Write data to a JSON file readable by CmdStan

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")
#> { #> "N": 5, #> "K": 2, #> "x": [ #> [0.552235993548325, 0.721685253131368], #> [1.40374671287315, -0.278162254251497], #> [0.512051509623765, -0.524699374531002], #> [0.660479109910809, 0.0625388737657775], #> [-0.519175154088263, -0.450598871694098] #> ], #> "y": [16, 11, 7, 7, 6], #> "z": [1, 0] #> }
# 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")
#> { #> "x": [ #> [1, 2, 3], #> [4, 5, 6] #> ] #> }