rpy2 | Interface to use R from Python

by rpy2 Python Version: 3.5.16 License: GPL-2.0

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | rpy2 Summary

rpy2 is a Python library typically used in Data Science applications. rpy2 has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has high support. You can install using 'pip install rpy2' or download it from GitHub, PyPI.

The project's webpage is here:

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Quality

Security

License

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Support

rpy2 has a highly active ecosystem.

It has 402 star(s) with 63 fork(s). There are 8 watchers for this library.

There were 2 major release(s) in the last 6 months.

There are 124 open issues and 757 have been closed. On average issues are closed in 1266 days. There are 7 open pull requests and 0 closed requests.

It has a negative sentiment in the developer community.

The latest version of rpy2 is 3.5.16

Quality

rpy2 has 0 bugs and 0 code smells.

Security

rpy2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

rpy2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

rpy2 is licensed under the GPL-2.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

rpy2 releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed rpy2 and discovered the below as its top functions. This is intended to give you an instant insight into rpy2 implemented functionality, and help decide if they suit your requirements.

Creates a closure from a function
Make an external pointer
Append an object to the list
Create a function from a Python object
Yield information about the system
Iterates over the tags
Add include directory
Extend the elements from the iterable
Wrapper for _show_files
List attributes
Return a pretty representation of the table
Read data from a csv file
Return a pretty representation of the object
Find an expression in the environment
Read n lines from buffer
Convert numpy array to rdata
Call given keyvals
Return the class of this expression
Test the sumr function
Returns the docstring for the given function
Evaluate the given arguments
Imports an R package
Create an API builder
Convert a pandas object to a pandas Series
Wrap r_func
Populates the meta data for the package

Get all kandi verified functions for this library.

rpy2 Key Features

No Key Features are available at this moment for rpy2.

rpy2 Examples and Code Snippets

No Code Snippets are available at this moment for rpy2.

Community Discussions

Trending Discussions on rpy2

Why I am getting ModuleNotFoundError when I make an Exe file for tkinter GUI?

How to plot R's vegan::procrustes using Python (SciPy, NumPy, and Matplotlib)?

capturing the residual from felm in original dataframe and passing to Python

How to transfer a vector from Python to R (and back) after having done some R specific computations

Unable to import rpy2, VSCode in WSL windows subsytem for linux

Using rpy2 to check if I have the latest version of an R package installed

Multipoint(df['geometry']) key error from dataframe but key exist. KeyError: 13 geopandas

rpy2 installation on macbook on Jupyter Notebook

How to select R installation when using rpy2 on conda?

Strange behaviour with string passing to rpy2 - deleting leading zeros from string

QUESTION

Why I am getting ModuleNotFoundError when I make an Exe file for tkinter GUI?

Asked 2022-Apr-01 at 23:30

I have a simple code to use the LHS design of the experiment, and it works fine.

...

ANSWER

Answered 2022-Apr-01 at 23:30

I found the answer for my post.

It seems it makes difference where to put mycode.py file and using the pyinstaller.

The file needs to be where your python is installed, in the scripts folder. Then, we can use pyinstaller mycode.py.

Source https://stackoverflow.com/questions/71709468

QUESTION

How to plot R's vegan::procrustes using Python (SciPy, NumPy, and Matplotlib)?

Asked 2022-Mar-08 at 15:36

I'm following the vegan tutorial on procrustes analysis:

https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/procrustes

...

ANSWER

Answered 2022-Jan-27 at 03:09

It's not exactly the same, but I think it's pretty close.

I brought the varespec data into Python for this. Then tried to mimic the actions that the vegan package (and your code) took. Along those lines, I stuck to the object names you used (for the most part).

There has to be an easier way to do this.

Source https://stackoverflow.com/questions/70870829

QUESTION

capturing the residual from felm in original dataframe and passing to Python

Asked 2022-Feb-10 at 16:18

I am running R via Python using %load_ext rpy2.ipython.

...

ANSWER

Answered 2022-Feb-10 at 16:18

The issue is that with lm the residuals return a named vector, whereas with felm, it is returning a matrix with single column

Source https://stackoverflow.com/questions/71068528

QUESTION

How to transfer a vector from Python to R (and back) after having done some R specific computations

Asked 2021-Dec-26 at 17:52

Let's say I have a vector x1 as a numpy array in the python environment. I want to transfert that vector to the R environment, do some computations using R specific functions and then get another vector x2 and then want to transfer x2 back to python as a numpy array. The goal is to have the following output:

...

ANSWER

Answered 2021-Oct-15 at 19:19

Here is an option with pyper

Source https://stackoverflow.com/questions/69589107

QUESTION

Unable to import rpy2, VSCode in WSL windows subsytem for linux

Asked 2021-Nov-21 at 22:47

Looking for help on using rpy2 in python script with vscode from WSL. I can't get the import to work.

If i try to run the following code:

...

ANSWER

Answered 2021-Nov-21 at 22:30

There is no module or sub-package rpackages in rpy2, so the error message when trying to import it is expected.

The error about a circular a partially initialized module is surprising. Do you happen to have a directory called rpy2 where you are running this from? Python would try to import that directory.

Source https://stackoverflow.com/questions/70058804

QUESTION

Using rpy2 to check if I have the latest version of an R package installed

Asked 2021-Nov-13 at 20:18

I have the following method that checks whether an R package is installed. This helps me avoid installing the package every time I run the code.

I want to add functionality so we can check if the R package is installed AND if it's the latest version. I've had a look at the rpy2 documentation though and I can't see a way to do this.

I was wondering if anyone had any ideas on how I can achieve this? Cheers

...

ANSWER

Answered 2021-Nov-13 at 20:18

You can use two other functions available in utils to get versions of installed and available packages and compare the two to get an answer. The relevant R code is provided in https://stackoverflow.com/a/2563683, which can be translated to Python as below:

Source https://stackoverflow.com/questions/69941743

QUESTION

Multipoint(df['geometry']) key error from dataframe but key exist. KeyError: 13 geopandas

Asked 2021-Oct-11 at 14:51

data source: https://catalog.data.gov/dataset/nyc-transit-subway-entrance-and-exit-data

I tried looking for a similar problem but I can't find an answer and the error does not help much. I'm kinda frustrated at this point. Thanks for the help. I'm calculating the closest distance from a point.

...

ANSWER

Answered 2021-Oct-11 at 14:21

geopandas 0.10.1

have noted that your data is on kaggle, so start by sourcing it
there really is only one issue shapely.geometry.MultiPoint() constructor does not work with a filtered series. Pass it a numpy array instead and it works.
full code below, have randomly selected a point to serve as gpdPoint

Source https://stackoverflow.com/questions/69521034

QUESTION

rpy2 installation on macbook on Jupyter Notebook

Asked 2021-Oct-04 at 12:29

Trying to install rpy2 modules on terminal and there is no action.

Trying to directly install rpy2 on cell

...

ANSWER

Answered 2021-Oct-04 at 12:29

Your example is showing just R code without any python functions used.

Option 1 (easy, without jupyter and python)

If you really do not need Jupyter and python, you can just create documents with R code cells and text in between using RMarkdon inside RStudio.

Option 2 (hard, with jupyter and python)

install R and python
install Jupyter
install rpy2 using ! pip install rpy2 inside a jupyter cell
Run R code within the notebook:

Source https://stackoverflow.com/questions/69433924

QUESTION

How to select R installation when using rpy2 on conda?

Asked 2021-Sep-19 at 23:49

tl;dr Can I configure rpy2 so that it loads the conda installation instead of the system one?

My issue

When I run rpy2 it uses the system installation of R, but it introspects and loads libraries from my conda installation of R. This has various side effects such as segfaults and so on...

Reproduction

I have an installation of R on a Ubuntu 18 server, that my sysadmin has installed. I want to use conda with python and rpy2 to make sure I can select versions somewhat freely.

Below, you can see I am in a conda environment called (rnvp), that rpy2 identifies the 4.0.5 conda installation of R, but that the rpy2.robjects library loads the system R installation instead, which is 4.0.3.

When running the situation script, I get the below

...

ANSWER

Answered 2021-Aug-26 at 12:02

Recompile rpy2 locally, with a linker flag to explicate which R library to link to.

Inspired by the blog post https://thomas-cokelaer.info/blog/2012/01/installing-rpy2-with-different-r-version-already-installed/ I decided to recompile rpy2 from source, and supply the R path as an environment variable to the compilation.

Source https://stackoverflow.com/questions/68936589

QUESTION

Strange behaviour with string passing to rpy2 - deleting leading zeros from string

Asked 2021-Aug-25 at 11:34

I am trying to call a python string variable within a rpy2 script. The variable is supposed to have the shape "01".

I encountered the following behaviour:

...

ANSWER

Answered 2021-Aug-14 at 22:20

Looking at the strings passed to rpy2 for evaluation as R code should make what is happening clear.

In the first case that string of R code is:

Source https://stackoverflow.com/questions/68714092

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install rpy2

pip should work out of the box:. The package has optional depencies providing specific functionalities not otherwise required to use the rest of rpy2.