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": [
#>     [1.39067866394794, 0.962441316104017],
#>     [-0.473566508639385, -0.892862153643971],
#>     [-2.10865772647623, 0.757598190570521],
#>     [-0.366087824635297, -0.120402278774405],
#>     [1.44942517823716, -0.444483690720062]
#>   ],
#>   "y": [5, 11, 1, 9, 11],
#>   "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]
#>   ]
#> }