Read a hub config file into R

Usage

read_config(
  hub_path,
  config = c("tasks", "admin", "model-metadata-schema"),
  silent = FALSE
)

Arguments

hub_path: Either a character string path to a local Modeling Hub directory or an object of class <SubTreeFileSystem> created using functions arrow::s3_bucket() or arrow::gs_bucket() by providing a string S3 or GCS bucket name or path to a Modeling Hub directory stored in the cloud. For more details consult the Using cloud storage (S3, GCS) in the arrow package.
config: Type of config file to read. One of "tasks", "admin" or "model-metadata-schema". Default is "tasks".
silent: Logical. If TRUE, suppress warnings. Default is FALSE.

Value

The contents of the config file as an R list. If possible, the output is further converted to a <config> class object before returning. Note that "model-metadata-schema" files are never converted to a <config> object.

Examples

# Read config files from local hub
hub_path <- system.file("testhubs/simple", package = "hubUtils")
read_config(hub_path, "tasks")
#> $schema_version
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
#> 
#> $rounds
#> $rounds[[1]]
#> $rounds[[1]]$round_id_from_variable
#> [1] TRUE
#> 
#> $rounds[[1]]$round_id
#> [1] "origin_date"
#> 
#> $rounds[[1]]$model_tasks
#> $rounds[[1]]$model_tasks[[1]]
#> $rounds[[1]]$model_tasks[[1]]$task_ids
#> $rounds[[1]]$model_tasks[[1]]$task_ids$origin_date
#> $rounds[[1]]$model_tasks[[1]]$task_ids$origin_date$required
#> NULL
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$origin_date$optional
#> [1] "2022-10-01" "2022-10-08"
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$target
#> $rounds[[1]]$model_tasks[[1]]$task_ids$target$required
#> [1] "wk inc flu hosp"
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$target$optional
#> NULL
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$horizon
#> $rounds[[1]]$model_tasks[[1]]$task_ids$horizon$required
#> [1] 1
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$horizon$optional
#> [1] 2 3 4
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$location
#> $rounds[[1]]$model_tasks[[1]]$task_ids$location$required
#> NULL
#> 
#> $rounds[[1]]$model_tasks[[1]]$task_ids$location$optional
#>  [1] "US" "01" "02" "04" "05" "06" "08" "09" "10" "11" "12" "13" "15" "16" "17"
#> [16] "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32"
#> [31] "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "44" "45" "46" "47" "48"
#> [46] "49" "50" "51" "53" "54" "55" "56" "72" "78"
#> 
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$output_type_id
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$output_type_id$required
#> NULL
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$output_type_id$optional
#> [1] NA
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$value
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$value$type
#> [1] "integer"
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$mean$value$minimum
#> [1] 0
#> 
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$output_type_id
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$output_type_id$required
#>  [1] 0.010 0.025 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500
#> [13] 0.550 0.600 0.650 0.700 0.750 0.800 0.850 0.900 0.950 0.975 0.990
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$output_type_id$optional
#> NULL
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$value
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$value$type
#> [1] "integer"
#> 
#> $rounds[[1]]$model_tasks[[1]]$output_type$quantile$value$minimum
#> [1] 0
#> 
#> 
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_id
#> [1] "wk inc flu hosp"
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_name
#> [1] "Weekly incident influenza hospitalizations"
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_units
#> [1] "count"
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_keys
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_keys$target
#> [1] "wk inc flu hosp"
#> 
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$target_type
#> [1] "continuous"
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$is_step_ahead
#> [1] TRUE
#> 
#> $rounds[[1]]$model_tasks[[1]]$target_metadata[[1]]$time_unit
#> [1] "week"
#> 
#> 
#> 
#> 
#> 
#> $rounds[[1]]$submissions_due
#> $rounds[[1]]$submissions_due$relative_to
#> [1] "origin_date"
#> 
#> $rounds[[1]]$submissions_due$start
#> [1] -6
#> 
#> $rounds[[1]]$submissions_due$end
#> [1] 1
#> 
#> 
#> 
#> $rounds[[2]]
#> $rounds[[2]]$round_id_from_variable
#> [1] TRUE
#> 
#> $rounds[[2]]$round_id
#> [1] "origin_date"
#> 
#> $rounds[[2]]$model_tasks
#> $rounds[[2]]$model_tasks[[1]]
#> $rounds[[2]]$model_tasks[[1]]$task_ids
#> $rounds[[2]]$model_tasks[[1]]$task_ids$origin_date
#> $rounds[[2]]$model_tasks[[1]]$task_ids$origin_date$required
#> NULL
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$origin_date$optional
#> [1] "2022-10-15" "2022-10-22" "2022-10-29"
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$target
#> $rounds[[2]]$model_tasks[[1]]$task_ids$target$required
#> [1] "wk inc flu hosp"
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$target$optional
#> NULL
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$horizon
#> $rounds[[2]]$model_tasks[[1]]$task_ids$horizon$required
#> [1] 1
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$horizon$optional
#> [1] 2 3 4
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$location
#> $rounds[[2]]$model_tasks[[1]]$task_ids$location$required
#> NULL
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$location$optional
#>  [1] "US" "01" "02" "04" "05" "06" "08" "09" "10" "11" "12" "13" "15" "16" "17"
#> [16] "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32"
#> [31] "33" "34" "35" "36" "37" "38" "39" "40" "41" "42" "44" "45" "46" "47" "48"
#> [46] "49" "50" "51" "53" "54" "55" "56" "72" "78"
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$age_group
#> $rounds[[2]]$model_tasks[[1]]$task_ids$age_group$required
#> [1] "65+"
#> 
#> $rounds[[2]]$model_tasks[[1]]$task_ids$age_group$optional
#> [1] "0-5"   "6-18"  "19-24" "25-64"
#> 
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$output_type_id
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$output_type_id$required
#> NULL
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$output_type_id$optional
#> [1] NA
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$value
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$value$type
#> [1] "integer"
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$mean$value$minimum
#> [1] 0
#> 
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$output_type_id
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$output_type_id$required
#>  [1] 0.010 0.025 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 0.450 0.500
#> [13] 0.550 0.600 0.650 0.700 0.750 0.800 0.850 0.900 0.950 0.975 0.990
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$output_type_id$optional
#> NULL
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$value
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$value$type
#> [1] "integer"
#> 
#> $rounds[[2]]$model_tasks[[1]]$output_type$quantile$value$minimum
#> [1] 0
#> 
#> 
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_id
#> [1] "wk inc flu hosp"
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_name
#> [1] "Weekly incident influenza hospitalizations"
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_units
#> [1] "count"
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_keys
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_keys$target
#> [1] "wk inc flu hosp"
#> 
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$target_type
#> [1] "continuous"
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$is_step_ahead
#> [1] TRUE
#> 
#> $rounds[[2]]$model_tasks[[1]]$target_metadata[[1]]$time_unit
#> [1] "week"
#> 
#> 
#> 
#> 
#> 
#> $rounds[[2]]$submissions_due
#> $rounds[[2]]$submissions_due$relative_to
#> [1] "origin_date"
#> 
#> $rounds[[2]]$submissions_due$start
#> [1] -6
#> 
#> $rounds[[2]]$submissions_due$end
#> [1] 1
#> 
#> 
#> 
#> 
#> attr(,"schema_id")
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/tasks-schema.json"
#> attr(,"type")
#> [1] "tasks"
#> attr(,"class")
#> [1] "config" "list"  
read_config(hub_path, "admin")
#> $schema_version
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/admin-schema.json"
#> 
#> $name
#> [1] "Simple Forecast Hub"
#> 
#> $maintainer
#> [1] "Consortium of Infectious Disease Modeling Hubs"
#> 
#> $contact
#> $contact$name
#> [1] "Joe Bloggs"
#> 
#> $contact$email
#> [1] "j.bloggs@cidmh.com"
#> 
#> 
#> $repository_url
#> [1] "https://github.com/hubverse-org/example-simple-forecast-hub"
#> 
#> $hub_models
#> $hub_models[[1]]
#> $hub_models[[1]]$team_abbr
#> [1] "simple_hub"
#> 
#> $hub_models[[1]]$model_abbr
#> [1] "baseline"
#> 
#> $hub_models[[1]]$model_type
#> [1] "baseline"
#> 
#> 
#> 
#> $file_format
#> [1] "csv"     "parquet" "arrow"  
#> 
#> $timezone
#> [1] "US/Eastern"
#> 
#> attr(,"schema_id")
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/admin-schema.json"
#> attr(,"type")
#> [1] "admin"
#> attr(,"class")
#> [1] "config" "list"  

# Read config file from AWS S3 bucket hub
hub_path <- arrow::s3_bucket("hubverse/hubutils/testhubs/simple/")
read_config(hub_path, "admin")
#> ℹ Updating superseded URL `Infectious-Disease-Modeling-hubs` to `hubverse-org`
#> $schema_version
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/admin-schema.json"
#> 
#> $name
#> [1] "Simple Forecast Hub"
#> 
#> $maintainer
#> [1] "Consortium of Infectious Disease Modeling Hubs"
#> 
#> $contact
#> $contact$name
#> [1] "Joe Bloggs"
#> 
#> $contact$email
#> [1] "j.bloggs@cidmh.com"
#> 
#> 
#> $repository_url
#> [1] "https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub"
#> 
#> $hub_models
#> $hub_models[[1]]
#> $hub_models[[1]]$team_abbr
#> [1] "simple_hub"
#> 
#> $hub_models[[1]]$model_abbr
#> [1] "baseline"
#> 
#> $hub_models[[1]]$model_type
#> [1] "baseline"
#> 
#> 
#> 
#> $file_format
#> [1] "csv"     "parquet" "arrow"  
#> 
#> $timezone
#> [1] "US/Eastern"
#> 
#> attr(,"schema_id")
#> [1] "https://raw.githubusercontent.com/hubverse-org/schemas/main/v2.0.0/admin-schema.json"
#> attr(,"type")
#> [1] "admin"
#> attr(,"class")
#> [1] "config" "list"