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<?php |
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/** |
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* ---------------------------------------------------------------------- |
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* |
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* Copyright (c) 2012 Khaled Al-Shamaa. |
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* |
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* http://www.ar-php.org |
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* |
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* PHP Version 5 |
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* |
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* ---------------------------------------------------------------------- |
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* @desc We aim in Al-Kashi project to provide a rich package full of statistical |
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* functions useful for online business intelligent and data mining, possible |
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* applications may include an online log file analysis, Ad's and Campaign |
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* statistics, or survey/voting results on-fly analysis. |
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* |
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* @category Math |
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* @package Kashi |
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* @author Khaled Al-Shamaa <khaled.alshamaa@gmail.com> |
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* @copyright 2012 Khaled Al-Shamaa |
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* |
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* @license GPL <http://www.gnu.org/licenses/gpl.txt> |
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* @version 1.0.0 released in March 5, 2012 |
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* @link http://www.ar-php.org/stats/al-kashi |
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*/ |
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class Kashi |
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{ |
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private $values = array(); |
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private $dataset = array(); |
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public function __construct() |
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{ |
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} |
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public function __destruct() |
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{ |
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} |
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/** |
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* Compute the arithmetic mean, and is calculated by adding a group of numbers |
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* and then dividing by the count of those numbers. |
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* For example, the mean of 2, 3, 3, 5, 7, and 10 is 30 divided by 6, which is 5. |
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* |
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* @param array List of float values for which you want to calculate the mean. |
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* |
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* @return float Arithmetic mean |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function mean() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$total = 0; |
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foreach ($this->values as $value) { |
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$total += $value; |
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} |
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return $total/count($this->values); |
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} |
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/** |
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* Compute the sample median which is the middle number of a group of numbers; that is, |
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* half the numbers have values that are greater than the median, and half the numbers |
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* have values that are less than the median. |
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* For example, the median of 2, 3, 3, 5, 7, and 10 is 4. |
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* |
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* @param array List of float values for which you want to calculate the median. |
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* |
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* @return float Sample median |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function median() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$list = $this->values; |
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sort($list); |
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$count = count($list); |
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if ($count % 2 == 0) { |
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$median = ($list[($count / 2) - 1] + $list[$count / 2]) / 2; |
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} else { |
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$median = $list[floor($count / 2)]; |
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} |
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return $median; |
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} |
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/** |
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* Compute the mode which is the most frequently occurring number in a group of numbers. |
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* For example, the mode of 2, 3, 3, 5, 7, and 10 is 3. |
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* |
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* @param array List of float values for which you want to calculate the mode. |
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* |
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* @return float Returns the most frequently occurring or repetitive value |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function mode() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$counter = array(); |
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foreach ($this->values as $value) { |
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if (isset($counter[$value])) { |
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$counter[$value]++; |
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} else { |
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$counter[$value] = 1; |
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} |
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} |
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return array_keys($counter, max($counter)); |
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} |
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/** |
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* Estimates variance based on a sample |
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* |
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* @param array List of float values corresponding to a sample of a population. |
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* |
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* @return float Returns the sample variance |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function variance() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$mean = $this->mean(); |
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$var = 0; |
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foreach ($this->values as $value) { |
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$var += ($value - $mean) * ($value - $mean); |
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} |
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$var = $var / (count($this->values) - 1); |
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return $var; |
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} |
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/** |
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* Compute the standard deviation based on a sample. The standard deviation is a measure of |
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* how widely values are dispersed from the average value (the mean). |
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* |
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* @param array List of float values for which you want to calculate the standard deviation. |
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* |
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* @return float Returns the standard deviation |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function sd() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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return sqrt($this->variance()); |
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} |
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/** |
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* Compute the skewness of a distribution. Skewness characterizes the degree of asymmetry of |
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* a distribution around its mean. Positive skewness indicates a distribution with an asymmetric |
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* tail extending toward more positive values. Negative skewness indicates a distribution with |
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* an asymmetric tail extending toward more negative values. |
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* |
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* @param array List of float values for which you want to calculate the skewness. |
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* |
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* @return float Returns the skewness of a distribution |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function skew() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$mean = $this->mean(); |
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$sd = $this->sd(); |
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$n = count($this->values); |
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$skew = 0; |
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foreach ($this->values as $value) { |
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$skew += pow(($value - $mean) / $sd, 3); |
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} |
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$skew = ($skew * $n) / (($n - 1) * ($n - 2)); |
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// skew standard error = sqrt(6 / $n) |
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// skew is significant if its value exceed 2 * sqrt(6 / $n) |
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return $skew; |
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} |
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/** |
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* Compute the kurtosis of a distribution. Kurtosis characterizes the relative peakedness or |
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* flatness of a distribution compared with the normal distribution. Positive kurtosis indicates |
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* a relatively peaked distribution. Negative kurtosis indicates a relatively flat distribution. |
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* |
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* @param array List of float values for which you want to calculate the kurtosis. |
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* |
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* @return float Returns the kurtosis of a distribution |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function kurt() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$mean = $this->mean(); |
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$sd = $this->sd(); |
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$n = count($this->values); |
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$kurt = 0; |
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foreach ($this->values as $value) { |
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$kurt += pow(($value - $mean) / $sd, 4); |
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} |
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$kurt = ($kurt * $n * ($n + 1)) / (($n - 1) * ($n - 2) * ($n - 3)); |
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$kurt = $kurt - ((3 * ($n - 1) * ($n - 1)) / (($n - 2) * ($n - 3))); |
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// kurt standard error = sqrt(24 / $n) |
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// kurt is significant if its value exceed 2 * sqrt(24 / $n) |
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return $kurt; |
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} |
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/** |
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* Compute the coefficients of variation |
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* |
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* @param array List of float values for which you want to calculate the coefficients of variation. |
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* |
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* @return float Returns the coefficients of variation |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function cv() |
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{ |
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if (func_num_args() > 0) { |
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$this->values = func_get_arg(0); |
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} |
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$mean = $this->mean(); |
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$sd = $this->sd(); |
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$cv = ($sd / $mean) * 100; |
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return $cv; |
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} |
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/** |
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* Compute the covariance, the average of the products of deviations for each data point pair. |
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* Use covariance to determine the relationship between two data sets. For example, you can |
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* examine whether greater income accompanies greater levels of education. |
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* |
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* @param array $x First list of float values |
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* @param array $y Second list of float values |
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* |
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* @return float Returns the covariance |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function cov($x, $y) |
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{ |
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$meanX = $this->mean($x); |
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$meanY = $this->mean($y); |
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$count = count($x); |
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$total = 0; |
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for ($i=0; $i<$count; $i++) { |
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$total += ($x[$i] - $meanX) * ($y[$i] - $meanY); |
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} |
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return (1 / ($count - 1)) * $total; |
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} |
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/** |
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* Compute the correlation coefficient. Use the correlation coefficient to determine the |
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* relationship between two properties. It uses different measures of association, all |
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* in the range [-1, 1] with 0 indicating no association. |
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* |
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* @param array $x First list of float values |
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* @param array $y Second list of float values |
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* |
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* @return float Returns the correlation coefficient |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function cor($x, $y) |
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{ |
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$cov = $this->cov($x, $y); |
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$sdX = $this->sd($x); |
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$sdY = $this->sd($y); |
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return $cov / ($sdX * $sdY); |
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} |
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/** |
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* Test of the null hypothesis that true correlation is equal to 0 |
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* |
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* @param array $r Correlation value |
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* @param array $n Number of observations |
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* |
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* @return float Returns null hypothesis probability: true correlation is equal to 0 |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function corTest($r, $n) |
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{ |
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$t = $r / sqrt((1 - ($r * $r)) / ($n - 2)); |
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$result = $this->tDist($t, $n - 2); |
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return $result; |
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} |
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/** |
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* Compute the simple linear regression fits a linear model to represent |
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* the relationship between a response (or y-) variate, and an explanatory |
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* (or x-) variate. |
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* |
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* @param array $x Specifies the name of the explanatory (or x-) variate. |
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* @param array $y Specifies the name of the response (or y-) variate. |
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* |
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* @return array Returns [intercept], [sploe], and [r-square] as float values |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function lm($x, $y) |
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{ |
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$meanX = $this->mean($x); |
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$meanY = $this->mean($y); |
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$n = count($x); |
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$nominator = 0; |
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$denominator = 0; |
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for ($i=0; $i<$n; $i++) { |
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$nominator += ($x[$i] - $meanX) * ($y[$i] - $meanY); |
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$denominator += ($x[$i] - $meanX) * ($x[$i] - $meanX); |
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} |
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$b = $nominator / $denominator; |
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$a = $meanY - $b * $meanX; |
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// Total sum of squares (ss) and Residual sum of squares (rss) |
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$ss = 0; |
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$rss = 0; |
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for ($i=0; $i<$n; $i++) { |
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$ss += pow($y[$i] - $meanY, 2); |
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$est = $a + ($b * $x[$i]); |
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$rss += pow($y[$i] - $est, 2); |
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} |
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// R-square value |
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$r2 = 1 - ($rss / $ss); |
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return array('intercept'=>$a, 'slope'=>$b, 'r-square'=>$r2); |
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} |
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/** |
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* Compute the Student's t-Test value to determine whether two samples are likely |
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* to have come from the same two underlying populations that have the same mean |
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* |
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* @param array $a First list of float values |
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* @param array $b Second list of float values |
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* @param boolean $paired Logical indicating whether you want a paired t-test |
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* |
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* @return float Returns the associated with a Student's t-Test |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function tTest ($a, $b, $paired=false) |
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{ |
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if ($paired == true) { |
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$count = count($a); |
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$diff = array(); |
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for ($i=0; $i<$count; $i++) { |
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$diff[$i] = $a[$i] - $b[$i]; |
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} |
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$mean = $this->mean($diff); |
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$var = $this->variance($diff); |
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$t = $mean / sqrt($var / $count); |
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} else { |
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$meanA = $this->mean($a); |
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$meanB = $this->mean($b); |
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$varA = $this->variance($a); |
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$varB = $this->variance($b); |
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$countA = count($a); |
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$countB = count($b); |
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$t = ($meanA - $meanB) / sqrt(($varA / $countA) + ($varB / $countB)); |
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} |
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return $t; |
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} |
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/** |
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* Returns the standard normal cumulative distribution function. The distribution |
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* has a mean of 0 (zero) and a standard deviation of one. Use this function in |
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* place of a table of standard normal curve areas. |
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* |
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* @param float $x Is the value for which you want the distribution. |
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* @param float $mean The distribution mean (default is zero). |
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* @param float $sd The distribution standard deviation (default is one). |
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* |
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* @return float the standard normal cumulative distribution function. |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function norm ($x, $mean=0, $sd=1) |
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{ |
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$y = (1 / sqrt(2 * pi())) * exp(-0.5 * pow($x, 2)); |
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return $y; |
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} |
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private function _zip ($q, $i, $j, $b) |
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{ |
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$zz = 1; |
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$z = $zz; |
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$k = $i; |
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while ($k <= $j) { |
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$zz *= $q * $k / ($k - $b); |
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$z += $zz; |
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$k += 2; |
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} |
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return $z; |
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} |
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/** |
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* Returns the Percentage Points (probability) for the Student t-distribution |
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* where a numeric value (t) is a calculated value of t for which the Percentage |
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* Points are to be computed. |
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* |
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* @param float $t Is the numeric value at which to evaluate the distribution. |
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* @param integer $n Is an integer indicating the number of degrees of freedom. |
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* @param integer $tail Specifies the number of distribution tails to return. |
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* If tail = 1, TDIST returns the one-tailed distribution. |
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* If tail = 2, TDIST returns the two-tailed distribution. |
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* |
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* @return float the Percentage Points (probability) for the Student t-distribution |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function tDist ($t, $n, $tail=1) |
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{ |
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$pj2 = pi() / 2; |
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$t = abs($t); |
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$rt = $t / sqrt($n); |
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$fk = atan($rt); |
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if ($n == 1) { |
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$result = 1 - $fk / $pj2; |
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} else { |
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$ek = sin($fk); |
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$dk = cos($fk); |
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if (($n % 2) == 1) { |
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$result = 1 - ($fk + $ek * $dk * $this->_zip($dk * $dk, 2, $n-3, -1)) / $pj2; |
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} else { |
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$result = 1 - $ek * $this->_zip($dk * $dk, 1, $n-3, -1); |
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} |
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} |
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return $result / $tail; |
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} |
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/** |
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* Returns the F probability distribution. You can use this function to determine |
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* whether two data sets have different degrees of diversity. |
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* |
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* @param float $f Is the value at which to evaluate the function. |
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* @param integer $df1 Is the numerator degrees of freedom. |
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* @param integer $df2 Is the denominator degrees of freedom. |
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* |
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* @return float the F probability distribution |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function fDist ($f, $df1, $df2) |
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{ |
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$pj2 = pi() / 2; |
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$x = $df2 / ($df1 * $f + $df2); |
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if (($df1 % 2) == 0) { |
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return $this->_zip(1 - $x, $df2, $df1 + $df2 - 4, $df2 - 2) * pow($x, $df2 / 2); |
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} |
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if (($df2 % 2) == 0) { |
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return 1 - $this->_zip($x, $df1, $df1 + $df2 - 4, $df1 - 2) * pow(1 - $x, $df1 / 2); |
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} |
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$tan = atan(sqrt($df1 * $f / $df2)); |
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$a = $tan / $pj2; |
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$sat = sin($tan); |
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$cot = cos($tan); |
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if ($df2 > 1) { |
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$a = $a + $sat * $cot * $this->_zip($cot * $cot, 2, $df2 - 3, -1) / $pj2; |
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} |
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if ($df1 == 1) { |
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return 1 - $a; |
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} |
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$c = 4 * $this->_zip($sat * $sat, $df2 + 1, $df1 + $df2 - 4, $df2 - 2) * $sat * pow($cot, $df2) / pi(); |
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if ($df2 == 1) { |
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return 1 - $a + $c / 2; |
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} |
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$k = 2; |
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while ($k <= ($df2 - 1) / 2) { |
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$c *= $k / ($k - 0.5); |
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$k++; |
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} |
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return 1 - $a + $c; |
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} |
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/** |
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* Return the probability of normal z value |
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* Adapted from a polynomial approximation in: |
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* Ibbetson D, Algorithm 209 |
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* Collected Algorithms of the CACM 1963 p. 616 |
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* |
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* @param float $z Is the value at which you want to evaluate the probability. |
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* |
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* @return float the probability of normal z value |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
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public function normCDF ($z) |
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{ |
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$max = 6; |
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|
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if ($z == 0) { |
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$x = 0; |
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} else { |
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$y = abs($z) / 2; |
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if ($y >= ($max / 2)) { |
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$x = 1; |
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} elseif ($y < 1) { |
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$w = $y * $y; |
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$x = ((((((((0.000124818987 * $w |
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- 0.001075204047) * $w + 0.005198775019) * $w |
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- 0.019198292004) * $w + 0.059054035642) * $w |
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- 0.151968751364) * $w + 0.319152932694) * $w |
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- 0.531923007300) * $w + 0.797884560593) * $y * 2; |
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} else { |
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$y -= 2; |
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$x = (((((((((((((-0.000045255659 * $y |
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+ 0.000152529290) * $y - 0.000019538132) * $y |
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- 0.000676904986) * $y + 0.001390604284) * $y |
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- 0.000794620820) * $y - 0.002034254874) * $y |
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+ 0.006549791214) * $y - 0.010557625006) * $y |
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+ 0.011630447319) * $y - 0.009279453341) * $y |
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+ 0.005353579108) * $y - 0.002141268741) * $y |
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+ 0.000535310849) * $y + 0.999936657524; |
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} |
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} |
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|
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if ($z > 0) { |
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$result = ($x + 1) / 2; |
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} else { |
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$result = (1 - $x) / 2; |
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} |
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return $result; |
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} |
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|
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/** |
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* Returns the one-tailed probability of the chi-squared distribution. The chi-squared |
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* distribution is associated with a chi-squared test. Use the chi-squared test to |
|
* compare observed and expected values. |
|
* Adapted from: |
|
* Hill, I. D. and Pike, M. C. Algorithm 299 |
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* Collected Algorithms for the CACM 1967 p. 243 |
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* Updated for rounding errors based on remark in |
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* ACM TOMS June 1985, page 185 |
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* |
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* @param float $x Is the value at which you want to evaluate the distribution. |
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* @param integer $df Is the number of degrees of freedom. |
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* |
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* @return float the probability of the chi-squared distribution |
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* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
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*/ |
|
public function chiDist ($x, $df) |
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{ |
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define(LOG_SQRT_PI, log(sqrt(pi()))); |
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define(I_SQRT_PI, 1 / sqrt(pi())); |
|
|
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if ($x <= 0 || $df < 1) { |
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$result = 1; |
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} |
|
|
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$a = $x / 2; |
|
|
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if ($df % 2 == 0) { |
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$even = true; |
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} else { |
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$even = false; |
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} |
|
|
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if ($df > 1) { |
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$y = exp(-1 * $a); |
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} |
|
|
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if ($even) { |
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$s = $y; |
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} else { |
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$s = 2 * $this->normCDF(-1 * sqrt($x)); |
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} |
|
|
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if ($df > 2) { |
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$x = ($df - 1) / 2; |
|
|
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if ($even) { |
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$z = 1; |
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} else { |
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$z = 0.5; |
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} |
|
|
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if ($a > 20) { |
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if ($even) { |
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$e = 0; |
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} else { |
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$e = LOG_SQRT_PI; |
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} |
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|
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$c = log($a); |
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|
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while ($z <= $x) { |
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$e += log($z); |
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$s += exp($c * $z - $a - $e); |
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$z += 1; |
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} |
|
|
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$result = $s; |
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} else { |
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if ($even) { |
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$e = 1; |
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} else { |
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$e = I_SQRT_PI / sqrt($a); |
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} |
|
|
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$c = 0; |
|
|
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while ($z <= $x) { |
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$e *= ($a / $z); |
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$c += $e; |
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$z += 1; |
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} |
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|
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$result = $c * $y + $s; |
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} |
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} else { |
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$result = $s; |
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} |
|
|
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return $result; |
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} |
|
|
|
/** |
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* Performs chi-squared contingency table tests and goodness-of-fit tests. |
|
* |
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* Example: |
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* <code> |
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* $table['Automatic'] = array('4 Cylinders' => 3, '6 Cylinders' => 4, '8 Cylinders' => 12); |
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* $table['Manual'] = array('4 Cylinders' => 8, '6 Cylinders' => 3, '8 Cylinders' => 2); |
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* |
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* $results = $stats->chiTest($table); |
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* </code> |
|
* |
|
* @param array $table Specifies the two-way, n x m table containing the counts |
|
* |
|
* @return array [chi] => the value the chi-squared test statistic |
|
* [df] => the degrees of freedom of the approximate chi-squared distribution of the test statistic. |
|
* [expected] => the expected counts under the null hypothesis. |
|
* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
|
*/ |
|
public function chiTest ($table) |
|
{ |
|
$total = 0; |
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$chi = 0; |
|
|
|
foreach ($table as $category => $row) { |
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foreach ($row as $sample => $cell) { |
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if (isset($rows[$category])) { |
|
$rows[$category] += $cell; |
|
} else { |
|
$rows[$category] = $cell; |
|
} |
|
|
|
if (isset($cols[$sample])) { |
|
$cols[$sample] += $cell; |
|
} else { |
|
$cols[$sample] = $cell; |
|
} |
|
|
|
$total += $cell; |
|
} |
|
} |
|
|
|
$r = count($rows); |
|
$c = count($cols); |
|
$df = ($r - 1) * ($c - 1); |
|
|
|
$expected = array(); |
|
|
|
foreach ($table as $category => $row) { |
|
foreach ($row as $sample => $cell) { |
|
// fo frequency of the observed value |
|
// fe frequency of the expected value |
|
$fo = $cell; |
|
$fe = ($rows[$category] * $cols[$sample]) / $total; |
|
$chi += pow($fo - $fe, 2) / $fe; |
|
|
|
$expected[$category][$sample] = $fe; |
|
} |
|
} |
|
|
|
return array('chi'=>$chi, 'df'=>$df, 'expected'=>$expected); |
|
} |
|
|
|
/** |
|
* Returns the inverse of the standard normal cumulative distribution. |
|
* The distribution has a mean of zero and a standard deviation of one. |
|
* This is an implementation of the algorithm published at: |
|
* http://home.online.no/~pjacklam/notes/invnorm/ |
|
* |
|
* @param float $p Is a probability corresponding to the normal distribution. |
|
* |
|
* @return float Inverse of the standard normal cumulative distribution, with a probability of $p |
|
* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
|
*/ |
|
function inverseNormCDF($p) { |
|
/* coefficients for the rational approximants for the normal probit: */ |
|
$a1 = -3.969683028665376e+01; |
|
$a2 = 2.209460984245205e+02; |
|
$a3 = -2.759285104469687e+02; |
|
$a4 = 1.383577518672690e+02; |
|
$a5 = -3.066479806614716e+01; |
|
$a6 = 2.506628277459239e+00; |
|
$b1 = -5.447609879822406e+01; |
|
$b2 = 1.615858368580409e+02; |
|
$b3 = -1.556989798598866e+02; |
|
$b4 = 6.680131188771972e+01; |
|
$b5 = -1.328068155288572e+01; |
|
$c1 = -7.784894002430293e-03; |
|
$c2 = -3.223964580411365e-01; |
|
$c3 = -2.400758277161838e+00; |
|
$c4 = -2.549732539343734e+00; |
|
$c5 = 4.374664141464968e+00; |
|
$c6 = 2.938163982698783e+00; |
|
$d1 = 7.784695709041462e-03; |
|
$d2 = 3.224671290700398e-01; |
|
$d3 = 2.445134137142996e+00; |
|
$d4 = 3.754408661907416e+00; |
|
|
|
$p_low = 0.02425; |
|
$p_high = 1.0 - $p_low; |
|
|
|
if(0 < $p && $p < $p_low) { |
|
/* rational approximation for the lower region */ |
|
$q = sqrt(-2 * log($p)); |
|
$x = ((((($c1 * $q + $c2) * $q + $c3) * $q + $c4) * $q + $c5) * $q + $c6) / (((($d1 * $q + $d2) * $q + $d3) * $q + $d4) * $q + 1); |
|
} elseif ($p_low <= $p && $p <= $p_high) { |
|
/* rational approximation for the central region */ |
|
$q = $p - 0.5; |
|
$r = $q * $q; |
|
$x = ((((($a1 * $r + $a2) * $r + $a3) * $r + $a4) * $r + $a5) * $r + $a6) * $q / ((((($b1 * $r + $b2) * $r + $b3) * $r + $b4) * $r + $b5) * $r + 1); |
|
} else { |
|
/* rational approximation for the upper region */ |
|
$q = sqrt(-2 * log(1 - $p)); |
|
$x = -((((($c1 * $q + $c2) * $q + $c3) * $q + $c4) * $q + $c5) * $q + $c6) / (((($d1 * $q + $d2) * $q + $d3) * $q + $d4) * $q + 1); |
|
} |
|
|
|
/* |
|
The relative error of the approximation has |
|
absolute value less than 1.15 × 10-9. One iteration of |
|
Halley's rational method (third order) gives full machine precision. |
|
|
|
if(0 < $p && $p < 1) { |
|
$e = 0.5 * erfc(-$x / sqrt(2)) - $p; |
|
$u = $e * sqrt(2 * pi()) * exp($x * $x / 2); |
|
$x = $x - $u / (1 + $x * $u / 2); |
|
} |
|
*/ |
|
|
|
return $x; |
|
} |
|
|
|
/** |
|
* Returns the t-value of the Student's t-distribution as a function of |
|
* the probability and the degrees of freedom. This is an implementation |
|
* of the algorithm in: |
|
* G. W. Hill. "Algorithm 396: Student's t-Quantiles." Communications |
|
* of the ACM 13(10):619--620. ACM Press, October, 1970. |
|
* |
|
* @param float $p Is the probability associated with the two-tailed Student's t-distribution. |
|
* @param integer $n Is the number of degrees of freedom with which to characterize the distribution. |
|
* |
|
* @return float t-value of the Student's t-distribution for the terms above (i.e. $p and $n). |
|
* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
|
*/ |
|
function inverseTCDF($p, $n) { |
|
if($n == 1) { |
|
$p *= M_PI_2; |
|
$result = cos($p) / sin($p); |
|
} else { |
|
$a = 1 / ($n - 0.5); |
|
$b = 48 / ($a * $a); |
|
$c = ((20700 * $a / $b - 98) * $a - 16) * $a + 96.36; |
|
$d = ((94.5 / ($b + $c) - 3) / $b + 1) * sqrt($a * M_PI_2) * $n; |
|
$y = pow(2 * $d * $p, 2 / $n); |
|
|
|
if ($y > (0.05 + $a)) { |
|
/* asymptotic inverse expansion about the normal */ |
|
$x = $this->inverseNormCDF($p * 0.5); |
|
$y = $x * $x; |
|
|
|
if ($n < 5) { |
|
$c += 0.3 * ($n - 4.5) * ($x + 0.6); |
|
} |
|
|
|
$c = (((0.05 * $d * $x - 5) * $x - 7) * $x - 2) * $x + $b + $c; |
|
$y = (((((0.4 * $y + 6.3) * $y + 36) * $y + 94.5) / $c - $y - 3) / $b + 1) * $x; |
|
$y *= $a * $y; |
|
|
|
if ($y > 0.002) { |
|
$y = exp($y) - 1; |
|
} else { |
|
$y += 0.5 * $y * $y; |
|
} |
|
} else { |
|
$y = ((1 / ((($n + 6) / ($n * $y) - 0.089 * $d - 0.822) * ($n + 2) * 3) + 0.5 / ($n + 4)) * $y - 1) * ($n + 1) / ($n + 2) + 1 / $y; |
|
} |
|
|
|
$result = sqrt($n * $y); |
|
} |
|
|
|
return $result; |
|
} |
|
|
|
/** |
|
* Returns the Shannon or Simpson index value |
|
* http://en.wikipedia.org/wiki/Diversity_index |
|
* |
|
* @param array $abundances Associated array where keys refer to the categories and values refer to the observation counts in each category. |
|
* @param string $index Which index you would like to calculate ["shannon"|"simpson"] (default is "shannon") |
|
* @param float $base Base of the logarithmic transformation used in the Shannon index (default is M_E) |
|
* |
|
* @return float The index (either Shannon or Simpson as selected in the $index parameter) |
|
* @author Khaled Al-Sham'aa <khaled.alshamaa@gmail.com> |
|
*/ |
|
public function diversity ($abundances, $index='shannon', $base=M_E) |
|
{ |
|
$index = strtolower($index); |
|
$N = array_sum($abundances); |
|
|
|
// Calculate the proportion of characters belonging to each category |
|
foreach ($abundances as $key=>$value) { |
|
$P["$key"] = $value / $N; |
|
} |
|
|
|
$result = 0; |
|
|
|
if ($index == 'shannon') { |
|
foreach ($P as $key=>$value) { |
|
$result += $value * log($value, $base); |
|
} |
|
$result = -1 * $result; |
|
} elseif ($index == 'simpson') { |
|
if ($N < 20) { |
|
foreach ($abundances as $key=>$value) { |
|
$result += $value * ($value - 1); |
|
} |
|
$result = $result / ($N * ($N - 1)); |
|
} else { |
|
foreach ($P as $key=>$value) { |
|
$result += $value * $value; |
|
} |
|
} |
|
} |
|
|
|
return $result; |
|
} |
|
} |
