rstan: stan_rdump – R documentation

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stan_rdump

Dump the data for a Stan model to R dump file in the limited format that Stan can read.

Description

This function takes a vector of names of R objects and outputs text representations of the objects to a file or connection. The file created by stan_rdump is typically used as data input of the Stan package (http://mc-stan.org/) or sourced into another R session. The usage of this function is very similar to dump in R.

Usage

stan_rdump(list, file = "", append = FALSE, 
          envir = parent.frame(),
          width = options("width")$width, 
          quiet = FALSE)

Arguments

`list`	A vector of character string: the names of one or more R objects to be dumped. See the note below.
`file`	Either a character string naming a file or a connection. `""` indicates output to the console.
`append`	Logical: if `TRUE` and `file` is a character string, output will be appended to `file`; otherwise, it will overwrite the contents of `file`.
`envir`	The environment to search for objects.
`width`	The width for maximum characters on a line. The output is broken into lines with `width.`
`quiet`	Whether to suppress warning messages that would appear when a variable is not found or not supported for dumping (not being numeric or it would not be converted to numeric) or a variable name is not allowed in Stan.

Value

An invisible character vector containing the names of the objects that were dumped.

Note

stan_rdump only dumps numeric data, which first can be a scalar, vector, matrix, or (multidimensional) array. Additional types supported are logical (TRUE and FALSE), factor, data.frame and a specially structured list.

The conversion for logical variables is to map TRUE to 1 and FALSE to 0. For factor variable, function as.integer is used to do the conversion (If we want to transform a factor f to approximately its original numeric values, see the help of function factor and do the transformation before calling stan_rdump). In the case of data.frame, function data.matrix is applied to the data frame before dumping. See the notes in stan for the specially structured list, which will be converted to array before dumping.

stan_rdump will check whether the names of objects are legal variable names in Stan. If an illegal name is found, data will be dumped with a warning. However, passing the name checking does not necessarily mean that the name is legal. More details regarding rules of variable names in Stan can be found in Stan's manual.

If objects with specified names are not found, a warning will be issued.

References

The Stan Development Team Stan Modeling Language User's Guide and Reference Manual. http://mc-stan.org.

Examples

# set variables in global environment
a <- 17.5
b <- c(1,2,3)
# write variables a and b to file ab.data.R in temporary directory
stan_rdump(c('a','b'), file.path(tempdir(), "ab.data.R"))
unlink(file.path(tempdir(), "ab.data.R"))

x <- 1; y <- 1:10; z <- array(1:10, dim = c(2,5)) 
stan_rdump(ls(pattern = '^[xyz]'), file.path(tempdir(), "xyz.Rdump"))
cat(paste(readLines(file.path(tempdir(), "xyz.Rdump")), collapse = '\n'), '\n')
unlink(file.path(tempdir(), "xyz.Rdump"))

rstan

R Interface to Stan

v2.21.2

GPL (>= 3)

Authors

Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Sebastian Weber [aut], Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Modrak Martin [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R, R/dynGet.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), John Maddock [cph] (gamma.hpp), Paul Bristow [cph] (gamma.hpp), Nikhar Agrawal [cph] (gamma.hpp), Christopher Kormanyos [cph] (gamma.hpp), Bronder Steve [ctb]

Initial release

2020-07-27