jarnorfb / epysurv Goto Github PK

E       rpy2.rinterface.RRuntimeError: Error in algo.farrington.data.glm(dayToConsider = dayToConsider, b = control$b,  : 
E         Some reference values did not exist (index<1).

import pandas as pd
import pytest

from epysurv.models.timepoint import FarringtonFlexible

def test_farrington_weekly_example():

    model = FarringtonFlexible()

    total_periods = 100
    test_size = 20
    case_count = 10

    # set up some weekly data
    dates = pd.date_range('2017-07-09', periods=total_periods, freq='7D')
    # just make this constant (but this also fails with random or real case count values)
    case_counts = [case_count] * total_periods

    df = pd.DataFrame({'n_cases': case_counts}, index = dates)

    train_data = df[:-1 * test_size]
    test_data = df[-1 * test_size:]

    # make sure we can fit and predict
    model.fit(train_data)
    _ = model.predict(test_data)

def test_farrington_weekly_example():
    
        model = FarringtonFlexible()
    
        total_periods = 100
        test_size = 20
        case_count = 10
    
        # set up some weekly data
        dates = pd.date_range('2017-07-09', periods=total_periods, freq='7D')
        # just make this constant (but this also fails with random or real case count values)
        case_counts = [case_count] * total_periods
    
        df = pd.DataFrame({'n_cases': case_counts}, index = dates)
    
        train_data = df[:-1 * test_size]
        test_data = df[-1 * test_size:]
    
        # make sure we can fit and predict
        model.fit(train_data)
>       _ = model.predict(test_data)

test_farrington_specific_example.py:26: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
..\epysurv\models\timepoint\_base.py:131: in predict
    surveillance_result = self._call_surveillance_algo(r_instance, detection_range)
..\epysurv\models\timepoint\farrington.py:166: in _call_surveillance_algo
    surv = surveillance.farringtonFlexible(sts, control=control)
C:\anaconda3\envs\epysurv-dev\lib\site-packages\rpy2\robjects\functions.py:178: in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = R object with classes: ('function',) mapped to:
<DocumentedSTFunction - Python:0x000001C714FD1608 / R:0x000001C70F26E4A8>
args = (R object with classes: ('sts',) mapped to:
<RS4 - Python:0x000001C7151F5548 / R:0x000001C70FF061F0>,)
kwargs = {'control': R object with classes: ('list',) mapped to:
<ListVector - Python:0x000001C7152E92C8 / R:0x000001C71400440...ect with classes: ('character',) mapped to:
<StrVector - Python:0x000001C715468C88 / R:0x000001C7149A7E00>
['delta']}
new_args = [R object with classes: ('sts',) mapped to:
<RS4 - Python:0x000001C7151F5548 / R:0x000001C70FF061F0>]
new_kwargs = {'control': R object with classes: ('list',) mapped to:
<ListVector - Python:0x000001C7152E92C8 / R:0x000001C71400440...ect with classes: ('character',) mapped to:
<StrVector - Python:0x000001C715471C88 / R:0x000001C7149A7E00>
['delta']}
k = 'control'
v = R object with classes: ('list',) mapped to:
<ListVector - Python:0x000001C7152E92C8 / R:0x000001C714004408>
[IntVect...ject with classes: ('character',) mapped to:
<StrVector - Python:0x000001C715478F48 / R:0x000001C7149A7E00>
['delta']

    def __call__(self, *args, **kwargs):
        new_args = [conversion.py2ri(a) for a in args]
        new_kwargs = {}
        for k, v in kwargs.items():
            new_kwargs[k] = conversion.py2ri(v)
>       res = super(Function, self).__call__(*new_args, **new_kwargs)
E       rpy2.rinterface.RRuntimeError: Error in algo.farrington.data.glm(dayToConsider = dayToConsider, b = control$b,  : 
E         Some reference values did not exist (index<1).

conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - python=3.7 -> vc[version='>=14,<15.0a0']
  - vc=9
Use "conda search <package> --info" to see the dependencies for each package.
During handling of the above exception, another exception occurred:
`conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform win-64: {"vc[version='>=14,<15.0a0']", 'vc=9'}`