Table 1 Six core commands in the package which a user will use when specifying, running, and analyzing a model
From: IxPopDyMod: an R package to write, run, and analyze tick population and infection dynamics models
Command | Inputs | Description |
|---|---|---|
config | cycle, initial_population, steps, preds, max_duration | This command makes a configuration object which is used to run the model. It is a convenient way to make the model shareable. These configs can be modified to run the model under different climate, host community scenarios, or different parameter values |
life_cycle | Multiple transitions | The life cycle object is required for the config. It specifies the tick life cycle as a series of transitions between life stages |
transition | from, to, fun, transition_type, mortality_type, parameters, predictors | A transition is a single step in the tick life cycle, from one life stage to the next. Each transition is either a probability of a tick going from one life stage to the next (e.g. probability a questing tick finds a host) or the duration of time that transition takes (e.g. how long it takes a developing egg to hatch). These probabilities or durations are given as a function (can be constant) which could have parameters and/or take predictors |
run | config | This command runs the model from a config object |
growth_rate | run output | This command calculates the daily growth rate of a population from the output of run |
annual_growth_rate | run output | This command calculates the annual growth rate of a population from the output of run |