Error using number as argument to R function in RPy2

Question

I am attempting to use the mutual information function from the R package tseriesChaos on a time series and find the first minimum in order to determine the optimum delay for a delay embedding of the time series. I have written the following function to accomplish this:

def determine_lag(tseries, plot):
numpser = numpy.asarray(tseries)
n = numpser.size
bins = 1 + math.log(n, 2)
z = 500 
emi = numpy.array(tseriesChaos.mutual(tseries, bins, z, plot))
x = emi[0]
it = numpy.nditer(emi)
while not it.finished:
    y = it[0]
    num = it.index
    if y > x:
        lag = num
        break
    else:
        x = y
    it.iternext()
else:
    showwarning(title='Error', message='No minimum found, delay set to 50')
    failed = True
    lag = 50
return lag, failed

where tseries is the time series as extracted by soundfile.read elsewhere and plot is either TRUE or FALSE .

When attempting to use the function, however, an error seems to occur in the translation of the arguments for the R function. The output is as follows:

Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/local/Cellar/python3/3.6.4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/tkinter/__init__.py", line 1699, in __call__
return self.func(*args)
File "/Users/BrandonPlay/Soundbed 0.3/master.py", line 177, in Start
self.lag, failed = determine_lag(self.tseries, do_plot)
File "/Users/BrandonPlay/Soundbed 0.3/master.py", line 49, in determine_lag
emi = numpy.array(tseriesChaos.mutual(tseries, bins, z, plot))
File "/Users/BrandonPlay/Library/Python/3.6/lib/python/site-packages/rpy2/robjects/functions.py", line 178, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/Users/BrandonPlay/Library/Python/3.6/lib/python/site-packages/rpy2/robjects/functions.py", line 102, in __call__
new_args = [conversion.py2ri(a) for a in args]
File "/Users/BrandonPlay/Library/Python/3.6/lib/python/site-packages/rpy2/robjects/functions.py", line 102, in <listcomp>
new_args = [conversion.py2ri(a) for a in args]
File "/Users/BrandonPlay/Library/Python/3.6/lib/python/site-packages/rpy2/robjects/numpy2ri.py", line 72, in numpy2ri
if not o.dtype.isnative:
AttributeError: 'float' object has no attribute 'dtype'

From what I can tell, this error occurs when the function in RPy2 which converts the arguments to R objects to pass to the R function encounters the argument z . The current setup, where z is assigned outside the function call, was in an attempt to fix the error; previously, I had simply stated the number as the argument within the function call.

I really do not even remotely understand why the argument converter should be having difficulty with a simple integer argument, especially since bins is also an integer and processes fine.

Does anybody know why this might be happening?

Answer 1

As it turns out, the problem was occurring because I had activated numpy2ri incorrectly earlier in the program, assigning it to py2ri instead of using numpy2ri.activate() , thus overwriting the normal py2ri routine which converts non-numpy objects into r objects. I discovered this in trying to fix a raft of similar errors by turning everything into numpy objects, including using numpy.array([numpy.int_(some_number)]) for simple integer arguments. Strangely, numpy2ri.activate() never worked, instead giving an error something like class function has no method activate , which is very weird given that that's how the docs tell you to do it. Eventually, I removed numpy2ri entirely and just converted the tseries numpy array directly into an R vector beforehand using tmseries = robjects.FloatVector(tseries.tolist()) .