com.github.jessemull.microflex.bigintegerflex.stat.SampleStandardDeviationBigInteger Maven / Gradle / Ivy

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Microplate library for parsing wet lab data.
There is a newer version: 1.0.4
/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

/* -------------------------------- Package -------------------------------- */

package com.github.jessemull.microflex.bigintegerflex.stat;

/* ----------------------------- Dependencies ------------------------------ */

import java.math.BigDecimal;
import java.math.MathContext;
import java.util.List;

import com.github.jessemull.microflex.util.ImmutableMathUtil;

/**
 * This class calculates the sample standard deviation of big integer plate 
 * stacks, plates, wells and well sets as the square root of the unbiased sample 
 * variance.
 * 
 * 


 * 
 * Statistical operations can be performed on stacks, plates, sets and wells using
 * standard or aggregated functions. Standard functions calculate the desired
 * statistic for each well in the stack, plate or set. Aggregated functions aggregate
 * the values from all the wells in the stack, plate or set and perform the statistical
 * operation on the aggregated values. Both standard and aggregated functions can
 * be performed on a subset of data within the stack, plate, set or well.
 * 
 * 


 * 
 * The methods within the MicroFlex library are meant to be flexible and the
 * descriptive statistic object supports operations using a single stack, plate,
 * set or well as well as collections and arrays of stacks, plates, sets or wells. 
 *  
 * 
 *    
 *    
 *    
 *    
 *    
 *       
 *       
 *       
 *       
 *    
 *    
 *       
 *       
 *       
 *       
 *    
 * Operation Beginning
Index Length of
Subset Input/Output

 *          
 *             
 *                
 *             
 *          Standard  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *             
 *                
 *             
 *          Accepts a single well, set, plate or stack as input
Calculates the statistic for each well in a well, set, plate or stack  
 *       

 *          
 *             
 *                
 *             
 *          Aggregated  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *              
 *                
 *             
 *          Accepts a single well/set/plate/stack or a collection/array of wells/sets/plates/stacks as input
Aggregates the data from all the wells in a well/set/plate/stack and calculates the statistic using the aggregated data  
 *       
 * 
 * @author Jesse L. Mull
 * @update Updated Oct 18, 2016
 * @address http://www.jessemull.com
 * @email [email protected]
 */
public class SampleStandardDeviationBigInteger extends DescriptiveStatisticBigIntegerContext {
	
	/**
     * Calculates the standard deviation.
     * @param    List    the list
     * @param    MathContext         the math context
     * @return                       the result
     */
	public BigDecimal calculate(List list, MathContext mc) {

        BigDecimal sum = new BigDecimal(0.0);
    	BigDecimal mean = mean(list, mc);
        
    	for(BigDecimal bd : list) {
    		BigDecimal difference = bd.subtract(mean);
    		sum = sum.add(difference.pow(2, mc));
    	}
    	
    	sum = sum.divide(new BigDecimal(list.size() - 1), mc);
    	
    	return ImmutableMathUtil.sqrt(sum);
    }    
	
    /**
     * Calculates the standard deviation of the values between the beginning 
     * and ending indices.
     * @param    List    the list
     * @param    int                 beginning index of subset
     * @param    int                 length of subset
     * @param    MathContext         the math context
     * @return                       the result
     */
    public BigDecimal  calculate(List list, int begin, int length, MathContext mc) {
        return calculate(list.subList(begin, begin + length), mc);
    }

    /**
     * Calculates the mean.
     * @param    List    the list
     * @param    MathContext         the math context
     * @return                       the result
     */
    private BigDecimal mean(List list, MathContext mc) {
        
        BigDecimal sum = new BigDecimal(0.0);
        
        for(BigDecimal bd : list) {
        	sum = sum.add(bd);
        }
        
        return sum.divide(new BigDecimal(list.size()));
    }

}