Added setup.py and README descriptions

README.md

@@ -1 +1,17 @@
-# pyroconductor
+# pyroconductor
+
+A high-level interface to access commonly-used R tools from python using the low-level r2py. Goal is to 'iron out' r2py conversion interfaces (e.g. like those provided by `pandas2ri`) and even manually create pythonic interfaces for R functions and objects that are hard to automatically translate.
+
+Install by simply doing:
+
+```bash
+python setup.py install
+```
+
+To use `your.favorite.r.package` in a python script, simply call:
+
+```python
+import pyroconductor as pyr
+
+pyr.your_favorite_r_package.function_in_package(args)
+```

__init__.py

@@ -0,0 +1,36 @@
+import numpy as np
+from rpy2 import robjects as ro
+from rpy2.robjects import pandas2ri
+from rpy2.robjects.functions import Function, SignatureTranslatedFunction
+from rpy2.robjects.vectors import DataFrame, ListVector, Vector
+
+pandas2ri.activate()
+
+def _convert_to_python(x):
+    if isinstance(x, DataFrame):
+        return pandas2ri.ri2py_dataframe(x)
+    elif isinstance(x, ListVector) or isinstance(x, Vector):
+        return [_convert_to_python(item) for item in x]
+    else:
+        return np.array(x)
+
+class R(object):
+    def __getattribute__(self, attr):
+        try:
+            return super(R, self).__getattribute__(attr)
+        except AttributeError as ae:
+            orig_ae = str(ae)
+
+        try:
+            return self.__getitem__(attr)
+        except LookupError:
+            raise AttributeError(orig_ae)
+
+    def __getitem__(self, item):
+        res = ro.r.__getitem__(item)
+        if isinstance(res, Function) or\
+                isinstance(SignatureTranslatedFunction):
+            return lambda *args, **kwargs: _convert_to_python(res(*args, **kwargs))
+        else:
+            return res
+r = R()

corpcor.py

@@ -0,0 +1,13 @@
+from rpy2 import robjects
+from rpy2.robjects import pandas2ri
+import numpy as np
+pandas2ri.activate()
+
+def cov_shrink(data_array, weights=None, **kwargs):
+    robjects.r('library(corpcor)')
+    if weights is None:
+        res = robjects.r['cov.shrink'](data_array, **kwargs)
+    else:
+        res = robjects.r['cov.shrink'](data_array, w=robjects.FloatVector(weights),
+                                       **kwargs)
+    return np.array(res)

glasso.py

@@ -0,0 +1,9 @@
+from rpy2 import robjects
+from rpy2.robjects import pandas2ri
+import numpy as np
+pandas2ri.activate()
+
+def glasso(s, rho):
+    robjects.r('library(glasso)')
+    cov, prec, loglik, errflg, approx, dl, niter = robjects.r['glasso'](s, rho)
+    return np.array(cov), np.array(prec), loglik[0], errflg[0], approx[0], dl[0], niter[0]

setup.py

@@ -0,0 +1,11 @@
+from setuptools import setup
+
+setup(name='pyroconductor',
+        version='0.1',
+        description='High level interface to access R from python leveraging r2py.',
+        author='Pablo Cordero',
+        author_email='[email protected]',
+        url='https://github.com/dimenwarper/pyroconductor',
+        packages=['corpcor', 'glasso'],
+        install_requires=['numpy', 'scipy', 'rpy2', 'pandas', 'matplotlib']
+        )