes) compartment. See Details.
gamma_U: Time-varying parameters for the Erlang rate parameter of the duration of the delay from hospital admission to diagnosis for those not confirmed on admission. Note this duration is a single-stage Erlang. See Details.
gamma_PCR_pre: Time-varying parameters for the Erlang rate parameter the duration of PCR pre-positivity affecting REACT and ONS infection prevalence. See Details.
gamma_PCR_pos: Time-varying parameters for the Erlang rate parameter the duration of PCR positivity affecting REACT and ONS infection prevalence. See Details.

Value

A list of parameter values

Time-varying parameters

Every time varying parameter has the same format, which can be NULL (in which case a default single value is used) or a list with date and value for changes in the parameter. If value is scalar then date can be NULL or missing. If value is a vector then date must be a vector of sircovid dates of the same length as value.