simulate_from_data_delay: Simulate from equilibrium, with delays in treatment

In SwissTPH/VivaxModelR: Simulation of Plasmodium Vivax dynamics

Simulate from equilibrium, with delays in treatment

Description

Uses the compartmental model to simulate a trajectory, starting from equilibrium variable

Usage

simulate_from_data_delay(
  df,
  from_equilibrium = TRUE,
  initial_states = NULL,
  f = 1/72,
  gamma = 1/223,
  r = 1/60,
  maxtime,
  year,
  rcd = FALSE,
  referral = FALSE,
  mda = FALSE,
  rcd_at_baseline = FALSE,
  sto = FALSE,
  sto_method = "exact",
  runs = 1,
  seeds = NULL
)

Arguments

df	a dataframe containing the data, with one column called I containing the proportion of infectious individuals (U0+Ul+Tl+T0) at equilibrium, one column called lambda containing the transmission rate, and one variable called id which identifies uniquely each row in the dataset. Additional optional variables are: rho (reporting rate), delta (importation rate) intervention levels in the past (when lambda was calculated): alpha.old (effective care), beta.old (proportion of liver stage cure), omega.old (intensity of vector control) intervention levels in the future (in the simulation): alpha.new (effective care), beta.new (proportion of liver stage cure), omega.new (intensity of vector control)
from_equilibrium	boolean indicating if the model is run from equilibrium (TRUE, default) or from a pre-specified initial condition, which should be specified in initial_states
initial_states	given initial condition, as a dataframe containing the variables "Ul_init", "U0_init", "Sl_init", "S0_init", "Tl_init", "T0_init", "h_init", with one variable called id which identifies uniquely each row in the dataset. This input is not used when from_equilibrium=TRUE (default).
f	relapse frequency
gamma	liver clearance rate
r	blood clearance rate
maxtime	number of time steps for simulation
year	if TRUE, aggregates the outputs per year (h would be in cases per person year). if FALSE, returns daily outputs (h would be in cases per person day).
rcd	a boolean indicating if the model including reactive case detection should be used. Default (FALSE) is the model without RCD
referral	a boolean indicating if the rcd model includes referral. Default (FALSE) is the model without referral for RCD. This parameter is used only if rcd==TRUE.
mda	a boolean indicating if the model including mass drug administration (MDA) prophylaxis should be used. Default (FALSE) is the model without MDA
rcd_at_baseline	a boolean indicating if the model was calibrated using the RCD model (i.e. there is some RCD at baseline already). Default (FALSE) is the model without RCD at baseline
sto	a boolean indicating if the stochastic model is used. Default (FALSE) is the deterministic (ODE) model
sto_method	a scalarindicating which simulation method is used. Default ("exact") is Gillespie's direct method. Other options are "approximate" (tau-leap) or "mixed". cf. the documentation of the TiPS package for more information.
runs	number of draws of the stochastic model
seeds	a vector of the length of runs containing the seeds for each simulation (don't use "0" which has another use in TiPS)

Details

If alpha is not provided in df, alpha=0. If beta is not provided in df, beta=1. If rho is not provided in df, rho=1. If omega is not provided in df, omega=1. If delta is not provided in df, delta=0.

Value

A dataframe with the simulated state variables for each parameter combination in df

Examples

mydata=data.frame(incidence=c(23,112),lambda=c(0.0063,0.0071),I=c(0.017,0.12),id=c(1,2))
mydata$rho=c(0.18,0.13)
mydata$beta.old=c(0.43,0.42)
mydata$alpha.old=c(0.17, 0.12)
mydata$delta=c(0,0)
mydata$omega.old=c(1,1)
mydata$sigma.old=c(1/15,1/15)
simulate_from_data_delay(df=mydata, f=1/69, gamma=1/383, r=1/60,maxtime=2000,year=TRUE)

SwissTPH/VivaxModelR documentation built on Feb. 14, 2024, 11:27 a.m.