Write data to a JSON file readable by CmdStan
write_stan_json(data, file, always_decimal = FALSE)
(list) A named list of R objects.
(string) The path to where the data file should be written.
(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.
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
.
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]
#> ]
#> }