First go

mostly generated by o1-mini based on a sample JSON file. I went through by hand and fixed most of the obvious issues. Will return tomorrow.

DESCRIPTION

@@ -35,6 +35,7 @@ Imports:
     jsonlite,
     rlang,
     rstan,
+    S7,
     tidybayes
 Additional_repositories:
     https://stan-dev.r-universe.dev

R/config.R

@@ -0,0 +1,211 @@
+#' Exclusions Class
+#'
+#' Represents exclusion criteria for the pipeline.
+#'
+#' @slot path A string specifying the path to a CSV file containing exclusion
+#' data. It should include at least the columns: `reference_date`,
+#' `report_date`, ' `state_abb`, `disease`.
+Exclusions <- S7::new_class(
+  "Exclusions",
+  properties = list(
+    path = class_character
+  )
+)
+
+#' GenerationInterval Class
+#'
+#' Represents the generation interval parameters.
+#'
+#' @slot path A string specifying the path to the generation interval CSV file.
+#' @slot blob_storage_container Optional. The name of the blob storage container
+#' to get it from. If NULL, will look locally.
+GenerationInterval <- S7::new_class(
+  "GenerationInterval",
+  properties = list(
+    path = class_character,
+    blob_storage_container = class_character
+  )
+)
+
+#' DelayInterval Class
+#'
+#' Represents the delay interval parameters.
+#'
+#' @slot path A string specifying the path to the delay interval CSV file.
+#' @slot blob_storage_container Optional. The name of the blob storage container
+#' to get it from. If NULL, will look locally.
+DelayInterval <- S7::new_class(
+  "DelayInterval",
+  properties = list(
+    path = class_character,
+    blob_storage_container = class_character
+  )
+)
+
+#' RightTruncation Class
+#'
+#' Represents the right truncation parameters.
+#'
+#' @slot path A string specifying the path to the right truncation CSV file.
+#' @slot blob_storage_container Optional. The name of the blob storage container
+#' to get it from. If NULL, will look locally.
+RightTruncation <- S7::new_class(
+  "RightTruncation",
+  properties = list(
+    path = class_character,
+    blob_storage_container = class_character
+  )
+)
+
+#' Parameters Class
+#'
+#' Holds all parameter-related configurations for the pipeline.
+#'
+#' @slot generation_interval An instance of `GenerationInterval` class.
+#' @slot delay_interval An instance of `DelayInterval` class.
+#' @slot right_truncation An instance of `RightTruncation` class.
+Parameters <- S7::new_class(
+  "Parameters",
+  properties = list(
+    generation_interval = class_GenerationInterval,
+    delay_interval = class_DelayInterval,
+    right_truncation = class_RightTruncation
+  )
+)
+
+#' RtPrior Class
+#'
+#' Represents the Rt prior parameters.
+#'
+#' @slot mean A numeric value representing the mean of the Rt prior.
+#' @slot sd A numeric value representing the standard deviation of the Rt prior.
+RtPrior <- S7::new_class(
+  "RtPrior",
+  properties = list(
+    mean = class_numeric,
+    sd = class_numeric
+  )
+)
+
+#' GpPrior Class
+#'
+#' Represents the Gaussian Process prior parameters.
+#'
+#' @slot alpha_sd A numeric value representing the standard deviation of the
+#' alpha parameter in the GP prior.
+GpPrior <- S7::new_class(
+  "GpPrior",
+  properties = list(
+    alpha_sd = class_numeric
+  )
+)
+
+#' Priors Class
+#'
+#' Holds all prior-related configurations for the pipeline.
+#'
+#' @slot rt An instance of `RtPrior` class.
+#' @slot gp An instance of `GpPrior` class.
+Priors <- S7::new_class(
+  "Priors",
+  properties = list(
+    rt = class_RtPrior,
+    gp = class_GpPrior
+  )
+)
+
+#' Data Class
+#'
+#' Represents the data-related configurations.
+#'
+#' @slot path A string specifying the path to the data Parquet file.
+#' @slot blob_storage_container Optional. The name of the blob storage container
+#' to which the data file will be uploaded. If NULL, no upload will occur.
+#' @slot report_date A list of strings representing report dates.
+#' @slot reference_date A list of strings representing reference dates.
+#' @slot production_date A list of strings representing production dates.
+Data <- S7::new_class(
+  "Data",
+  properties = list(
+    path = class_character,
+    blob_storage_container = class_character,
+    report_date = class_list,
+    reference_date = class_list,
+    production_date = class_list
+  )
+)
+
+#' SamplerOpts Class
+#'
+#' Represents the sampler options for the pipeline.
+#'
+#' @slot cores An integer specifying the number of CPU cores to use.
+#' @slot chains An integer specifying the number of Markov chains.
+#' @slot iter_warmup An integer specifying the number of warmup iterations.
+#' @slot iter_sampling An integer specifying the number of sampling iterations.
+#' @slot adapt_delta A numeric value for the target acceptance probability.
+#' @slot max_treedepth An integer specifying the maximum tree depth for the
+#' sampler.
+SamplerOpts <- S7::new_class(
+  "SamplerOpts",
+  properties = list(
+    cores = class_integer,
+    chains = class_integer,
+    iter_warmup = class_integer,
+    iter_sampling = class_integer,
+    adapt_delta = class_numeric,
+    max_treedepth = class_integer
+  )
+)
+
+#' Config Class
+#'
+#' Represents the complete configuration for the pipeline.
+#'
+#' @slot job_id A string specifying the job.
+#' @slot task_id A string specifying the task.
+#' @slot min_reference_date A Date object representing the minimum reference
+#' date.
+#' @slot max_reference_date A Date object representing the maximum reference
+#' date.
+#' @slot disease A string specifying the disease being modeled.
+#' @slot geo_value A string specifying the geographic value, usually a state.
+#' @slot geo_type A string specifying the geographic type, usually "state".
+#' @slot data An instance of `Data` class containing data configurations.
+#' @slot seed An integer for setting the random seed.
+#' @slot horizon An integer specifying the forecasting horizon.
+#' @slot priors An instance of `Priors` class containing prior configurations.
+#' @slot parameters An instance of `Parameters` class containing parameter
+#' configurations.
+#' @slot sampler_opts An instance of `SamplerOpts` class containing sampler
+#' options.
+#' @slot exclusions An instance of `Exclusions` class containing exclusion
+#' criteria.
+#' @slot config_version A numeric value specifying the configuration version.
+#' @slot quantile_width A list of numeric values representing the desired
+#' quantiles.
+#' @slot model A string specifying the model to be used.
+#' @slot report_date A Date object representing the report date.
+Config <- S7::new_class(
+  "Config",
+  properties = list(
+    job_id = class_character,
+    task_id = class_character,
+    min_reference_date = class_Date,
+    max_reference_date = class_Date,
+    disease = class_character,
+    geo_value = class_character,
+    geo_type = class_character,
+    data = class_Data,
+    seed = class_integer,
+    horizon = class_integer,
+    priors = class_Priors,
+    parameters = class_Parameters,
+    sampler_opts = class_SamplerOpts,
+    exclusions = class_Exclusions,
+    config_version = class_numeric,
+    quantile_width = class_list,
+    model = class_character,
+    report_date = class_Date
+  )
+)