PypeR

PypeR

ypeR

PypeR (PYthon-piPE-R, originally names as Rinpy - R in Python) allows people to use R in Python through PIPE.

The package can be downloaded at:

• PyPI - the Python Package Index.
• SourceForge

While PypeR will be first distributed on the above two databases, it can also been download in some other locations, which are possibly have a few days lagging behind for a newly distributed version:

• Softpedia
• DownloadPlex
• WareSeeker
• FamousWhy
• ClickCop

For installation, please see README

For upgrading LOG, please see CHANGES

Known problems or bugs in the current distribution:

1. Some errors in command strings sent to R can be fatal to PypeR!
   For example, incomplete command strings, typically, missing quotes or parentheses, will lead to a dead waiting: R is waiting for more input from Python while Python is trying to getting output from R.

   	>>> from pyper import *
   	>>> r = R()
   	>>> r('a <- 10 / (3 + 2')
   					

   In Such cases, the user has to press "Ctrl - C" to break the pipe, and restart R again. So far I have no idea for a solution for this problem.
   

   For suggestions or supports, please email to    "Xiao-Qin Xia"<x q x i a 7 0 @ g m a i l . c o m>

    

   README: PypeR Please refer to http://www.webarray.org/softwares/PypeR/ for bug fixes. Requirements: Python 2.3 or later. PypeR can run with different Python implementations: Python 2.X.X Python 3.X.X Jython IronPython For installation: # python setup.py install or # easy_install PypeR or # pip install PypeR To upgrade to the newest version: # python setup.py install or # easy_install --upgrade PypeR or # pip install --upgrade PypeR Known issues: 1. Problem: cannot run with IronPython on mono. Platform: tested on Ubuntu-10.04, mono 2.4.4, IronPython 2.6 Beta 2 DEBUG (2.6.0.20) on .NET 2.0.50727.1433 Behavior: report "TypeError: Cannot cast from source type to desination type." Reason: This happens when call a function found in the dict "str_func", e.g. "str_func[type(obj)](obj)". Most likely it is caused by a bug of IronPython (or mono?). Solution: It is possible to use IF...ELIF...ESLE to replace the dict "str_func". However it will make the function "Str4R" much longer than it is now. For Help: Please see the documents of the module, class, and methods For example: The script "test.py" covers all the typical uses of PypeR Citation: @article{Xia:McClelland:Wang:2010:JSSOBK:v35c02, author = "Xiao-Qin Xia and Michael McClelland and Yipeng Wang", title = "PypeR, A Python Package for Using R in Python", journal = "Journal of Statistical Software, Code Snippets", volume = "35", number = "2", pages = "1--8", day = "30", month = "7", year = "2010", CODEN = "JSSOBK", ISSN = "1548-7660", bibdate = "2010-03-23", URL = "http://www.jstatsoft.org/v35/c02", accepted = "2010-03-23", acknowledgement = "", keywords = "", submitted = "2009-10-23", } FAQs: 1. Q: I got error message when trying to use PypeR: >>> from pyper import * >>> r = R() Traceback (most recent call last): ...... "WindowsError: [Error 2] The system cannot find the file specified" >>> A: Usually this means PypeR cannot find the R program on Windows. There is two ways to tell PypeR where R is. E.g., R is installed at "C:\Program Files\R\R-2.11.1". method 1 - initialize R with full path: >>> r = R(RCMD="C:\\Program Files\\R\\R-2.11.1\\bin\\R") method 2 - add "C:\\Program Files\\R\\R-2.11.1\\bin" into the PATH environmental variable: (1) Right click "My Computer" on Windows XP (or "Computer" on Windows 7), either on your desktop or in your start menu. (2) Click "Properties" (3) In Windows 7, click "Advanced System Settings" on the left. (4) In the "Advanced" tab, click the "Environment Variables" button. (5) Double-click the PATH variable, and add your R path to the list. Entries are separated by semicolons. For example: %WinDir%\System32;C:\Program Files\R\R-2.11.1\bin 2. Q: What is the differences between r("myvar"), r["myvar"], r.myvar, r.get("myvar", "a wild value"), and r.assign("myvar", "a new value")? A: These forms serve for different purpose: (1) r("myvar") Here "myvar" is a R variable name or a complex R expression. This equals to type myvar on the R terminal. The information displayed on the terminal will be returned as a Python string. (2) r["myvar"] This form can be used to get values from R, or set value for a R variable. If it is used to get value from R, "myvar" can be a R variable name or a complex R expression, and this will return the value of "myvar" instead of the output on STDOUT. To set value for the R variable, the form is: r["myvar"] = "something" here "myvar" should be valid R variable name. (3) r.myvar This form is similar to r["myvar"], but diffs in two aspects: a) myvar have to following Python's name convention too. b) IMPORTANT: if myvar is a attribute of the python object r, it will override (shield) the variable myvar in R! (4) r.get("myvar", "a wild value") This form is similar to r["myvar"], but it can only be used to get values from R. If there is no variable "myvar" in R, the value "a wild value" will be returned (5) r.assign("myvar", "a new value") This form is used to assign value ("a new value") to a R variable ("myvar"). Here "myvar" should be a valid R variable name. 3. Q: How can I get a named list in R returned as a dict, - just as been done in RPy? A: Due to named R list allows replicated names, while Python dictionary does not, conversion of R named list to Python dictionary may lead to lost of data. That is why PypeR return a list of tuples (name, value) for R named list. However it is possible to get dictionary returned since PypeR 1.0.2: method 1: >>> r.get("myvar", use_dict=True) method 2: >>> r.use_dict = True >>> r.myvar If this failed, please update your PypeR with the newest version.

   CHANGES: LOG of Changes of PypeR Changes between version PypeR-1.1.0 to PypeR-1.1.1: on Wed Oct 10 11:07:27 CST 2012 1. Added support to Pandas Series and DataFrame. (Thanks Joost Delsman very much for providing codes for this purpose!) 2. Addressed some compatibility problems for Python 2.7 on Windows. (Many users provided helps!) 3. Addressed a potential problem related to one-element tuple in conversion of R data frames to Python objects. (Thank Matt Knox for point this out and provide a solution.) 4. Addressed the row-column confusion in conversion of R arrays to Python objects. 5. Added supports to some special data, e.g. NaN and Inf. 6. More clear codes for test (in test.py). Changes between version PypeR-1.0.4 to PypeR-1.1.0: on Mon Sep 13 14:22:47 PDT 2010 1. Removed the module "pipeio.py" (the modification to the subprocess package by Josiah Carlson). Therefore, the package "pywin32" is no longer need on Windows. 2. Comparing to PypeR-1.0.X, which can only run with Python-2.X.X (>= 2.4), now PypeR runs with Python 2.X.X (>= 2.3), Python 3.X.X, Jython, and IronPython. 3. The parameters "wait0" and "wait" have been cancelled for the "R" class and the "runR" function. Now R can be initialized a little faster. Changes between version PypeR-1.0.3 to PypeR-1.0.4: on Thu Sep 9 09:53:05 PDT 2010 1. Fixed the bug in parsing R command with backslash or space in the PATH - now the following code works: >>> r = R(RCMD="C:\\Program Files\\R\\R-2.X.X\\bin\\R") Changes between version PypeR-1.0.2 to PypeR-1.0.3: on Fri Sep 3 16:30:12 PDT 2010: 1. Fixed the bug in passing R values to Python which happens on Windows aftersome library (e.g. "fastICA") change newline from '\r\n' to '\n'. 2. Fixed the bug in passing R values with the backslash character ('\') to Python. 3. Fixed the bug on Windows in parsing user library for R. 4. change the default value for parameter "use_dict". Now "use_dict" can be one of the three values: None, True, False. None is the default value, which allows a Python dictionary returned for R named list without replicated name, or a Python list if replicated names exist. Here is some examples: >>> from pyper import * >>> r = R() # the default value for use_dict is None >>> r('a <- list(aa=3, bb=4, cc=5, aa=6)') # with replicated name "aa" 'try({a <- list(aa=3, bb=4, cc=5, aa=6)})\r\n' >>> r.a [('aa', 3), ('bb', 4), ('cc', 5), ('aa', 6)] >>> r.get('a', use_dict=False) [('aa', 3), ('bb', 4), ('cc', 5), ('aa', 6)] >>> r.get('a', use_dict=True) {'aa': 6, 'cc': 5, 'bb': 4} >>> r.use_dict = True # change the default value from None to True >>> r.a {'aa': 6, 'cc': 5, 'bb': 4} >>> r.get('a') {'aa': 6, 'cc': 5, 'bb': 4} >>> r.get('a', use_dict=False) [('aa', 3), ('bb', 4), ('cc', 5), ('aa', 6)] >>> r.get('a', use_dict=None) # "None" here means that r.use_dict should be used! {'aa': 6, 'cc': 5, 'bb': 4} >>> r.use_dict = None # recover the default value >>> r.a [('aa', 3), ('bb', 4), ('cc', 5), ('aa', 6)] Changes between version PypeR-1.0.1 to PypeR-1.0.2: on Fri Sep 3 2010: 1. Fix bugs in converting logical data in R to Python 2. R Objects other than factor, NULL, vector, matrix, data.frame, or list, will be converted to character using the function as.character 3. add the optional parameter "use_dict" for the R class and for the "get" method of the R class. Changes between version PypeR-1.0 to PypeR-1.0.1: 1. Redict stderr to stdout for R. This can be disabled by setting "return_err=False" when initialize a R instance, e.g., "r = R(return_err=False)" 2. In order that user settings can be used by R, R is launched with arguments "--quiet --no-save --no-restore" instead of "--vanilla", which equal to "--no-save --no-restore --no-site-file --no-init-file --no-environ". 3. A version variable is added for the module: __version__ = 1.01 4. Suppressed the popup terminal window on Windows. 5. Added the user-specific library PATH in IDLE on Windows.