Logistic regression results different in Scikit python and R?

Question

I was running logistic regression on iris dataset on both R and Python.But both are giving different results(coefficients,intercept and scores).

#Python codes.
    In[23]: iris_df.head(5)
    Out[23]: 
     Sepal.Length  Sepal.Width  Petal.Length  Petal.Width  Species
    0           5.1          3.5           1.4          0.2        0
    1           4.9          3.0           1.4          0.2        0
    2           4.7          3.2           1.3          0.2        0
    3           4.6          3.1           1.5          0.2        0
    In[35]: iris_df.shape
    Out[35]: (100, 5)
    #looking at the levels of the Species dependent variable..

        In[25]: iris_df['Species'].unique()
        Out[25]: array([0, 1], dtype=int64)

    #creating dependent and independent variable datasets..

        x = iris_df.ix[:,0:4]
        y = iris_df.ix[:,-1]

    #modelling starts..
    y = np.ravel(y)
    logistic = LogisticRegression()
    model = logistic.fit(x,y)
    #getting the model coefficients..
    model_coef= pd.DataFrame(list(zip(x.columns, np.transpose(model.coef_))))
    model_intercept = model.intercept_
    In[30]: model_coef
    Out[36]: 
                  0                  1
    0  Sepal.Length  [-0.402473917528]
    1   Sepal.Width   [-1.46382924771]
    2  Petal.Length    [2.23785647964]
    3   Petal.Width     [1.0000929404]
    In[31]: model_intercept
    Out[31]: array([-0.25906453])
    #scores...
    In[34]: logistic.predict_proba(x)
    Out[34]: 
    array([[ 0.9837306 ,  0.0162694 ],
           [ 0.96407227,  0.03592773],
           [ 0.97647105,  0.02352895],
           [ 0.95654126,  0.04345874],
           [ 0.98534488,  0.01465512],
           [ 0.98086592,  0.01913408],

R codes.

> str(irisdf)
'data.frame':   100 obs. of  5 variables:
 $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
 $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
 $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 $ Species     : int  0 0 0 0 0 0 0 0 0 0 ...

 > model <- glm(Species ~ ., data = irisdf, family = binomial)
Warning messages:
1: glm.fit: algorithm did not converge 
2: glm.fit: fitted probabilities numerically 0 or 1 occurred 
> summary(model)

Call:
glm(formula = Species ~ ., family = binomial, data = irisdf)

Deviance Residuals: 
       Min          1Q      Median          3Q         Max  
-1.681e-05  -2.110e-08   0.000e+00   2.110e-08   2.006e-05  

Coefficients:
               Estimate Std. Error z value Pr(>|z|)
(Intercept)       6.556 601950.324       0        1
Sepal.Length     -9.879 194223.245       0        1
Sepal.Width      -7.418  92924.451       0        1
Petal.Length     19.054 144515.981       0        1
Petal.Width      25.033 216058.936       0        1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 1.3863e+02  on 99  degrees of freedom
Residual deviance: 1.3166e-09  on 95  degrees of freedom
AIC: 10

Number of Fisher Scoring iterations: 25

Due to convergence problem,i increased the maximum iteration and gave epsilon as 0.05.

> model <- glm(Species ~ ., data = irisdf, family = binomial,control = glm.control(epsilon=0.01,trace=FALSE,maxit = 100))
> summary(model)

Call:
glm(formula = Species ~ ., family = binomial, data = irisdf, 
    control = glm.control(epsilon = 0.01, trace = FALSE, maxit = 100))

Deviance Residuals: 
       Min          1Q      Median          3Q         Max  
-0.0102793  -0.0005659  -0.0000052   0.0001438   0.0112531  

Coefficients:
             Estimate Std. Error z value Pr(>|z|)
(Intercept)     1.796    704.352   0.003    0.998
Sepal.Length   -3.426    215.912  -0.016    0.987
Sepal.Width    -4.208    123.513  -0.034    0.973
Petal.Length    7.615    159.478   0.048    0.962
Petal.Width    11.835    285.938   0.041    0.967

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 1.3863e+02  on 99  degrees of freedom
Residual deviance: 5.3910e-04  on 95  degrees of freedom
AIC: 10.001

Number of Fisher Scoring iterations: 12

#R scores..
> scores = predict(model, newdata = irisdf, type = "response")
> head(scores,5)
           1            2            3            4            5 
2.844996e-08 4.627411e-07 1.848093e-07 1.818231e-06 2.631029e-08 

Both the scores,intercept and coefficients are completely different in R and python.Which one is correct and I want to proceed in python.Now having confusion which results are accurate.

Answer 1

UPDATED The problem is that there exists perfect separation along the petal width variable. In other words, this variable can be used to perfectly predict whether a sample in the given dataset is setosa or versicolor. This breaks the loglikelihood maximization estimation used in logistic regression in R. The problem is that the loglikelihood can be driven very high by taking the coefficient of petal width to the infinity.

Some background and strategies are discussed here .

There is also a good thread on CrossValidated discussing strategies.

So why does the sklearn LogisticRegression work? Because it employs "regularized logistic regression". The regularization penalizes estimating large values for parameters.

In the example below, I use the Firth's bias-reduced method of logistic regression package, logistf, to produce a converged model.

library(logistf)

iris = read.table("path_to _iris.txt", sep="\t", header=TRUE)
iris$Species <- as.factor(iris$Species)
sapply(iris, class)

model1 <- glm(Species ~ ., data = irisdf, family = binomial)
# Does not converge, throws warnings.

model2 <- logistf(Species ~ ., data = irisdf, family = binomial)
# Does converge.

ORIGINAL Based on the std.error and z-values in the R solution, I think you have a bad model specification. A z-value of close to 0 essentially tells you there is no correlation between the model and the dependent variable. So this is a nonsensical model.

My first thought is that you need to transform that Species field into a categorical variable. It is an int type in your example. Try using as.factor

How to convert integer into categorical data in R?