SWI-Prolog interface to R
Nicos Angelopoulos
Abstract
This article documents the package R, a library to talk to R system for Statistical Computing.

## 1 R.pl: R session

author
  Nicos Angelopoulos
version
  0:0:7
See also
  - `ensure_loaded(library('../doc/packages/examples/R/r_demo.pl'))`
  - http://www.r-project.org/
copyright
  Nicos Angelopoulos
license
  GPL+SWI-exception or Artistic 2.0

This library facilitates interaction with the R system for statistical computing. It assumes an R executable in $PATH or can be given a location to a functioning R executable (see r_bin/1 and r_open/1 for details on how R is located). R is ran as a slave with Prolog writing on and reading from the associated streams. Multiple sessions can be managed simultaneously. Each has 3 main components: a name or alias, a term structure holding the communicating streams and a number of associated data items.

The library attempts to ease the translation between prolog terms and R inputs. Thus, Prolog term `x <- c(1,2,3)` is translated to atomic `'x <- c(1,2,3)'` which is then passed on to R. That is, `<-` is a defined/recognised operator. `X <- c(1,2,3)`, where X is a variable, instantiates X to the list `[1,2,3]`. Also 'Atom' <- [x1,...,xn] translates to R code: Atom <- `c(x1,...,xn)`. Currently vectors, matrices and (R)-lists are translated in this fashion. The goal "A <- B" translates to `r_in( A <- B )`.

Although the library is primarily meant to be used as a research tool, it still provides access to many functions of the R system that may render it useful to a wider audience. The library provides access to R's plethora of vector and scalar functions. We adicipate that of particular interest to Prolog programmers might be the fact that the library can be used to create plots from Prolog objects. Notably creating plots from lists of numbers.

There is a known issue with X11 when R is started without --interactive. `R.pl` runs by default the --interactive flag and try to surpress echo output. If you do get weird output, try giving to r_open, option `with(non_interactive)`. This is suboptimal for some tasks, but might resolve other issues. There is a issue with Macs, where --interactive doesnot work. On Macs, you should use `with(non_interactive)`. This can also be achieved using settings/2.

These capabilities are illustrated in the following example :

    rtest :-
         r_open,
         y <- rnorm(50),
         r_print( y ),
         x <- rnorm(y),
         r_in( x11(width=5,height=3.5) ),
         r_in( plot(x,y) ),
         write( 'Press Return to continue...' ), nl,
         read_line_to_codes( user_input, _ ),
         r_print( 'dev.off()' ),
         Y <- y,
         write( y(Y) ), nl,
         findall( Zx, between(1,9,Zx), Z ),
         z <- Z,
         r_print( z ),
         cars <- c(1, 3, 6, 4, 9),
         r_in(pie(cars)),
         write( 'Press Return to continue...' ), nl,
         read_line_to_codes( user_input, _ ),
         r_close.

r_bin(?Rbin)
  Register the default R location, +Rbin, or interrogate the current location: -Rbin. When interrogating Rbin is bound to the R binary that would be used by an r_open/0. The order of search is: registered location, environment variable 'R_BIN' and path defined. On unix systems path defined is the first R executable in $PATH. On MS wins it is the latest Rterm.exe found by `expand_file_name( 'C:/Program Files/R/R-*/bin/Rterm.exe', Candidates )`. The value Rbin `==` `retract` retracts the current registered location. Rbin `==` `test`, succeeds if an R location has been registered.
r_open
  Open a new R session. Same as `r_open( [] )`.
r_start
  Only start and session via r_open/1, if no open session existss.
r_open(+Opts)
  Open a new R session with optional list of arguments. Opts should be a list of the following
  alias(Alias)
    Name for the session. If absent or a variable an opaque term is generated.
  assert(A)
    Assert token. By default session opened last is the default session (see default_r_session/1). Using A = `z` will push the session to the bottom of the pile.
  at_r_halt(RHAction)
    R slaves used to halt when they encounter an error. This is no longer the case but this option is still present in case it is useful in the future. This option provides a handle to changing the behaviour of the session when a halt of the R-slave occurs. RHAction should be one of `abort`, `fail`, call/1, call_ground/1, `reinstate` or `restart`. Default is `fail`. When RHAction is `reinstate`, the history of the session is used to roll-back all the commands sent so far. At `restart' the session is restarted with same name and options, but history is not replayed.
  copy(CopyTo, CopyWhat)
    Records interaction with R to a file/stream. CopyTo should be one of `null`, `stream(Stream)`, OpenStream, AtomicFile, `once(File)` or `many(File)`. In the case of `many(File)`, file is opened and closed at each write operation. CopyWhat should be one of `both`, `in`, `out` or `none`. Default is no recording (CopyTo = `null`).
  ssh(Host)
  ssh(Host, Dir)
    Run R on Host with start directory Dir. Dir defaults to /tmp. Not supported on MS Windows.
  rbin(Rbin)
    R executable location to use for this open operation. If the option is not present binary registered with r_bin/1 and environment variable R_BIN are examined for the full location of the R binary. In MS windows Rbin should point to Rterm.exe. Also see r_bin/1.
  with(With)
    With is in [environ,non_interactive,restore,save]. The default behaviour is to start the R executable with flags `interactive --no-environ --no-restore --no-save`. For each With value found in Opts the corresponding `--no-` flag is removed. In the case of non_interactive, it removes the default --interactive. This makes the connection more robust, and allows proper x11 plots in linux. However you get alot all the echos of what you pipe in, back from R.
r_close
  Close the default R session.
r_close(+R)
  Close the named R session.
r_in(+Rcmd)
  Push Rcmd to the default R session. Output and Errors will be printed to the terminal.
r_in(+R, +Rcmd)
  As r_in/1 but for session R.
r_push(+Rcmd)
  As r_in/1 but does not consume error or output streams.
r_push(+R, +Rcmd)
  As r_push/1 but for named session.
r_out(+Rcmd, -Lines)
  Push Rcmd to default R session and grab output lines Lines as a list of code lists.
r_out(+R, +Rcmd, -Lines)
  As r_out/2 but for named session R.
r_err(+Rcmd, -Lines, -ErrLines)
  Push Rcmd to default R session and grab output lines Lines as a list of code lists. Error lines are in ErrLines.
r_err(+R, +Rcmd, -Lines, -ErrLines)
  As r_err/3 but for named session R.
r_print(+X)
  A shortcut for `r_in( print(X) )`.
r_print(+R, +X)
  As r_print/1 but for named session R.
r_lines_print(+Lines)
  Print a list of code lists (Lines) to the user_output. Lines would normally be read of an R stream.
r_lines_print(+Lines, +Type)
  As r_lines_print/1 but Type declares whether to treat lines as output or error response. In the latter case they are written on user_error and prefixed with '!'.
r_lines_print(+Lines, +Type, +Stream)
  As r_lines_print/3 but Lines are written on Stream.
r_lib(+L)
  A shortcut for `r_in( library(X) )`.
r_lib(+R, +L)
  As r_lib/1 but for named session R.
r_flush
  Flush default R's output and error on to the terminal.
r_flush(+R)
  As r_flush/0 but for session R.
r_flush_onto(+SAliases, -Onto)
  Flush stream aliases to code lists Onto. SAliases should be one of, or a list of, [output,error].
r_flush_onto(+R, +SAliases, -Onto)
  As r_flush_onto/2 for specified session R.
current_r_session(?R)
  True if R is the name of current R session. Can be used to enumerate all open sessions.
current_r_session(?R, ?S, ?D)
  True if R is an open session with streams S and data D (see introduction to the library).
default_r_session(?R)
  True if R is the default session.
r_streams_data(+SId, +Streams, -S)
  True if Streams is an R session streams structure and S is its stream corresponding to identifier SId, which should be one of [input,output,error].
r_session_data(+DId, +Data, -Datum)
  True if Data is a structure representing R session associated data and Datum is its data item corresponding to data identifier DId. DId should be in [at_r_halt,copy_to,copy_this,interactive,version,opts].
r_history
  Print on user_output the history of the default session.
r_history(-H)
  H unifies to the history list of the Rcmds fed into the default session. Most recent command appears at the head of the list.
r_history(?R, -H)
  As r_history/1 but for named session R. It can be used to enumerate all histories. It fails when no session is open.
r_session_version(-Version)
  Installed version. Version is of the form Major:Minor:Fix, where all three are integers.
r_verbosity(?Level)
  Set, +Level, or interrogate, -Level, the verbosity level. +Level could be `false` (=0), `true` (=3) or an integer in {0,1,2,3}. 3 being the most verbose. The default is 0. -Level will instantiate to the current verbosity level, an integer in {0,1,2,3}.
r_bin_version(-Version)
  Get the version of R binary identified by r_bin/1. Version will have the same structure as in r_session_version/1 ie M:N:F.
r_bin_version(+Rbin, -Version)
  Get the version of R binary identified by +Rbin. Version will have the same structure as in r_session_version/1 ie M:N:F.
[multifile]settings(+Setting, +Value)
  Multifile hook-predicate that allows for user settings to sip through. Currently the following are recognised:
  r_open_opt
    These come after any options given explicitly to r_open/1. For example on a Mac to avoid issue with --interactive use the following before querring r_open/0,1.

        :- multifile settings/2.
        r_session:settings(r_open_opt,with(non_interactive)).

  atom_is_r_function
    expands atoms such as x11 to r function calls x11()
  r_function_def(+Function)
    where Function is an R function. This hook allows default argument values to R functions. Only Arg=Value pairs are allowed.

        :- multifile settings/2.
        r_session:settings(r_function_def(x11),width=5).

# Index

?
current_r_session/1
current_r_session/3
default_r_session/1
r_bin/1
r_bin_version/1
r_bin_version/2
r_close/0
r_close/1
r_err/3
r_err/4
r_flush/0
r_flush/1
r_flush_onto/2
r_flush_onto/3
r_history/0
r_history/1
r_history/2
r_in/1
r_in/2
r_lib/1
r_lib/2
r_lines_print/1
r_lines_print/2
r_lines_print/3
r_open/0
r_open/1
r_out/2
r_out/3
r_print/1
r_print/2
r_push/1
r_push/2
r_session_data/3
r_session_version/1
r_start/0
r_streams_data/3
r_verbosity/1
settings/2