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Python调用R编程——rpy2
在Python调用R，最常见的方式是使用rpy2模块。
The package is made of several sub-packages or modules:
Importing R packages is often the first step when running R code, and rpy2 is providing a function rpy2.robjects.packages.importr() that makes that step very similar to importing Python packages.
We mentioned earlier that rpy2 is running an embedded R. This is may be a little abstract, so there is an object rpy2.robjects.r to make it tangible.
The __getitem__() method of rpy2.robjects.r, gets the R object associated with a given symbol
The object r is also callable , and the string passed in a call is evaluated as R code.
An R object has a string representation that can be used directly into R code to be evaluated.
In R, data are mostly represented by vectors, even when looking like scalars. When looking closely at the R object pi used previously, we can observe that this is in fact a vector of length 1.
Creating R vectors can be achieved simply.
The easiest way to create such objects is to do it through R functions.
Calling R functions is disappointingly similar to calling Python functions.
By default, calling R functions return R objects.
Linear models
Creating an R vector or matrix, and filling its cells using Python code
This module should be the right pick for casual and general use. Its aim is to abstract some of the details and provide an intuitive interface to both Python and R programmers.
The instance can be seen as the entry point to an embedded R process. The elements that would be accessible from an equivalent R environment are accessible as attributes of the instance.
When safety matters most, we recommend using __getitem__() to get a given R object.
Storing the object in a python variable will protect it from garbage collection, even if deleted from the objects visible to an R user.
Just like it is the case with RPy-1.x, on-the-fly evaluation of R code contained in a string can be performed by calling the r instance.
The astute reader will quickly realize that R objects named by python variables can be plugged into code through their R representation.
R environments can be described to the Python user as an hybrid of a dictionary and a scope.
The first of all environments is called the Global Environment, that can also be referred to as the R workspace.
Assigning a value to a symbol in an environment has been made as simple as assigning a value to a key in a Python dictionary.
An environment is also iter-able, returning all the symbols (keys) it contains.
R functions exposed by rpy2's high-level interface can be used:
This is all looking fine and simple until R arguments with names such as na.rm are encountered. By default, this is addressed by having a translation of ‘.’ (dot) in the R argument name into a ‘_’ in the Python argument name.
In Python one can write:
R is capable of introspection, and can return the arguments accepted by a function through the function formals().
The method Function.rcall() is an alternative way to call an underlying R function.
For tasks such as modelling and plotting, an R formula can be a terse, yet readable, way of expressing what is wanted.
The class robjects.Formula is representing an R formula.
Other options are:
This is achieved by the R functions library() and require() (attaching the namespace of the package to the R search path).
Beside functions and environments, most of the objects an R user is interacting with are vector-like. For example, this means that any scalar is in fact a vector of length one.
The class Vector has a constructor:
Creating vectors can be achieved either from R or from Python.
When the vectors are created from R, one should not worry much as they will be exposed as they should by rpy2.robjects.
When one wants to create a vector from Python, either the class Vector or the convenience classes IntVector, FloatVector, BoolVector, StrVector can be used.
Extracting, Python-style
The python __getitem__() method behaves like a Python user would expect it for a vector (and indexing starts at zero).
Extracting, R-style
Access to R-style extracting/subsetting is granted though the two delegators rx and rx2, representing the R functions [ and [[ respectively.
Assigning, Python-style
Since vectors are exposed as Python mutable sequences, the assignment works as for regular Python lists.
In R vectors can be named, that is elements of the vector have a name.
Assigning, R-style
The attributes rx and rx2 used previously can again be used:
For the sake of complete compatibility with R, arguments can be named (and passed as a dict or rpy2.rlike.container.TaggedList).
In S/Splus/R special NA values can be used in a data vector to indicate that fact, and rpy2.robjects makes aliases for those available as data objects NA_Logical, NA_Real, NA_Integer, NA_Character, NA_Complex .
To expose that to Python, a delegating attribute ro is provided for vector-like objects.
R vectors can have a name given to all or some of the elements. The property names can be used to get, or set, those names.
Array
In R, arrays are simply vectors with a dimension attribute. That fact was reflected in the class hierarchy with robjects.Array inheriting from robjects.Vector.
Matrix
A Matrix is a special case of Array. As with arrays, one must remember that this is just a vector with dimension attributes (number of rows, number of columns).
DataFrame
In rpy2.robjects, DataFrame represents the R class data.frame.
Creating a DataFrame can be done by:
The DataFrame constructor accepts either an rinterface.SexpVector (with typeof equal to VECSXP, that is, an R list) or any Python object implementing the method items() (for example dict or rpy2.rlike.container.OrdDict).
To create a DataFrame and be certain of the clumn order order, an ordered dictionary can be used:
Here again, Python’s __getitem__() will work as a Python programmer will expect it to:
The DataFrame is composed of columns, with each column being possibly of a different type:
The approach followed in rpy2 has 2 levels (rinterface and robjects), and conversion functions help moving between them.
R vectors are mapped to Python objects implementing the methods __getitem__() / __setitem__() in the sequence protocol so elements can be accessed easily.
R functions are mapped to Python objects implementing the __call__() so they can be called just as if they were functions.
R environments are mapped to Python objects implementing __getitem__() / __setitem__() in the mapping protocol so elements can be accessed similarly to in a Python dict.
In its high-level interface rpy2 is using a conversion system that has the task of convertion objects between the following 3 representations: - lower-level interface to R (rpy2.rinterface level), - higher-level interface to R (rpy2.robjects level) - other (no rpy2) representations
R vectors or arrays can be converted to numpy arrays using numpy.array() or numpy.asarray().
The activation (and deactivation) of the automatic conversion of numpy objects into rpy2 objects can be made with:
求助，R语言在python中调用问题
你使用的方法没有问题。r.mydose()调用后返回的东西不是报错，是因为mydose这个function返回值就是NULL,所以rpy就相应的返回了rpy2.rinterface.NULL，没有问题。以上是我的测试nofunc是一个什么也不做的functionhello是输出Hello world的function
如何通过PypeR来实现在Python中调用R
如何通过PypeR来实现在Python中调用R
In [1]: # LOAD PYTHON PACKAGES
In [2]: import pandas as pd
In [3]: import pyper as pr
In [4]: # READ DATA
In [5]: data = pd.read_table("/home/liuwensui/Documents/data/csdata.txt", header = 0)
In [6]: # CREATE A R INSTANCE WITH PYPER
In [7]: r = pr.R(use_pandas = True)
In [8]: # PASS DATA FROM PYTHON TO R
In [9]: r.assign("rdata", data)
In [10]: # SHOW DATA SUMMARY
In [11]: print r("summary(rdata)")
try({summary(rdata)})
LEV_LT3 TAX_NDEB COLLAT1 SIZE1
Min. :0.00000 Min. : 0.0000 Min. :0.0000 Min. : 7.738
1st Qu.:0.00000 1st Qu.: 0.3494 1st Qu.:0.1241 1st Qu.:12.317
Median :0.00000 Median : 0.5666 Median :0.2876 Median :13.540
Mean :0.09083 Mean : 0.8245 Mean :0.3174 Mean :13.511
3rd Qu.:0.01169 3rd Qu.: 0.7891 3rd Qu.:0.4724 3rd Qu.:14.751
Max. :0.99837 Max. :102.1495 Max. :0.9953 Max. :18.587
PROF2 GROWTH2 AGE LIQ
Min. :0.0000158 Min. :-81.248 Min. : 6.00 Min. :0.00000
1st Qu.:0.0721233 1st Qu.: -3.563 1st Qu.: 11.00 1st Qu.:0.03483
Median :0.1203435 Median : 6.164 Median : 17.00 Median :0.10854
Mean :0.1445929 Mean : 13.620 Mean : 20.37 Mean :0.20281
3rd Qu.:0.1875148 3rd Qu.: 21.952 3rd Qu.: 25.00 3rd Qu.:0.29137
Max. :1.5902009 Max. :681.354 Max. :210.00 Max. :1.00018
IND2A IND3A IND4A IND5A
Min. :0.0000 Min. :0.0000 Min. :0.00000 Min. :0.00000
1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:0.00000 1st Qu.:0.00000
Median :1.0000 Median :0.0000 Median :0.00000 Median :0.00000
Mean :0.6116 Mean :0.1902 Mean :0.02692 Mean :0.09907
3rd Qu.:1.0000 3rd Qu.:0.0000 3rd Qu.:0.00000 3rd Qu.:0.00000
Max. :1.0000 Max. :1.0000 Max. :1.00000 Max. :1.00000
In [12]: # LOAD R PACKAGE
In [13]: r("library(betareg)")
Out[13]: 'try({library(betareg)})\nLoading required package: Formula\n'
In [14]: # ESTIMATE A BETA REGRESSION
In [15]: r("m - betareg(LEV_LT3 ~ SIZE1 + PROF2 + GROWTH2 + AGE + IND3A, data = rdata, subset = LEV_LT3 0)")
Out[15]: 'try({m - betareg(LEV_LT3 ~ SIZE1 + PROF2 + GROWTH2 + AGE + IND3A, data = rdata, subset = LEV_LT3 0)})\n'
In [16]: # OUTPUT MODEL SUMMARY
In [17]: print r("summary(m)")
try({summary(m)})
Call:
betareg(formula = LEV_LT3 ~ SIZE1 + PROF2 + GROWTH2 + AGE + IND3A, data = rdata,
subset = LEV_LT3 0)
Standardized weighted residuals 2:
Min 1Q Median 3Q Max
-7.2802 -0.5194 0.0777 0.6037 5.8777
Coefficients (mean model with logit link):
Estimate Std. Error z value Pr(|z|)
(Intercept) 1.229773 0.312990 3.929 8.53e-05 ***
SIZE1 -0.105009 0.021211 -4.951 7.39e-07 ***
PROF2 -2.414794 0.377271 -6.401 1.55e-10 ***
GROWTH2 0.003306 0.001043 3.169 0.00153 **
AGE -0.004999 0.001795 -2.786 0.00534 **
IND3A 0.688314 0.074069 9.293 2e-16 ***
Phi coefficients (precision model with identity link):
Estimate Std. Error z value Pr(|z|)
(phi) 3.9362 0.1528 25.77 2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Type of estimator: ML (maximum likelihood)
Log-likelihood: 266.7 on 7 Df
Pseudo R-squared: 0.1468
Number of iterations: 25 (BFGS) + 2 (Fisher scoring)
In [18]: # CALCULATE MODEL PREDICTION
In [19]: r("beta_fit - predict(m, link = 'response')")
Out[19]: "try({beta_fit - predict(m, link = 'response')})\n"
In [20]: # SHOW PREDICTION SUMMARY IN R
In [21]: print r("summary(beta_fit)")
try({summary(beta_fit)})
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.1634 0.3069 0.3465 0.3657 0.4007 0.6695
In [22]: # PASS DATA FROM R TO PYTHON
In [23]: pydata = pd.DataFrame(r.get("beta_fit"), columns = ["y_hat"])
In [24]: # SHOW PREDICTION SUMMARY IN PYTHON
In [25]: pydata.y_hat.describe()
Out[25]:
count 1116.000000
mean 0.365675
std 0.089804
min 0.163388
25% 0.306897
50% 0.346483
75% 0.400656
max 0.669489
