Unify on "transitions" style step functions

[pearsonca]

Tasks:

• update contribution guidance @pearsonca
• all instructors: review and normalize their material
• intro materials: highlight this persective

Overview: Some implementations look like:

SI_open_model <- function(times, state, parms) {
  ## ... get out variables / params
  # Define differential equations
  dS <- -(beta * S * I) / N
  dI <- (beta * S * I) / N - gamma * I
  dR <- gamma * I
  return(list(c(dS, dI, dR)))
}

while others do

SI_open_model <- function(times, state, parms) {
  ## ... get out variables / params
  # Define transition rates
  infection <- (beta * S * I) / N
  recovery <- gamma * I
  return(list(c(dS = -infection, dI = infection - recovery, dR = recovery)))
}

In general, the "transitions" style should be preferred.