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Dynamic Variable Names

Source: R/flow_frame.R
mp_vars.Rd

Get the state, flow, and other dynamic variables in a model specification. Dynamic variables are any variable that is updated every time step. State and flow variables are special dynamic variables involved in compartmental models that have been explicitly represented using functions like mp_per_capita_flow that define flows among compartments (i.e., states).

Usage

mp_state_vars(spec, topological_sort = FALSE, loops = "^$", trans = "")

mp_flow_vars(spec, topological_sort = FALSE, loops = "^$", trans = "")

mp_state_flow_vars(spec, topological_sort = FALSE, loops = "^$", trans = "")

mp_dynamic_vars(spec)

mp_other_dynamic_vars(spec)

Arguments

spec

Model specification (mp_tmb_model_spec).

topological_sort

Should the states and flows be topologically sorted to respect the main direction of flow? The default is no topological sorting, which differs from mp_flow_frame.

loops

Pattern for matching the names of flows that make the flow model not a DAG, which is a critical assumption when topologically sorting the order of states and flows in the output. This is only relevant if topological_sort is used.

trans

Add a prefix to the names for indicating if a transformed version of the variables is preferred.

Value

Character vector of names of all requested variables.

Details

State and flow variables will be identical regardless of the state update method (e.g., mp_rk4), but other dynamic variables might appear for one particular state update method that does not appear for another. For example, the first Runge Kutta step for a state in a model with an mp_rk4 updater, will not appear with an mp_euler updater.

Functions

  • mp_state_vars(): Return character vector of all state variables.

  • mp_flow_vars(): Return the names of all variables that contain the absolute flow between compartments. The absolute flow is the magnitude of a flow per time step.

  • mp_state_flow_vars(): Union of mp_state_vars() and mp_flow_vars().

  • mp_dynamic_vars(): All variables that are updated once per time-step.

  • mp_other_dynamic_vars(): All variables that are updated once per time-step, excluding those that are state and flow variables.

Examples

si = mp_tmb_library("starter_models", "si", package = "macpan2")
(si
  |> mp_simulator(time_steps = 5L, mp_state_vars(si))
  |> mp_trajectory()
)
#>    matrix time row col     value
#> 1       I    1   0   0  1.198000
#> 2       S    1   0   0 98.802000
#> 3       I    2   0   0  1.434730
#> 4       S    2   0   0 98.565270
#> 5       I    3   0   0  1.717559
#> 6       S    3   0   0 98.282441
#> 7       I    4   0   0  2.055170
#> 8       S    4   0   0 97.944830
#> 9       I    5   0   0  2.457757
#> 10      S    5   0   0 97.542243