Public API

Types

# RCall.AnySxp — Type.

R "any" object

# RCall.BcodeSxp — Type.

R byte code

# RCall.BuiltinSxp — Type.

R built-in function

# RCall.CharSxp — Type.

R character string

# RCall.ClosSxp — Type.

R function closure

# RCall.CplxSxp — Type.

R complex vector

# RCall.DotSxp — Type.

R dot-dot-dot object

# RCall.EnvSxp — Type.

R environment

# RCall.ExprSxp — Type.

R expression vector

# RCall.ExtPtrSxp — Type.

R external pointer

# RCall.IntSxp — Type.

R integer vector

# RCall.LangSxp — Type.

R function call

# RCall.LglSxp — Type.

R logical vector

# RCall.ListSxp — Type.

R pairs (cons) list cell

# RCall.NilSxp — Type.

R NULL value

# RCall.PromSxp — Type.

R promise

# RCall.RObject — Type.

An RObject is a Julia wrapper for an R object (known as an "S-expression" or "SEXP"). It is stored as a pointer which is protected from the R garbage collector, until the RObject itself is finalized by Julia. The parameter is the type of the S-expression.

When called with a Julia object as an argument, a corresponding R object is constructed.

julia> RObject(1)
RObject{IntSxp}
[1] 1

julia> RObject(1:3)
RObject{IntSxp}
[1] 1 2 3

julia> RObject(1.0:3.0)
RObject{RealSxp}
[1] 1 2 3

# RCall.RawSxp — Type.

R byte vector

# RCall.RealSxp — Type.

R real vector

# RCall.S4Sxp — Type.

R S4 object

# RCall.SpecialSxp — Type.

R special function

# RCall.StrSxp — Type.

R vector of character strings

# RCall.Sxp — Type.

R symbolic expression (SxpPtr): these are represented by a pointer to a symbolic expression record (Sxp).

# RCall.SxpHead — Type.

R Sxp header: a pointer to this is used for unknown types.

# RCall.SymSxp — Type.

R symbol

# RCall.VecSxp — Type.

R list (i.e. Array{Any,1})

# RCall.WeakRefSxp — Type.

R weak reference

Methods

# Base.eltype — Function.

Element types of R vectors.

# Base.getindex — Function.

extract the value of symbol s in the environment e

extract the i-th element of LangSxp l

String indexing finds the first element with the matching name

Indexing into VectorSxp types uses Julia indexing into the vec result, except for StrSxp and the VectorListSxp types, which must apply sexp to the Ptr{Void} obtained by indexing into the vec result.

# Base.isascii — Function.

Determines the encoding of the CharSxp. This is determined by the 'gp' part of the sxpinfo (this is the middle 16 bits). * 0x00_0002_00 (bit 1): set of bytes (no known encoding) * 0x00_0004_00 (bit 2): Latin-1 * 0x00_0008_00 (bit 3): UTF-8 * 0x00_0040_00 (bit 6): ASCII

We only support ASCII and UTF-8.

# Base.length — Function.

Sxp methods for length return the R length.

Rf_xlength handles Sxps that are not vector-like and R's "long vectors", which have a negative value for the length member.

# Base.setindex! — Function.

assign value v to symbol s in the environment e

assign value v to the i-th element of LangSxp l

# RCall.NAel — Function.

NA element for each type

# RCall.ParseVector — Function.

A pure julia wrapper of R_ParseVector

# RCall.anyNA — Function.

Check if there are any NA values in the vector.

# RCall.bound — Function.

The R NAMED property, represented by 2 bits in the info field. This can take values 0,1 or 2, corresponding to whether it is bound to 0,1 or 2 or more symbols. See http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Named-objects-and-copying

# RCall.callJuliaExtPtr — Function.

The function called by R .External for Julia callbacks.

It receives a ListSxpPtr containing - a pointer to the function itself (ExtPtrSxpPtr) - a pointer to the Julia function (ExtPtrSxpPtr) - any arguments (as SxpPtr)

# RCall.dataptr — Function.

Pointer to start of the data array in a SEXPREC. Corresponds to DATAPTR C macro.

# RCall.decrefExtPtr — Function.

Called by the R finalizer.

# RCall.endEmbeddedR — Function.

endEmbeddedR()

Close embedded R session.

# RCall.findNamespace — Function.

find namespace by name of the namespace, it is not error tolerant.

# RCall.getAttrib — Function.

Return a particular attribute of an RObject

# RCall.getClass — Function.

Returns the class of an R object.

# RCall.getNames — Function.

Returns the names of an R vector.

# RCall.getNamespace — Function.

get namespace by name of the namespace. It is safer to be used than findNamespace as it checks bound.

# RCall.ijulia_displayplots — Function.

Called after cell evaluation. Closes graphics device and displays files in notebook.

# RCall.ijulia_setdevice — Function.

Set options for R plotting with IJulia.

The first argument should be a MIME object: currently supported are * MIME("image/png") [default] * MIME("image/svg+xml")

The remaining arguments (keyword only) are passed to the appropriate R graphics device: see the relevant R help for details.

# RCall.initEmbeddedR — Function.

initEmbeddedR()

This initializes an embedded R session. It should only be called when R is not already running (e.g. if Julia is running inside an R session)

# RCall.isFactor — Function.

Check whether an R variable is a factor variable

# RCall.isNA — Function.

Check if values correspond to R's sentinel NA values.

# RCall.isOrdered — Function.

Check whether an R variable is an ordered factor variable

# RCall.makeExternalPtr — Function.

Create an ExtPtrSxpPtr object

# RCall.makeNativeSymbol — Function.

Register a function pointer as an R NativeSymbol.

This is completely undocumented, so may break: we technically are supposed to use R_registerRoutines, but this is much easier for just 1 function.

# RCall.newEnvironment — Function.

newEnvironment([env])

Create a new environment which extends environment env (globalEnv by default).

# RCall.parse_rscript — Function.

Parses an inline R script, substituting invalid ":($(Expr(:incomplete, "incomplete: invalid string syntax")))

# RCall.preserve — Function.

Prevent garbage collection of an R object. Object can be released via release.

This is slower than protect, as it requires searching an internal list, but more flexible.

# RCall.protect — Function.

Stack-based protection of garbage collection of R objects. Objects are released via unprotect. Returns the same pointer, allowing inline use.

This is faster than preserve, but more restrictive. Really only useful inside functions.

# RCall.rcall — Function.

Evaluate a function in the global environment. The first argument corresponds to the function to be called. It can be either a FunctionSxp type, a SymSxp or a Symbol.

# RCall.rcopy — Function.

Evaluate and convert the result of a string as an R expression.

rcopy copies the contents of an R object into a corresponding canonical Julia type.

rcopy(T,p) converts a pointer p to a Sxp object to a native Julia object of type T.

rcopy(p) performs a default conversion.

# RCall.registerFinalizer — Function.

Register finalizer to be called by the R GC.

# RCall.release — Function.

Release object that has been gc protected by preserve.

# RCall.reval — Function.

Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning an RObject.

# RCall.reval_p — Function.

Evaluate an R symbol or language object (i.e. a function call) in an R try/catch block, returning a Sxp pointer.

Evaluate an R expression array iteratively.

# RCall.rlang — Function.

Create a function call from a function pointer and a list of arguments and return it as an RObject, which can then be evaulated

# RCall.rlang_p — Function.

Create a function call from a list of arguments

# RCall.rparse — Function.

Parse a string as an R expression, returning an RObject.

# RCall.rparse_p — Function.

Parse a string as an R expression, returning a Sxp pointer.

# RCall.rprint — Function.

Parse, evaluate and print the result of a string as an R expression.

Print the value of an Sxp using R's printing mechanism

# RCall.setAttrib! — Function.

Set a particular attribute of an RObject

# RCall.setClass! — Function.

Set the class of an R object.

# RCall.setNames! — Function.

Set the names of an R vector.

# RCall.sexp — Function.

Wrap a callable Julia object f an a R ClosSxpPtr.

Constructs the following R code

function(...) .External(juliaCallback, fExPtr, ...)

Wrap a Julia object an a R ExtPtrSxpPtr.

We store the pointer and the object in a const Dict to prevent it being removed by the Julia GC.

Create a StrSxp from an AbstractString

Create a CharSxp from a String.

Generic function for constructing Sxps from Julia objects.

Create a SymSxp from a Symbol

sexp(S,x) converts a Julia object x to a pointer to a Sxp object of type S.

sexp(x) performs a default conversion.

Convert a UnknownSxpPtr to an approptiate SxpPtr.

# RCall.sexp_arglist_dots — Function.

Create an argument list for an R function call, with a varargs "dots" at the end.

# RCall.sexpnum — Function.

The SEXPTYPE number of a Sxp

Determined from the trailing 5 bits of the first 32-bit word. Is a 0-based index into the info field of a SxpHead.

# RCall.tryEval — Function.

A pure julia wrapper of R_tryEval.

# RCall.unprotect — Function.

Release last n objects gc-protected by protect.

# RCall.unsafe_array — Function.

The same as unsafe_vec, except returns an appropriately sized array.

# RCall.unsafe_vec — Function.

Represent the contents of a VectorSxp type as a Vector.

This does not copy the contents. If the argument is not named (in R) or otherwise protected from R's garbage collection (e.g. by keeping the containing RObject in scope) the contents of this vector can be modified or could cause a memory error when accessed.

The contents are as stored in R. Missing values (NA's) are represented in R by sentinels. Missing data values in RealSxp and CplxSxp show up as NaN and NaN + NaNim, respectively. Missing data in IntSxp show up as -2147483648, the minimum 32-bit integer value. Internally a LglSxp is represented as Vector{Int32}. The convention is that 0 is false, -2147483648 is NA and all other values represent true.

Macros

# RCall.@R_str — Macro.

R"..."

An inline R expression, the result of which is evaluated and returned as an RObject.

It supports substitution of Julia variables and expressions via prefix with $ whenever not valid R syntax (i.e. when not immediately following another completed R expression):

R"glm(Sepal.Length ~ Sepal.Width, data=$iris)"

It is also possible to pass Julia expressions:

R"plot((anonymous function))"

All such Julia expressions are evaluated once, before the R expression is evaluated.

The expression does not support assigning to Julia variables, so the only way retrieve values from R via the return value.

# RCall.@rget — Macro.

Copies variables from R to Julia using the same name.

# RCall.@rimport — Macro.

Import an R Package as a Julia module. You can also use classic Python syntax to make an alias: @rimport *module-name* as *shorthand*

# RCall.@rlibrary — Macro.

Load all exported functions/objects of a R package to the current module.

# RCall.@rput — Macro.

Copies variables from Julia to R using the same name.

# RCall.@var_str — Macro.

Returns a variable named "str". Useful for passing keyword arguments containing dots.

Constants

# RCall.globalEnv — Constant.

R global Environment.

globalEnv[:x] = 1
globalEnv[:x]

# RCall.jtypExtPtrs — Constant.

Julia types (typically functions) which are wrapped in ExtPtrSxpPtr are stored here to prevent garbage collection by Julia.

# RCall.typs — Constant.

vector of R Sxp types