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Get the values each modeling task in a round allows

Source: R/get_round_value_sets_config.R
get_round_value_sets_config.Rd

Reads a round of a tasks.json config into one list per modeling task. Each list holds the values that modeling task allows in each task ID column and, for each output type, in the output_type_id column:

Usage

get_round_value_sets_config(
  config_tasks,
  round_id,
  required_vals_only = FALSE,
  force_output_types = FALSE,
  output_types = NULL,
  derived_task_ids = NULL,
  call = rlang::current_env()
)

Arguments

config_tasks

a list version of the content's of a hub's tasks.json config file, accessed through the "config_tasks" attribute of a <hub_connection> object or function read_config().

round_id

Character string. Round identifier. If the round is set to round_id_from_variable: true, IDs are values of the task ID defined in the round's round_id property of config_tasks. Otherwise should match round's round_id value in config.

required_vals_only

Logical. Whether to return only required values.

force_output_types

Logical. Whether to treat all output types as required, regardless of their is_required setting. Only affects the result when required_vals_only = TRUE.

output_types

Character vector of output type names to include. If NULL, all output types in the round are included.

derived_task_ids

Character vector of derived task ID names (task IDs whose values depend on other task IDs). Their values are returned as NA.

call

The execution environment of the function to name in error and warning messages. By default, messages name this function. Supply another environment, such as a wrapper function's environment, to name that function instead.

Value

A list with one element per modeling task in the round. Each element is a list of two:

  • task_ids: a named list with a vector of allowed values for each task ID in the round.

  • output_type_ids: a named list with a vector of allowed output type ID values for each output type in the modeling task. An output type with no required values is left out when required_vals_only = TRUE.

Details

[[1]]
  $task_ids
    $target   "wk flu hosp rate category"
    $horizon  0 1 2 3
    $location "US" "01" "02" ...
  $output_type_ids
    $pmf      "low" "moderate" "high" ...

The values are read from the config as follows:

  • required and optional values are combined into one vector, required values first. With required_vals_only = TRUE, only required values are kept.

  • A task ID a modeling task does not use is either listed as null or left out of that modeling task. Both are returned as NA, the value model output holds in that column. So are task IDs that have no required values when required_vals_only = TRUE, and derived task IDs.

  • In a round with round_id_from_variable: true, the task ID holding round IDs is set to round_id.

  • Output type IDs are read the same way for every schema version. From schema v4.0.0 onwards, an output type's is_required setting determines whether its output type IDs are required. Output types with no output type ID values are returned as NA. For mean and median, NA is the only valid value. For sample, NA stands in for sample IDs, which the config does not list.

Values keep the type they have in the config.

Examples

hub_path <- system.file("testhubs/v6/target_dir", package = "hubUtils")
config_tasks <- read_config(hub_path)
get_round_value_sets_config(config_tasks, round_id = "2022-10-22")
#> [[1]]
#> [[1]]$task_ids
#> [[1]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[1]]$task_ids$target
#> [1] "flu_hosp_rate_cat"
#> 
#> [[1]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[1]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[1]]$task_ids$target_end_date
#>  [1] "2022-10-22" "2022-10-29" "2022-11-05" "2022-11-12" "2022-11-19"
#>  [6] "2022-11-26" "2022-12-03" "2022-12-10" "2022-12-17" "2022-12-24"
#> [11] "2022-12-31" "2023-01-07" "2023-01-14"
#> 
#> 
#> [[1]]$output_type_ids
#> [[1]]$output_type_ids$pmf
#> [1] "low"       "moderate"  "high"      "very high"
#> 
#> 
#> 
#> [[2]]
#> [[2]]$task_ids
#> [[2]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[2]]$task_ids$target
#> [1] "flu_hosp_rate"
#> 
#> [[2]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[2]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[2]]$task_ids$target_end_date
#>  [1] "2022-10-22" "2022-10-29" "2022-11-05" "2022-11-12" "2022-11-19"
#>  [6] "2022-11-26" "2022-12-03" "2022-12-10" "2022-12-17" "2022-12-24"
#> [11] "2022-12-31" "2023-01-07" "2023-01-14"
#> 
#> 
#> [[2]]$output_type_ids
#> [[2]]$output_type_ids$cdf
#>  [1]  1  2  3  4  5  6  7  8  9 10 11 12
#> 
#> 
#> 
#> [[3]]
#> [[3]]$task_ids
#> [[3]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[3]]$task_ids$target
#> [1] "flu_hosp_inc"
#> 
#> [[3]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[3]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[3]]$task_ids$target_end_date
#>  [1] "2022-10-22" "2022-10-29" "2022-11-05" "2022-11-12" "2022-11-19"
#>  [6] "2022-11-26" "2022-12-03" "2022-12-10" "2022-12-17" "2022-12-24"
#> [11] "2022-12-31" "2023-01-07" "2023-01-14"
#> 
#> 
#> [[3]]$output_type_ids
#> [[3]]$output_type_ids$quantile
#>  [1] 0.025 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 0.975
#> 
#> [[3]]$output_type_ids$sample
#> [1] NA
#> 
#> [[3]]$output_type_ids$mean
#> [1] NA
#> 
#> 
#> 
# Set derived task IDs to NA
get_round_value_sets_config(
  config_tasks,
  round_id = "2022-10-22",
  derived_task_ids = "target_end_date"
)
#> [[1]]
#> [[1]]$task_ids
#> [[1]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[1]]$task_ids$target
#> [1] "flu_hosp_rate_cat"
#> 
#> [[1]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[1]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[1]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[1]]$output_type_ids
#> [[1]]$output_type_ids$pmf
#> [1] "low"       "moderate"  "high"      "very high"
#> 
#> 
#> 
#> [[2]]
#> [[2]]$task_ids
#> [[2]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[2]]$task_ids$target
#> [1] "flu_hosp_rate"
#> 
#> [[2]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[2]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[2]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[2]]$output_type_ids
#> [[2]]$output_type_ids$cdf
#>  [1]  1  2  3  4  5  6  7  8  9 10 11 12
#> 
#> 
#> 
#> [[3]]
#> [[3]]$task_ids
#> [[3]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[3]]$task_ids$target
#> [1] "flu_hosp_inc"
#> 
#> [[3]]$task_ids$horizon
#> [1] 1 2
#> 
#> [[3]]$task_ids$location
#> [1] "US" "01" "02"
#> 
#> [[3]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[3]]$output_type_ids
#> [[3]]$output_type_ids$quantile
#>  [1] 0.025 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 0.975
#> 
#> [[3]]$output_type_ids$sample
#> [1] NA
#> 
#> [[3]]$output_type_ids$mean
#> [1] NA
#> 
#> 
#> 
# Required values of a single output type only
get_round_value_sets_config(
  config_tasks,
  round_id = "2022-10-22",
  required_vals_only = TRUE,
  output_types = "pmf"
)
#> [[1]]
#> [[1]]$task_ids
#> [[1]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[1]]$task_ids$target
#> [1] NA
#> 
#> [[1]]$task_ids$horizon
#> [1] NA
#> 
#> [[1]]$task_ids$location
#> [1] NA
#> 
#> [[1]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[1]]$output_type_ids
#> [[1]]$output_type_ids$pmf
#> [1] "low"       "moderate"  "high"      "very high"
#> 
#> 
#> 
#> [[2]]
#> [[2]]$task_ids
#> [[2]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[2]]$task_ids$target
#> [1] NA
#> 
#> [[2]]$task_ids$horizon
#> [1] NA
#> 
#> [[2]]$task_ids$location
#> [1] NA
#> 
#> [[2]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[2]]$output_type_ids
#> named list()
#> 
#> 
#> [[3]]
#> [[3]]$task_ids
#> [[3]]$task_ids$reference_date
#> [1] "2022-10-22"
#> 
#> [[3]]$task_ids$target
#> [1] NA
#> 
#> [[3]]$task_ids$horizon
#> [1] NA
#> 
#> [[3]]$task_ids$location
#> [1] NA
#> 
#> [[3]]$task_ids$target_end_date
#> [1] NA
#> 
#> 
#> [[3]]$output_type_ids
#> named list()
#> 
#>