rpy2

I am implementing rpy2 code in Django and when I convert pandas dataframe into r dataframe my app starts crashing and giving error: Error: C stack usage 60820464 is too close to the limit otherwise app works fine as long as i don't convert. Is there any problem/mistake in my code? My code snippet: from .models import Values import pandas as pd from rpy2.robjects import pandas2ri pandas2ri.activate() def rpyset(request): filterdata = pd.DataFrame(list(Values.objects.all().values('val1','val2', 'val3', 'val4', 'val5', 'val6'))) r_dataframe = pandas2ri.py2ri(filterdata) # I want to pass r

When I run 'sudo pip install rpy2' I get the a lot of compilation errors. Here is the full dump of all the errors and here is an example except: Compilation parameters for rpy2's C components: include_dirs = ['/usr/share/R/include'] library_dirs = ['/usr/lib/R/lib'] libraries = ['R', 'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm'] extra_link_args = ['-Wl,--export-dynamic', '-fopenmp'] R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" building 'rpy2.rinterface._rinterface' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DR

I'm trying to make a simple call to a R package ( ks ) from within python through rpy2 . This is what I would like to achieve: import rpy2.robjects as robjects # Define two matrices. matrix1 = [[1,1,1,1], [3,3,3,3]] matrix2 = [[1,1,1,1], [3,3,3,3]] # Call 'ks' function to obtain p_value. p_val = robjects.r(''' library(ks) kde.test(x1=matrix1, x2=matrix2)$pvalue''') print p_val I tried following the documentation from rpy2 but it is very scarce. Any help would be appreciated. Gabriel Posting my own answer based on the one given by lgautier since that one did not work as is. I also made it a bit

I'm trying to use rpy2 to use the DESeq2 R/Bioconductor package in python. I actually solved my problem while writing my question (using do_slots allows access to the r objects attributes), but I think the example might be useful for others, so here is how I do in R and how this translates in python: In R I can create a "DESeqDataSet" from two data frames as follows: counts_data <- read.table("long/path/to/file", header=TRUE, row.names="gene") head(counts_data) ## WT_RT_1 WT_RT_2 prg1_RT_1 prg1_RT_2 ## aap-1 406 311 41 95 ## aat-1 5 8 2 0 ## aat-2 1 1 0 0 ## aat-3 13 12 0 1 ## aat-4 6 6 2 3 ##

I've encounter a problem when using rpy2 package to transform dataframe saved in R to Python. import os os.environ['R_HOME'] = '/Library/Frameworks/R.framework/Resources' import rpy2.robjects as ro from rpy2.robjects import pandas2ri # define a trivial dataframe in R ro.r('n = c(1,2)') ro.r("b = c(NA,'def')") ro.r("temp_df = data.frame(n,b)") # the dataframe in R shows missing value in one cell as NA temp_rdf = ro.r('temp_df') print(temp_rdf) n b 1 1 <NA> 2 2 def # yet the transformed Python dataframe replace the missing value with a string temp_pydf = pandas2ri.ri2py(temp_rdf) print(temp_pydf

I am trying to use the magic command in ipython, something I saw here: rpy2 slides I have done the following: import rpy2.ipython %load_ext rpy2.ipython But I get the following error: ImportError: dlopen(/Users/XXX/anaconda/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so, 2): Library not loaded: libicuuc.54.dylib Referenced from: /Users/XXX/anaconda/lib/python2.7/site-packages/rpy2/rinterface/_rinterface.so Reason: image not found Some relevant information: OS: MacOS Sierra Python: 2.7.12 iPython: IPython 5.1.0 rpy2: 2.8.3 Did the pip install singledispatch but the error still

What's the reason for the error when installing rpy2 on Ubuntu 12.04? easy_install rpy2 Searching for rpy2 Reading http://pypi.python.org/simple/rpy2/ Best match: rpy2 2.3.9 Downloading https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.9.tar.gz#md5=86851a56f637e7b87709eb2b91dc5075 Processing rpy2-2.3.9.tar.gz Running rpy2-2.3.9/setup.py -q bdist_egg --dist-dir /tmp/easy_install-DFDRi5/rpy2-2.3.9/egg-dist-tmp-7nyGO8 "/usr/lib/R/bin/R" CMD config --ldflags Invalid substring -fopenmp in string -Wl,--export-dynamic -fopenmp -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lrt -ldl -lm error: Setup

I'm trying to use ryp2 to do a logistic regression. I managed to execute it, but don't know how to extract the coefficients and p-values from the result. I don't want to print the values on the screen bu create a function to use them independently. import rpy2.robjects as ro mydata = ro.r['data.frame'] read = ro.r['read.csv'] head = ro.r['head'] summary = ro.r['summary'] mydata = read("http://www.ats.ucla.edu/stat/data/binary.csv") #cabecalho = head(mydata) formula = 'admit ~ gre + gpa + rank' mylogit = ro.r.glm(formula=ro.r(formula), data=mydata,family=ro.r('binomial(link="logit")')) #What