/*** DO NOT EDIT THIS LINE -----------------------------------------------------
Version: 2.1.2
Title: rcall
Description: seamless interactive __[R](https://cran.r-project.org/)__ in Stata.
The command automatically returns {help return:rclass} R objects with
_integer_, _numeric_, _character_, _logical_, _matrix_, _data.frame_, _list_, and _NULL_
classes to Stata. It also allows passing Stata variable, dataset,
macro, scalar, and matrix to R as well as load a dataframe from R
to Stata automatically,
which provides an automated reciprocal communication between Stata and R. For
more information and examples visit [rcall homepage](http://www.haghish.com/packages/Rcall.php).
----------------------------------------------------- DO NOT EDIT THIS LINE ***/
/***
Syntax
======
To call R from Stata use the following syntax
{p 8 16 2}
rcall [{help rcall##modes:{it:mode}}] [{cmd::}] [{it:R-command}]
{p_end}
the package also includes a few subcommands to facilitate integrating R in Stata
{p 8 16 2}
rcall [{help rcall##subcommand:{it:subcommand}}]
{p_end}
the following functions can be used to communicate data from Stata to R:
{synoptset 22 tabbed}{...}
{synopthdr:Function}
{synoptline}
{synopt:{opt st.scalar(name)}}passes a scalar to R{p_end}
{synopt:{opt st.matrix(name)}}passes a matrix to R{p_end}
{synopt:{opt st.var(varname)}}passes a numeric or string variable to R{p_end}
{synopt:{opt st.data(filename)}}passes Stata data to R. without _filename_, the currently loaded data is used. {p_end}
{synopt:{opt st.load(dataframe)}}loads data from R dataframe to Stata{p_end}
{synoptline}
{p2colreset}{...}
programmers can use __rcall_check__ to evaluate the required version of R or R packages:
{p 8 16 2}
{browse "http://www.haghish.com/packages/Rcall.php#check":{bf:rcall_check}} [{it:pkgname>=ver}] [{it:pkgname>=ver}] [...] , {opt r:version(ver)}
{p_end}
{marker modes}{...}
Modes
=====
The _mode_ changes the behavior of the package and it can be __vanilla__ or __sync__.
When the _mode_ is not specified, R is called interactively which is the default
mode. Finally, when the [{it:R-command}] is not specified, the console mode
will be executed which simulates R console within Stata results window for interactive
use. In all of these modes, __rcall__ returns _rclass_ objects from R to Stata. These
modes are summarized below:
{* the new Stata help format of putting detail before generality}{...}
{synoptset 22 tabbed}{...}
{synopthdr:Mode}
{synoptline}
{synopt: __[vanilla](http://www.haghish.com/packages/Rcall.php#vanilla_mode)__ }Calls R non-interactively. This mode is advised for programmers
who wish to embed R in Stata packages{p_end}
{synopt: __[sync](http://www.haghish.com/packages/Rcall.php#sync_mode)__ }executes R interactively and
synchronizes _matrices_ and _scalars_ between
R and Stata. Making a change in any of these objects in either Stata or
R will change the object in the other environment.
{p_end}
{synopt:[interactive](http://www.haghish.com/packages/Rcall.php#interactive_mode)}when the mode is not specified, R is called interactively
which memorizes the actions, objects available in the R memory, the attached
datasets, and the loaded packages. {p_end}
{synopt:[console](http://www.haghish.com/packages/Rcall.php#console_mode)}when the R command is not specified, R is called interactively
and in addition, R console is simulated within the results windows of Stata.
In the console mode users can type R commands directly in Stata and get the
results back interactively. Similarly, the results are returned to Stata
in the background and can be accessed in Stata when quiting the console
mode. {p_end}
{synoptline}
{p2colreset}{...}
{marker subcommand}{...}
Subcommands
=================
__rcall__ allows a few subcommands which provide several features to facilitate
working with the package interactivey. The subcommands are summarized in the
table below:
{* the new Stata help format of putting detail before generality}{...}
{synoptset 22 tabbed}{...}
{synopthdr:Subcommand}
{synoptline}
{synopt:[setpath](http://www.haghish.com/packages/Rcall.php#setpath_subcommand) {it:"path/to/R"}}permanently defines the path to executable
R on the machine.{p_end}
{synopt:[clear](http://www.haghish.com/packages/Rcall.php#clear_subcommand)}erases
the R memory and history in the interactive mode. {p_end}
{synopt:[describe](http://www.haghish.com/packages/Rcall.php#describe_subcommand)}returns
the R version and paths to R, RProfile, and Rhistory {p_end}
{synopt:[history](http://www.haghish.com/packages/Rcall.php#history_subcommand)}opens
__Rhistory.do__ in do-file editor which stores the history of the
interactive R session. {p_end}
{synopt:[site](http://www.haghish.com/packages/Rcall.php#site_subcommand)}opens
__Rprofile.site__ in do-file editor which is
used for customizing R when is called from Stata. {p_end}
{synoptline}
{p2colreset}{...}
Description
===========
__[R statistical language](https://cran.r-project.org/)__ is a free software
and programming langage for statistical computing and graphics.
The rcall package combines the power of R with Stata, allowing the
Stata users to call R interactively within Stata and communicate
data and analysis results between R and Stata simultaniously.
In other words, anytime an R code is executed, the R objects are available
for further manipulation in Stata.
R objects with
_numeric_, _integer_, _character_, _logical_, _matrix_, _list_, and _NULL_
classes are automatically returned to Stata as {help return:rclass}.
R objects with _data.frame_ class can be automatically loaded from R to
Stata using the __st.load()__ function (see below).
__rcall__ uses the __try__ function to evaluate the R code and
returns __r(rc)__ scalar which is an indicator for errors occuring in R. if __r(rc)__
equals zero, R has successfully executed the code. Otherwise, if __r(rc)__ equals
one an error has occured and __rcall__ will return the error message and break the
execution.
Communication from R to Stata
======================================
Stata automatically receives R objects as {help return:rclass} anytime
the rcall is executed. If R is running interactively
(i.e. without __vanilla__ subcommand), the previous objects still remain accessable
to Stata, unless they are changed or erased from R. Moreover, the packages
that you load from Stata in R remain loaded until you detach them.
Accessing R objects in Stata is simultanious which makes working with
rcall convenient. For example a _numeric_, or _string_ vector which is
defined in R, can be accessed in Stata as simple as calling the name of that
object withing {help rclass} i.e. __r(_objectname_)__.
A _numeric_ object example:
. rcall: a <- 100
. display r(a)
100
Without the __vanilla__ subcommand, the defined object remains in the memory of
R and consequently, returned to Stata anytime R is called.
. rcall: a
[1] 100
A _string_ object example:
. rcall: str <- "Hello World"
. display r(str)
Hello World
. rcall: str <- c("Hello", "World")
. display r(str)
"Hello" "World"
A _vector_ example:
. rcall: v <- c(1,2,3,4,5)
. display r(v)
1 2 3 4 5
A _matrix_ example:
. rcall: A = matrix(1:6, nrow=2, byrow = TRUE)
. mat list r(A)
r(A)[2,3]
c1 c2 c3
r1 1 2 3
r2 4 5 6
A _list_ example:
. rcall: mylist <- list(a=c(1:10))
. display r(mylist_a)
1 2 3 4 5 6 7 8 9 10
A _logical_ example:
. rcall: l <- T
. display r(l)
TRUE
A _NULL_ example:
. rcall: n <- NULL
. display r(n)
NULL
Regarding communicating R data set to Stata automatically, see the
__st.load(_dataframe_)__ function below.
Communication from Stata to R
======================================
For an ideal reciprocation between Stata and R, Stata should also easily
communicate variables to R. Local and global {help macro:macros} can be passed
within R code, since Stata automatically interprets them while it passes the
code to rcall command, as shown in the example below:
. global a 99
. rcall: (a <- $a)
[1] 99
In order to pass a {help scalar} from Stata to R, you can
use the __st.scalar()__ function as shown below:
. scalar a = 50
. rcall: (a <- st.scalar(a))
[1] 50
Similarly, Stata {help matrix:matrices} can be seamlessly passed to R using
the __st.matrix()__ function as shown below:
. matrix A = (1,2\3,4)
. matrix B = (96,96\96,96)
. rcall: C <- st.matrix(A) + st.matrix(B)
. rcall: C
[,1] [,2]
[1,] 97 98
[2,] 99 100
And of course, you can access the matrix from R in Stata as well:
. mat list r(C)
r(C)[2,2]
c1 c2
r1 97 98
r2 99 100
Passing variables from Stata to R is convenient, using the
__st.var(_varname_)__ function. Therefore, any analysis can be executed in R
simply by passing the variables required for the analysis from Stata to R:
. sysuse auto, clear
. rcall: dep <- st.var(price)
. rcall: pre <- st.var(mpg)
. rcall: lm(dep~pre)
Call:
lm(formula = dep ~ pre)
Coefficients:
(Intercept) pre
11267.3 -238.3
The rcall package also allows to pass Stata data to R within
__st.data(_{help filename}_)__ function. This function relies on the __readstata13__
package in R to load Stata data sets, without converting them to CSV or alike.
The __readstata13__ package
[is faster and more acurate then __foreign__ and __haven__ packages](http://www.haghish.com/stata-blog/?p=21)
and read Stata 13 and 14 datasets. This R package can be installed within Stata as follows:
. rcall: install.packages("readstata13", repos="http://cran.uk.r-project.org")
Specify the relative or absolute path to the data set to transporting data
from Stata to R. For example:
. rcall: data <- st.data(/Applications/Stata/ado/base/a/auto.dta)
. rcall: dim(data)
If the _filename_ is not specified, the function passes the currently loaded
data to R.
. sysuse auto, clear
. rcall: data <- st.data()
. rcall: dim(data)
[1] 74 12
Finally, the data can be imported from R to Stata automatically, using the
__st.load(_dataframe_)__ function. This function will automatically save a
Stata data set from R and load it in Stata by clearing the current data set,
if there is any. Naturally, you can have more control over converting variable
types if you write a proper code in R for exporting Stata data sets. Nevertheless,
the function should work just fine in most occasions:
. clear
. rcall: st.load(cars)
. list in 1/2
{c TLC}{hline 14}{c TRC}
{c |} speed dist {c |}
{c LT}{hline 14}{c RT}
1. {c |} 4 2 {c |}
2. {c |} 4 10 {c |}
{c BLC}{hline 14}{c BRC}
Remarks
=======
You should be careful with using Stata symbols in R. For example, the __$__
sign in Stata is preserved for global macros. To use this sign in R, you
should place a backslash before it to pass it to R. For example:
. rcall: head(cars\$speed)
Also, the object name in R can include a dot, for example:
. rcall: a.name <- "anything"
The rcall package returns scalars and locals which can only include
underscore in the names (e.g. a_name). rcall automatically converts
dots to underscore in the name. In the example above, if you type {cmd:return list}
in Stata, you would get a macro as follos:
. return list
r(a_name) : "anything"
To maximize the speed of calling R from Stata,
detach the packages that are no longer needed and also, drop all the objects
that are of no use for you. The more objects you keep in R memory,
the more time needed to automatically communicate those objects between
R and Stata.
Example
=================
Visit [rcall homepage](http://www.haghish.com/packages/Rcall.php) for more examples and
documentation.
Author
======
__E. F. Haghish__
Center for Medical Biometry and Medical Informatics
University of Freiburg, Germany
_and_
Department of Mathematics and Computer Science
University of Southern Denmark
haghish@imbi.uni-freiburg.de
[rcall Homepage](www.haghish.com/packages/Rcall.php)
Package Updates on [Twitter](http://www.twitter.com/Haghish)
- - -
This help file was dynamically produced by {help markdoc:MarkDoc Literate Programming package}
***/
*cap prog drop rcall
program define rcall , rclass
*version 12
// =========================================================================
// Syntax processing
// - if the [:] appears first, it means the rest are not modes or subcommands
// - Process the rcall inputs
// - If R path not defined, and "setpath" not specified, search R path
// =========================================================================
if "$rcallwarning" == "" {
di "{err:Warning}: rcall is no longer updated on SSC after version 2.1.2. visit" _n ///
`"{browse "https://github.com/haghish/rcall/"}"' ///
" to reinstall the package from GitHub"
global rcallwarning 1
}
macro drop RcallError
// -------------------------------------------------------------------------
// Search R path, if not specified
// =========================================================================
capture prog drop Rpath
capture Rpath
tokenize `"`macval(0)'"'
if `"`macval(1)'"' != "setpath" & `"`macval(1)'"' != "setpath:" {
if missing("$Rpath") {
if "`c(os)'" == "Windows" {
// 1- try both "Program Files" and "Program Files (86)"
// 2- Get the list of directories that begin with R-*
// 3- select the last one
local wd : pwd
capture quietly cd "C:\Program Files\R"
if _rc != 0 {
capture quietly cd "C:\Program Files (x86)\R"
if _rc != 0 {
display as err "R was not found on your system. Setup R path manually"
exit 198
}
}
local folder : pwd
local Rdir : dir "`folder'" dirs "R-*", respectcase
tokenize `"`Rdir'"'
while `"`1'"' != "" {
local newest_R `"`1'"'
macro shift
}
quietly cd `"`newest_R'\bin"'
local path : pwd
local path : display "`path'\R.exe"
*global Rpath : display "`path'"
quietly cd "`wd'"
}
// for linux and Mac try 2 possible default paths
else {
local path "/usr/bin/r"
capture confirm file "`path'"
if _rc != 0 {
local path "/usr/local/bin/R"
global Rpath : display "`path'"
}
}
if !missing("`debug'") {
di _n "{title:Path to R}" _n ///
"The path to R was {err:guessed} to be:" _n
display `"{err:`path'}"'
}
}
else {
local path = "$Rpath"
if !missing("`debug'") {
di _n "{title:Path to R}" _n ///
"The path to R was obtained from {err:Rpath.ado} to be:" _n
display `"{err:`path'}"'
}
}
capture confirm file "`path'"
if _rc != 0 {
di as txt "{p}R was expected in: `path'"
display as err "{bf:rcall} could not find R on your system"
err 198
}
}
// -------------------------------------------------------------------------
// Input processing
// =========================================================================
// Check if the command includes Colon in the beginning or not
// -----------------------------------------------------------
if substr(trim(`"`macval(0)'"'),1,1) == ":" {
local 0 : subinstr local 0 ":" ""
}
else {
//check WHY windows version requierd this tokenize here and Mac doesn't!
tokenize `"`macval(0)'"'
// debug mode (begining)
// ================
*if substr(trim(`"`macval(0)'"'),1,5) == "debug" {
if `"`macval(1)'"' == "debug" | `"`macval(1)'"' == "debug:" {
local 0 : subinstr local 0 "debug" ""
di as err `"02: `macval(0)'"'
tokenize `"`macval(0)'"' //reset
local debug debug
global debug 1
if !missing("`debug'") {
di _n "{title:[1/5] Debug mode}" _n ///
"Running rcall in debug mode"
}
}
// clear R memory
// ================
if `"`macval(0)'"' == "clear" | `"`macval(0)'"' == "clear:" {
capture erase .RData
capture findfile RProfile.R, path("`c(sysdir_plus)'r")
if _rc == 0 {
capture erase "`r(fn)'"
}
capture findfile Rhistory.do, path("`c(sysdir_plus)'r")
if _rc == 0 {
capture erase "`r(fn)'"
tempfile history
tempname knot
qui file open `knot' using "`history'", write text append
file write `knot' "// Rhistory initiated on `c(current_date)' `c(current_time)'" _n
qui file close `knot'
quietly copy "`history'" "`c(sysdir_plus)'r/Rhistory.do"
}
display as txt "(R memory cleared)"
exit
}
// describe R
// ================
if `"`macval(0)'"' == "describe" | `"`macval(1)'"' == "describe:" {
di as txt "{hline 79}"
di _col(10) "{bf:R path}:" _col(20) _c
di as txt `"{browse "`path'$Rpath"}"'
rcall vanilla: version = R.Version()\$version.string; ///
lst <- ls(globalenv());
di _col(7) "{bf:R version}:" _col(20) _c
if !missing("`r(version)'") di as txt "`r(version)'"
else di as err "R was not accessed!"
capture findfile RProfile.site, path("`c(sysdir_plus)'r")
if _rc == 0 {
di _col(7) "{bf:R profile}:" _col(20) _c
di as txt `"{browse "`r(fn)'"}"'
}
capture findfile Rhistory.do, path("`c(sysdir_plus)'r")
if _rc == 0 {
di _col(7) "{bf:R history}:" _col(20) _c
di as txt `"{browse "`r(fn)'"}"'
}
else {
tempfile history
tempname knot
qui file open `knot' using "`history'", write text append
file write `knot' "// Rhistory initiated on `c(current_date)' `c(current_time)'" _n
qui file close `knot'
quietly copy "`history'" "`c(sysdir_plus)'r/Rhistory.do"
di _col(7) "{bf:R History}:" _col(20) _c
di as txt "{browse `c(sysdir_plus)'r/Rhistory.do}"
}
di as txt "{hline 79}"
exit
}
// Synchronize mode
// ================
if `"`macval(1)'"' == "sync" | `"`macval(1)'"' == "sync:" {
local 0 : subinstr local 0 "sync" ""
global Rcall_synchronize_mode on
local mode sync
}
// Vanilla mode
// ============
*if substr(trim(`"`macval(0)'"'),1,7) == "vanilla" {
if `"`macval(1)'"' == "vanilla" | `"`macval(1)'"' == "vanilla:" {
local 0 : subinstr local 0 "vanilla" ""
local vanilla --vanilla
if !missing("`debug'") {
di _n "{title:Vanilla}" _n ///
"Running R in non-interactive batch mode"
}
local mode vanilla
}
// debug mode AGAIN (ending)
// =========================
*if substr(trim(`"`macval(0)'"'),1,5) == "debug" {
tokenize `"`macval(0)'"'
if `"`macval(1)'"' == "debug" | `"`macval(1)'"' == "debug:" {
local 0 : subinstr local 0 "debug" ""
di as err `"02: `macval(0)'"'
tokenize `"`macval(0)'"' //reset
local debug debug
global debug 1
if !missing("`debug'") {
di _n "{title:[1/5] Debug mode}" _n ///
"Running rcall in debug mode"
}
}
// Setpath
// =======
*else if substr(trim(`"`macval(0)'"'),1,7) == "setpath" {
if `"`macval(1)'"' == "setpath" | `"`macval(1)'"' == "setpath:" {
local 0 : subinstr local 0 "setpath" ""
confirm file `0'
tempfile Rpath
tempname knot
qui file open `knot' using "`Rpath'", write text replace
file write `knot' "program define Rpath" _n
file write `knot' `" global Rpath `macval(0)'"' _n
file write `knot' "end" _n
qui file close `knot'
qui copy "`Rpath'" "`c(sysdir_plus)'r/Rpath.ado", replace
if !missing("`debug'") {
di "{title:Memorizing R path}" _n ///
`"the {bf:Rpath.ado} was created to memorize the path to `macval(0)'"'
}
exit
}
// HISTORY
// =======
if `"`macval(1)'"' == "history" {
local 0 : subinstr local 0 "history" ""
capture findfile Rhistory.do, path("`c(sysdir_plus)'r")
if _rc == 0 {
*copy "`r(fn)'" Rhistory.do, replace
*display as txt `"(Rhistory coppied to {browse "./Rhistory.do"})"'
doedit "`r(fn)'"
}
else {
display as txt "(Rhistory is empty)"
}
exit
}
// SITE
// =======
if `"`macval(1)'"' == "site" {
local 0 : subinstr local 0 "site" ""
capture findfile Rprofile.site, path("`c(sysdir_plus)'r")
if _rc == 0 {
doedit "`r(fn)'"
}
else {
display as err "{bf:Rprofile.site} was not found!"
}
exit
}
// Check if the command includes Colon in the end
if substr(trim(`"`macval(0)'"'),1,1) == ":" {
local 0 : subinstr local 0 ":" ""
}
}
// -------------------------------------------------------------------------
// Execute interactive mode (including sync)
// =========================================================================
if trim(`"`0'"') == "" {
local mode interactive
global Rcall_interactive_mode on
// avoid the sync mode to get repeated in each trial
*if "$Rcall_synchronize_mode" == "on" {
* Rcall_synchronize
* global Rcall_synchronize_mode2 "on"
* macro drop Rcall_synchronize_mode
*}
if missing("`vanilla'") {
Rcall_interactive
}
else {
di as err "the {bf:vanilla} mode cannot be called interactively"
err 198
}
}
if !missing("`debug'") {
di _n "{title:R command}" _n ///
"The command that you wish to execute in {bf:R} is:" _n(2) ///
`"{err:`macval(0)'}"'
}
// -------------------------------------------------------------------------
// Create and update the history file
// =========================================================================
if missing("`vanilla'") {
capture findfile Rhistory.do, path("`c(sysdir_plus)'r")
if _rc == 0 {
tempname knot
qui file open `knot' using "`r(fn)'", write text append
if !missing(`"`macval(0)'"') {
file write `knot' `"rcall `mode': `macval(0)'"' _n
}
qui file close `knot'
}
else {
tempfile history
tempname knot
qui file open `knot' using "`history'", write text append
file write `knot' "// Rhistory initiated on `c(current_date)' `c(current_time)'" _n
if !missing(`"`macval(0)'"') {
file write `knot' `"rcall `mode': `macval(0)'"' _n
}
qui file close `knot'
quietly copy "`history'" "`c(sysdir_plus)'r/Rhistory.do"
}
}
// -------------------------------------------------------------------------
// Searching for Matrix
// =========================================================================
while strpos(`"`macval(0)'"',"st.matrix(") != 0 {
local br = strpos(`"`macval(0)'"',"st.matrix")
local l1 = substr(`"`macval(0)'"',1, `br'-1)
local l2 = substr(`"`macval(0)'"',`br',.)
local l2 : subinstr local l2 "st.matrix(" ""
local mt = strpos(`"`macval(l2)'"',")")
local mat = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
if !missing("`debug'") {
di _n "{title:st.matrix() function}" _n ///
"You wish to pass Matrix {bf:`mat'} to {bf:R}. This will call " ///
"the {bf:matconvert.ado} function, which returns:"
matconvert `mat'
}
qui matconvert `mat'
local l2 = `"`r(`mat')'"' + "`l2'"
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
}
// -------------------------------------------------------------------------
// Searching for Scalar
// =========================================================================
while strpos(`"`macval(0)'"',"st.scalar(") != 0 {
local br = strpos(`"`macval(0)'"',"st.scalar")
local l1 = substr(`"`macval(0)'"',1, `br'-1)
local l2 = substr(`"`macval(0)'"',`br',.)
local l2 : subinstr local l2 "st.scalar(" ""
local mt = strpos(`"`macval(l2)'"',")")
local sca = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
if !missing("`debug'") {
di _n "{title:st.scalar() function}" _n ///
"You wish to pass Scalar {bf:`sca'} to {bf:R}. This value is: "
display `sca'
}
local sca : display `sca'
//If scalar is string, add double quote
capture local test : display int(`sca')
if missing("`test'") & "`sca'" != "" {
local sca : display `"`sca'"'
local l2 = `"""' + `"`macval(sca)'"' + `"""' + `"`l2'"'
}
else if "`sca'" != "" {
local l2 = "`sca'" + "`l2'"
}
else {
local l2 = `"`sca'"' + "`l2'"
}
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
}
// -------------------------------------------------------------------------
// Searching for Data
// =========================================================================
while strpos(`"`macval(0)'"',"st.data(") != 0 {
local br = strpos(`"`macval(0)'"',"st.data")
local l1 = substr(`"`macval(0)'"',1, `br'-1)
local l2 = substr(`"`macval(0)'"',`br',.)
local l2 : subinstr local l2 "st.data(" ""
local mt = strpos(`"`macval(l2)'"',")")
local filename = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
local foreign 1 //load foreign package
//IF THE NAME HAS A PRANTHESIS...
if strpos(`"`macval(filename)'"',"(") != 0 {
local filename : di `"`macval(filename)')"'
local mt = strpos(`"`macval(l2)'"',")")
local filename2 = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
local filename : di `"`macval(filename)'`macval(filename2)'"'
}
if !missing("`debug'") {
di _n "{title:st.data() function}" _n ///
"You wish to pass Stata data {bf:`filename'} to {bf:R}..."
}
// Get rid of double quotes or add them!
cap local filename : display "`macval(filename)'"
if _rc != 0 local filename : display `macval(filename)'
//IF FILENAME IS MISSING
if missing("`filename'") {
if "`c(version)'" >= "14" {
qui saveold _st.data.dta, version(11) replace
}
else {
qui saveold _st.data.dta, replace
}
local dta : di "read.dta13(" `"""' "_st.data.dta" `"""' ")"
}
else {
confirm file "`filename'"
preserve
qui use "`filename'", clear
if "`c(version)'" >= "14" qui saveold _st.data.dta, version(11) replace
else qui saveold _st.data.dta, replace
local dta : di "read.dta13(" `"""' "_st.data.dta" `"""' ")"
restore
}
local l2 = `"`macval(dta)'"' + `"`macval(l2)'"'
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
}
// make sure readstata13 is installed and updated regularly
// -------------------------------------------------------------------------
if "`foreign'" == "1" {
capture rcall_check readstata13>=0.8.5
if _rc != 0 display as err "R package {bf:readstata13} version 0.8.3 " ///
"is required. Type:" _n "{p}R: install.packages(" ///
`""readstata13", repos="http://cran.uk.r-project.org")"'
// avoid slowing down rcall
global Rcall_check 1
}
// -------------------------------------------------------------------------
// Searching for Load Data
// =========================================================================
while strpos(`"`macval(0)'"',"st.load(") != 0 {
local br = strpos(`"`macval(0)'"',"st.load")
local l1 = substr(`"`macval(0)'"',1, `br'-1)
local l2 = substr(`"`macval(0)'"',`br',.)
local l2 : subinstr local l2 "st.load(" ""
local mt = strpos(`"`macval(l2)'"',")")
local loaddata = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
local foreign 1 //load foreign package
local forceload 1 //load data to stata
if !missing("`debug'") {
di as txt _n "{title:st.load() function}" _n ///
"You wish to force loading R data {bf:`loaddata'} to {bf:Stata}..." _n
}
//IF FILENAME IS MISSING
if missing("`loaddata'") {
display as err "data frame is not specified"
err 198
}
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
if !missing("`debug'") di _n `"`macval(0)'"'
}
// -------------------------------------------------------------------------
// Searching for variable
// =========================================================================
while strpos(`"`macval(0)'"',"st.var(") != 0 {
local br = strpos(`"`macval(0)'"',"st.var")
local l1 = substr(`"`macval(0)'"',1, `br'-1)
local l2 = substr(`"`macval(0)'"',`br',.)
local l2 : subinstr local l2 "st.var(" ""
local mt = strpos(`"`macval(l2)'"',")")
local mat = substr(`"`macval(l2)'"',1, `mt'-1)
local l2 = substr(`"`macval(l2)'"',`mt'+1, .)
if !missing("`debug'") {
di _n "{title:st.var() function}" _n ///
"You wish to pass variable {bf:`mat'} to {bf:R}. This will call " ///
"the {bf:varconvert.ado} function, which returns:"
varconvert `mat'
}
qui varconvert `mat'
if "`r(type)'" == "numeric" {
local l2 = "`r(`mat')'" + "`l2'"
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
}
if "`r(type)'" == "string" {
local l2 = `"`r(`mat')'"' + "`l2'"
local 0 = `"`macval(l1)'"' + `"`macval(l2)'"'
}
}
*local line : subinstr local line "$" "_", all //avoid "$" in name
// -------------------------------------------------------------------------
// Create temporary Rscript file
// =========================================================================
capture findfile stata.output.R, path("`c(sysdir_plus)'s")
if _rc != 0 {
di as err "stata.output.R script file not found. reinstall the package"
err 198
}
local source `r(fn)'
//Change the stata.output.R path in Windows
if "`c(os)'" == "Windows" {
local source : subinstr local source "\" "/", all
}
capture findfile Rprofile.site, path("`c(sysdir_plus)'r")
if _rc == 0 {
local RSite `r(fn)'
}
capture findfile RProfile.R, path("`c(sysdir_plus)'r")
if _rc == 0 {
local RProfile `r(fn)'
}
// get the path to PLUS/r
local plusR "`c(sysdir_plus)'r"
//Change the stata.output.R path in Windows
if "`c(os)'" == "Windows" {
local RProfile : subinstr local RProfile "\" "/", all
local RSite : subinstr local RProfile "\" "/", all
local plusR : subinstr local plusR "\" "/", all
}
tempfile Rscript
tempfile Rout
tempname knot
qui file open `knot' using "`Rscript'", write text replace
if "$Rcall_interactive_mode" != "on" {
if "$Rcall_synchronize_mode" == "on" {
Rcall_synchronize
file write `knot' "source('Rcall_synchronize')" _n
}
}
if !missing("`vanilla'") file write `knot' "rm(list=ls())" _n // erase memory temporarily
if !missing("`foreign'") file write `knot' "library(readstata13)" _n // load the readstata13 package
if !missing("`RSite'") & missing("`vanilla'") ///
file write `knot' "source('`RSite'')" _n
if !missing("`RProfile'") & missing("`vanilla'") ///
file write `knot' "source('`RProfile'')" _n // load the libraries
// -------------------------------------------------------------------------
// Handling Errors
//
// catch the errors and return proper error
// and only procede if the "rc" object is not missing
// =========================================================================
*file write `knot' `"`macval(0)'"' _n
if trim(`"`macval(0)'"') != "" {
file write `knot' "try({" `"`macval(0)'"' "})" _n
}
// if there was an error in R...
// -------------------------------------------------------------------------
file write `knot' `"if (class(.Last.value) != "try-error" ) {"' _n /// there was an error
///" print(.Last.value)" _n ///
" rc = 0" _n
if missing("`vanilla'") file write `knot' "save.image()" _n // save if mode is not vanilla
file write `knot' "} else {" _n ///
" rc = 1" _n ///
" error = geterrmessage()" _n ///
`" error = gsub("Error in try({ :", "Error:", error, fixed = T)"' _n ///
"}" _n(2)
// if R does not fail, it continues...
// -------------------------------------------------------------------------
file write `knot' "source('`source'')" _n
*file write `knot' `"plusR <- "`plusR'""' _n //source stata.output() before exit
file write `knot' `"stata.output("`plusR'", "`vanilla'")"' _n
//file write `knot' "rm(stata.output)" _n
//file write `knot' `"try(rm(stata.output, RProfile), silent=TRUE)"' _n
*if missing("`vanilla'") file write `knot' "save.image()" _n
if !missing("`forceload'") {
file write `knot' `"save.dta13(`loaddata', "' ///
`"file = "_load.data.dta", version = 11) "' _n
}
qui file close `knot'
if !missing("`debug'") {
di _n "{title:[2/5] Temporary R script}" _n ///
"{p}A temporary Rscript file was created to execute your command in " ///
"{bf:R}. The path to the temporary file is: " _n
display `"`Rscript'"'
di _n "{title:Investigate R script}" _n ///
"You can investigate the temporary R script file in debug mode." _n
capture erase _temporary_R_script.R
copy "`Rscript'" _temporary_R_script.R, replace
di "{browse _temporary_R_script.R}"
}
*cap erase 0PROCESS0.txt
*copy "`Rscript'" 0PROCESS0.txt, replace
// -------------------------------------------------------------------------
// Execute the command in R
// =========================================================================
//By default, the input commands are printed along with the output.
//To suppress this behavior, add options(echo = FALSE) at the beginning of
//infile, or use option --slave.
if missing("`vanilla'") local save "--save"
else local save "--no-save"
local Rcommand `""`path'" `vanilla' --slave `save' < "`Rscript'" > "`Rout'" "'
*local Rcommand `""`path'" `vanilla' --save < "`Rscript'" > "`Rout'" "'
if !missing("`debug'") {
di _n "{title:[3/5] Running R in batch mode}" _n ///
"The following command is executed in Stata:" _n
display `"{p}{err:shell `Rcommand'}"'
}
quietly shell `Rcommand'
capture confirm file stata.output
if _rc != 0 {
shell `Rcommand'
exit
}
if !missing("`debug'") {
di _n "{title:[4/5] R Output}" _n ///
"R output was generated. A copy is made in the debug mode..." _n
capture erase _temporary_R_output.txt
copy "`Rout'" _temporary_R_output.txt, replace
di "{browse _temporary_R_output.txt}"
}
// If data was loaded automatically, remove the temporary data file
if !missing("`foreign'") capture qui erase _st.data.dta
type "`Rout'"
if !missing("`debug'") {
di _n "{title:[5/5] rclass return}" _n ///
"The final step is returning objects from R to Stata" _n
di "{browse stata.output}"
}
// This has to be an engine for itself
// -------------------------------------------------------------------------
// Returning objects to Stata
// =========================================================================
// ???: AVOID returning in console mode
call_return using "stata.output" , `debug'
return add
// If data was loaded automatically, remove the temporary data file
if !missing("`forceload'") {
capture confirm file _load.data.dta
if _rc != 0 {
di as err "{bf:R} failed to export Stata data set"
exit
}
else {
quietly use _load.data.dta, clear
capture qui erase _load.data.dta
}
}
// Erase globals
macro drop Rpath
macro drop Rcall_synchronize_mode
// stop rcall execution if error has occured
// -------------------------------------------------------------------------
if "$RcallError" == "1" {
macro drop RcallError
if "$Rcall_interactive_mode" != "on" {
error 1
}
}
macro drop debug
end
// -------------------------------------------------------------------------
// CREATE help file
// =========================================================================
*markdoc rcall.ado, export(sthlp) replace