BART Serialization Routines

BART models contains external pointers to C++ objects, which means they cannot be correctly serialized to .Rds from an R session in their default state. This group of serialization functions allow us to convert between C++ data structures and a persistent JSON representation. The CppJson class wraps a performant C++ JSON API, and the functions saveBARTModelToJson and createBARTModelFromJson save to and load from this format. This representation, of course, also relies on external C++ pointers, so in order to save and reload BART models across sessions, we provide two other interfaces.

saveBARTModelToJsonString converts a BART model to an in-memory string containing the model's JSON representation and createBARTModelFromJsonString converts this representation back to a BART model object.

saveBARTModelToJsonFile and createBARTModelFromJsonFile save or reload a BART model directly to / from a .json file.

Finally, for cases in which multiple BART models have been sampled (for instance, multiple processes run via doParallel), we offer createBARTModelFromCombinedJson and createBARTModelFromCombinedJsonString for loading a new combined BART model from a list of BART JSON objects / strings.

Usage

saveBARTModelToJson(object)

saveBARTModelToJsonFile(object, filename)

saveBARTModelToJsonString(object)

createBARTModelFromJson(json_object)

createBARTModelFromJsonFile(json_filename)

createBARTModelFromJsonString(json_string)

createBARTModelFromCombinedJson(json_object_list)

createBARTModelFromCombinedJsonString(json_string_list)

Arguments

object

Object of type bartmodel containing draws of a BART model and associated sampling outputs.

filename

String of filepath, must end in ".json"

json_object

Object of type CppJson containing Json representation of a BART model

json_filename

String of filepath, must end in ".json"

json_string

JSON string dump

json_object_list

List of objects of type CppJson containing Json representation of a BART model

json_string_list

List of JSON strings which can be parsed to objects of type CppJson containing Json representation of a BART model

Value

saveBARTModelToJson return an object of type CppJson. saveBARTModelToJsonString returns a string dump of the BART model's JSON representation. saveBARTModelToJsonFile returns nothing, but writes to the provided filename.

createBARTModelFromJson, createBARTModelFromJsonFile, createBARTModelFromJsonString, createBARTModelFromCombinedJson, and createBARTModelFromCombinedJsonString all return objects of type bartmodel.

Examples

# Generate data
n <- 100
p <- 5
X <- matrix(runif(n*p), ncol = p)
y <- X[,1] + rnorm(n, 0, 1)

# Sample BART model
bart_model <- bart(X_train = X, y_train = y, num_gfr = 0,
                   num_burnin = 0, num_mcmc = 10)

# Save to in-memory JSON
bart_json <- saveBARTModelToJson(bart_model)
# Save to JSON string
bart_json_string <- saveBARTModelToJsonString(bart_model)
# Save to JSON file
tmpjson <- tempfile(fileext = ".json")
saveBARTModelToJsonFile(bart_model, file.path(tmpjson))

# Reload BART model from in-memory JSON object
bart_model_roundtrip <- createBARTModelFromJson(bart_json)
# Reload BART model from JSON string
bart_model_roundtrip <- createBARTModelFromJsonString(bart_json_string)
# Reload BART model from JSON file
bart_model_roundtrip <- createBARTModelFromJsonFile(file.path(tmpjson))
unlink(tmpjson)
# Reload BART model from list of JSON objects
bart_model_roundtrip <- createBARTModelFromCombinedJson(list(bart_json))
# Reload BART model from list of JSON strings
bart_model_roundtrip <- createBARTModelFromCombinedJsonString(list(bart_json_string))