write_stan_json: Write data to a JSON file readable by CmdStan

In stan-dev/cmdstanr: R Interface to 'CmdStan'

Write data to a JSON file readable by CmdStan

Description

Write data to a JSON file readable by CmdStan

Usage

write_stan_json(data, file, always_decimal = FALSE)

Arguments

data	(list) A named list of R objects.
file	(string) The path to where the data file should be written.
always_decimal	(logical) Force generate non-integers with decimal points to better distinguish between integers and floating point values. If TRUE all R objects in data intended for integers must be of integer type.

Details

write_stan_json() performs several conversions before writing the JSON file:

• logical -> integer (TRUE -> 1, FALSE -> 0)

• data.frame -> matrix (via data.matrix())

• list -> array

• table -> vector, matrix, or array (depending on dimensions of table)

The list to array conversion is intended to make it easier to prepare the data for certain Stan declarations involving arrays:

• ⁠vector[J] v[K]⁠ (or equivalently ⁠array[K] vector[J] v ⁠ as of Stan 2.27) can be constructed in R as a list with K elements where each element a vector of length J

• ⁠matrix[I,J] v[K]⁠ (or equivalently ⁠array[K] matrix[I,J] m ⁠ as of Stan 2.27 ) can be constructed in R as a list with K elements where each element an IxJ matrix

These can also be passed in from R as arrays instead of lists but the list option is provided for convenience. Unfortunately for arrays with more than one dimension, e.g., ⁠vector[J] v[K,L]⁠ (or equivalently ⁠array[K,L] vector[J] v ⁠ as of Stan 2.27) it is not possible to use an R list and an array must be used instead. For this example the array in R should have dimensions KxLxJ.

Examples

x <- matrix(rnorm(10), 5, 2)
y <- rpois(nrow(x), lambda = 10)
z <- c(TRUE, FALSE)
data <- list(N = nrow(x), K = ncol(x), x = x, y = y, z = z)

# write data to json file
file <- tempfile(fileext = ".json")
write_stan_json(data, file)

# check the contents of the file
cat(readLines(file), sep = "\n")


# demonstrating list to array conversion
# suppose x is declared as `vector[3] x[2]` (or equivalently `array[2] vector[3] x`)
# we can use a list of length 2 where each element is a vector of length 3
data <- list(x = list(1:3, 4:6))
file <- tempfile(fileext = ".json")
write_stan_json(data, file)
cat(readLines(file), sep = "\n")

stan-dev/cmdstanr documentation built on May 1, 2024, 7:17 a.m.