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Model Files

Source: R/model_files.R
ModelFiles.Rd

Construct objects for accessing and caching model definition files.

Usage

ModelFiles(
  model_directory,
  csv_reader = CSVReader,
  json_reader = JSONReader,
  txt_reader = TXTReader
)

Arguments

model_directory

String giving a path to a directory containing the following files, variables.csv, derivations.json, flows.csv, and settings.json, described by this spec.

csv_reader

Class inheriting from Reader for reading csv files.

json_reader

Class inheriting from Reader for reading json files.

txt_reader

Class inheriting from Reader for reading txt files.

Examples

d = system.file("starter_models", "seir_symp_vax", package = "macpan2")
m = ModelFiles(d)
m$flows()
#>    from  to      flow       type from_partition to_partition flow_partition
#> 1     S   E       foi per_capita            Epi          Epi            Epi
#> 2     E   I     alpha per_capita            Epi          Epi            Epi
#> 3     I   R     gamma per_capita            Epi          Epi            Epi
#> 4 unvax vax dose_rate per_capita            Vax          Vax            Vax
#>    from_to_partition from_flow_partition to_flow_partition
#> 1                Vax                                  Null
#> 2                Vax                                  Null
#> 3                Vax                Symp              Null
#> 4 Epi.Symp.SympStruc                                  Null
expander = FlowExpander(m)
expander$expand_flows()
#>                        from                       to                     flow
#> 1     S..unstructured.unvax    E..unstructured.unvax  foi..unstructured.unvax
#> 2     S..unstructured.unvax    E..unstructured.unvax    foi..unstructured.vax
#> 3       S..unstructured.vax      E..unstructured.vax  foi..unstructured.unvax
#> 4       S..unstructured.vax      E..unstructured.vax    foi..unstructured.vax
#> 5     E..unstructured.unvax   I.mild.component.unvax     alpha..unstructured.
#> 6     E..unstructured.unvax I.severe.component.unvax     alpha..unstructured.
#> 7       E..unstructured.vax     I.mild.component.vax     alpha..unstructured.
#> 8       E..unstructured.vax   I.severe.component.vax     alpha..unstructured.
#> 9    I.mild.component.unvax    R..unstructured.unvax    gamma.mild.component.
#> 10 I.severe.component.unvax    R..unstructured.unvax  gamma.severe.component.
#> 11     I.mild.component.vax      R..unstructured.vax    gamma.mild.component.
#> 12   I.severe.component.vax      R..unstructured.vax  gamma.severe.component.
#> 13    S..unstructured.unvax      S..unstructured.vax ..unstructured.dose_rate
#> 14    E..unstructured.unvax      E..unstructured.vax ..unstructured.dose_rate
#> 15   I.mild.component.unvax     I.mild.component.vax ..unstructured.dose_rate
#> 16 I.severe.component.unvax   I.severe.component.vax ..unstructured.dose_rate
#> 17    R..unstructured.unvax      R..unstructured.vax ..unstructured.dose_rate
#>          type
#> 1  per_capita
#> 2  per_capita
#> 3  per_capita
#> 4  per_capita
#> 5  per_capita
#> 6  per_capita
#> 7  per_capita
#> 8  per_capita
#> 9  per_capita
#> 10 per_capita
#> 11 per_capita
#> 12 per_capita
#> 13 per_capita
#> 14 per_capita
#> 15 per_capita
#> 16 per_capita
#> 17 per_capita