transition {IxPopDyMod}

Create a transition object

Description

A transition object represents a single transition between two tick life stages, or the mortality rate from a life stage.

Usage

transition(
  from,
  to,
  fun,
  transition_type,
  mortality_type = NULL,
  predictors = NULL,
  parameters = list()
)

Arguments

from

The name of the life stage a tick is transitioning from.

to

The name of the life stage a tick is transitioning to, or NULL if the transition is representing mortality.

fun

The transition function to evaluate. The inputs of the function are predictors and parameters. The output is the daily probability of completing the transition, for "probability" transitions, or the daily rate the transition takes place, for "duration" transitions.

transition_type

One of: "probability": the evaluated transition is interpreted as the daily fraction of ticks that complete the transition. Ticks remain in the original life stage if they do not complete a transition or undergo mortality. "duration": the transition is complete on the first day that the cumulative sum of the evaluated transition is greater than or equal to 1. No ticks remain in the original life stage at the end of a transition - they either complete the transition or die.

mortality_type

One of: NULL: the default, indicating that the transition is not mortality. "per_day": indicates that the evaluated transition is the fraction of ticks that dies each day. "throughout_transition": only valid for "duration" type transitions, where it indicates that the evaluated transition is the fraction of ticks that die throughout the entire transition.

predictors

Optional, a named list of predictor_spec objects that specify how any predictor data should be used in evaluating fun. The names are matched with the formal args to fun to determine which input in fun each predictor will be passed to.

parameters

Optional, a parameters object, or a named list of numeric vectors.

Value

a transition object