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Module: LogisticRegression Bio/Tools/Classification/LogisticRegression.py

LogisticRegression.py

This module provides code for doing logistic regressions.

Classes: LogisticRegression Holds information for a LogisticRegression classifier.

Functions: train Train a new classifier. calculate Calculate the probabilities of each class, given an observation. classify Classify an observation into a class.

Imported modules   
from Bio.Tools import listfns
Functions   
calculate
classify
train
  calculate 
calculate ( lr,  x )

calculate(lr, x) -> list of probabilities

Calculate the probability for each class. lr is a LogisticRegression object. x is the observed data. Returns a list of the probability that it fits each class.

  classify 
classify ( lr,  x )

classify(lr, x) -> 1 or 0

Classify an observation into a class.

  train 
train (
        xs,
        ys,
        update_fn=None,
        typecode=None,
        )

train(xs, ys[, update_fn]) -> LogisticRegression

Train a logistic regression classifier on a training set. xs is a list of observations and ys is a list of the class assignments, which should be 0 or 1. xs and ys should contain the same number of elements. update_fn is an optional callback function that takes as parameters that iteration number and log likelihood.

Exceptions   
AssertionError, "Didn't converge."
ValueError, "Classes should be 0's and 1's"
ValueError, "No observations or observation of 0 dimension."
ValueError, "xs and ys should be the same length."
Classes   
LogisticRegression

Holds information necessary to do logistic regression


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