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Christina Azodi
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#' Generating time-dependent parameters
#'
#' Function to generate parameter values for the time range of the simulation
#' that can change over time.
#'
#' @param nstep Number of time steps to generate parameter values for.
#' @param vals List of parameter values to include over the nsteps.
#' @param timing List of the step numbers at which to start changes, with the
#' last number reflecting when to hit the last parameter value in vals.
#'
#' @return list of parameter values for length t
#'
vary_param <- function(nstep = nstep, vals = vals, timing = timing) {
stopifnot(length(vals) == length(timing))
y <- list()
for(t in seq(1:nstep)){
if(t <= timing[1]){ # If before first jump set to val[1]
y.t <- vals[1]
}else if(t > tail(timing, n=1)){ # If after last jump set to val[-1]
y.t <- tail(vals, n=1)
}else{ # If intermediate step, calculate...
for(j in (2:length(timing))){
if(t > timing[j - 1] & t <= timing[j]){
start <- vals[j - 1]
end <- vals[j]
start_t <- timing[j - 1]
end_t <- timing[j]
y.t <- start - (t-start_t)*(start - end)/(end_t - start_t)
}
}
}
y <- append(y, y.t)
}
return(unlist(y))
}