In PredictiveEcology/SpaDES.Workshops: Training workshops for ecological modeling with SpaDES

knitr::opts_chunk$set(echo = TRUE, eval = FALSE)

Loops: what are they and why use them?

• fundamental programming units (most languages have them)
• used to repeat a set of instructions, without "duplicating" code
• often used in ecology to iterate something over "time"
• usually, each 'time-step' depends on the previous one. Note in the examples below, how we start an age object at 1, and increment it at each step of time, or t. In both cases time and t are the loop counters, but only in the second case is the counter being effectively "used" inside the loop.

Loop example in R

age <- 1
for (time in 1:10) {
  age <- age + 1
}

• initialise a storage vector
• define time boundaries
• define the increment
• define the content (what's done)

From loops to events

• In R, we try to avoid loops because:
• they are slow
• they make code harder to share amongst users

From loops to events

• It's easy to think about "events" in ecology

In SpaDES, events are first defined, then scheduled to happen at a particular point in time:

Events in SpaDES

## initialisation
age <- 1                              

## boundaries
times = list(start = 1, end = 10) 

## event definition (content)
aging <- function(age) {
  age <- age + 1                
}

## event execution and scheduling
events <- {
  doEvent("aging")
  scheduleEvent("aging", when = now + 1)
}

Events in SpaDES

• Event execution and scheduling in SpaDES use same components of a for-loop: initialize, bounds, step, content

• This creates an event queue

What would that sequence look like?

1. what is happening now
2. What are the next thing(s) in the queue

#     eventTime moduleName  eventType
#  1:         0       loop       init
#  2:         0       loop addOneYear
#  3:         1       loop addOneYear
#  4:         2       loop addOneYear
#  5:         3       loop addOneYear
#  6:         4       loop addOneYear
#  7:         5       loop addOneYear
#  8:         6       loop addOneYear
#  9:         7       loop addOneYear
# 10:         8       loop addOneYear
# 11:         9       loop addOneYear
# 12:        10       loop addOneYear 

Why contain the iterated code in a function?

• iterated code remains isolated from execution and scheduling - cleaner, more organised
• easier to share
• easier to change and update - modular!

PredictiveEcology/SpaDES.Workshops documentation built on Jan. 30, 2021, 6:52 p.m.