EpiModelHIV ‐ code conventions - EpiModel/EpiModeling GitHub Wiki

Work In Progress

Module Structure

new_module <- function(dat, at) {
  ##Inputs
  # Attributes
  an.attribute <- get_attr(dat, "an.attribute")

  # Parameters
  a.param <- get_param(dat, "a.param")

  ## Process
  an.attribute <- an.attribute + a.param

  ## Output
  # Attributes
  dat <- set_attr(dat, "an.attribute", an.attribute)

  # Epi Trackers
  dat <- set_epi(dat, "high.attributes", at, an.attribute > 10)

  return(dat)
}

Naming

• parameters are lower.dot.case
• attributes are lower.dot.case
• variables in a module are lower_snake_case
• functions are lower_snake_case

Name conventions

Try to follow the below example:

new disease xyz

• xyz: 0-1; presence of the disease

• xyz.tx: 0-1; presence of treatment for xyz`

• xyz.dx: 0-1; xyz` diagnosed

• xyz.sympt: 0-1; xyz` with symptoms

• xyz.count: 0-Inf; number of time infected by xyz`

• xyz.tst.last: time step; last time xyz was testd

• xyz.dx.last: time step; last time xyz was diagnosed

• xyz.stage: 0-N; stage of xyz

• xyz.prob: [0, 1]; probability of getting xyz

• xyz.tx.int: 0-N; duration of xyz treatment in timestep

• xyz.sympt.prob: [0, 1]; probability of having xyz symptoms