526 lines
16 KiB
Plaintext
526 lines
16 KiB
Plaintext
;; @module stat.lsp
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;; @description Basic statistics and plotting library
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;; @version 3.0 - Eliminated plot functions and f-prob which now is built-in as prob-f
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;; @version 3.1 - Documentation changes
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;; @version 3.2 - Documentation, mention built-in 'stats' function since 10.4.2
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;;
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;; @author Lutz Mueller, 2001-2014
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;; <h2>Functions for statistics</h2>
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;; To use this module it has to be loaded at the beginning of the
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;; program file:
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;; <pre>
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;; (load (append (env "NEWLISPDIR") "/modules/stat.lsp"))
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;; ; or shorter
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;; (module "stat.lsp")
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;; </pre>
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;; All functions work on integers and floats or a mix of both. <lists> are normal
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;; LISP lists. <matrices> are lists of lists, one list for each row in the
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;; two dimensional data matrix. See the function 'stat:matrix' on how to make matrices
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;; from lists.
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;;
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;; In version 3.0 of 'stat.lsp' the usage for Gnuplot the stat:plot and stat:plotXY
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;; functions has been eliminated. Instead use the module 'plot.lsp' shipped with all binary and
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;; source distributions. The F-distribution function 'f-prob' has also been eliminated
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;; instead use one of new the built-in 'prob-f' or 'crit-f' functions.
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;;
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;; The documention contains only the call patterns. See the source for more
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;; documentation.
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;;
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;; <h2>Summary of functions</h2><br>
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;; <h3>General uni- and bi- variate statistics</h3>
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;; <pre>
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;; stat:sum - sum of a vector of numbers (see also built-in stats since 10.4.2)
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;; stat:mean - arithmetik mean of a vector of numbers (see also built-in stats since 10.4.2)
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;; stat:var - estimated variance of numbers in a vector sample
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;; stat:sdev - estimated standard deviation of numbers in a vector (see also built-in stats since 10.4.2)
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;; stat:sum-sq - sum of squares of a data vector
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;; stat:sum-xy - sum of products of a two data vectors
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;; stat:corr - correlation coefficient between two vectors (built-in since 10.4.2)
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;; stat:cov - covariance of two number vectors
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;; stat:sum-d2 - sum of squared differences of a vector from its mean
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;; stat:sum-d2xy - sum of squared diffferences of two vectors
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;; stat:regression - calculates the intecept and slope of a regression estimate
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;; stat:fit - return the fitted line using regression coefficients
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;; stat:moments - calulates 1st to 3rd moments from a vector of numbers
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;; </pre>
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;; <h3>Multi variate statistics</h3>
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;; <pre>
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;; stat:multiple-reg - calculates a multiple regression
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;; stat:cov-matrix - calculates a covariance matrix
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;; stat:corr-matrix - calculates a correlation matrix
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;; </pre>
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;; <h3>Time series</h3>
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;; <pre>
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;; stat:smooth - smoothes a vector of numbers
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;; stat:lag - calcultes a difference list with specified lag
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;; stat:cumulate - cumulate a data vector
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;; stat:power - calculate the power spectrum of a time series
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;; </pre>
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;; <h3>Matrix and list utilities</h3>
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;; <pre>
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;; stat:matrix - make a matrix from column vectors
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;; stat:diagonal - make a diagonal matrix
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;; stat:get-diagonal - return the diagonal of a matrix in a vector
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;; stat:mat-map - map a binary function on to matrices
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;; </pre>
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(if (< (sys-info -2) 10111)
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(constant (global 'term) name))
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;; @syntax (stat:corr <X> <Y>)
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;; @param <X> A list of numbers.
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;; @param <Y> A list of numbers.
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;; @return Correlation coefficient of lists <X> and <Y>.
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;; A 'corr' native function is built into newLISP since 10.4.2.
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;; @syntax (stat:cov <X> <Y>)
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;; @param <X> A list of numbers.
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;; @param <Y> A list of numbers.
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;; @return Covariance of data in lists <X> and <Y>
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;; @syntax (stat:cov-matrix <X>)
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;; @param <X> A matrix of numbers.
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;; @return Covariance matrix of <X> with <N> rows and <k> columns.
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;; @syntax (stat:corr-matrix <X>)
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;; @param <X> A matrix of numbers.
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;; @return Correlation matrix of <X> with <N> rows and <k> columns.
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;; @syntax (stat:cumulate <X>)
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;; @param <X> A list of numbers.
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;; @return The cumulated list of <X>.
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;; @syntax (stat:diagonal <item> <N>)
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;; @param <item> The diagonal element.
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;; @return A diagonal matrix of length <N> with <item> in the diagonal.
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;; @syntax (stat:fit <X> <Y>)
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;; @param <X> A list of numbers.
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;; @param <Y> A list of numbers.
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;; @return fitted line based on '(stat:regression X Y)'.
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;; @syntax (stat:f-prob <F> <df1> <df2>)
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;; @param <F> The variance ratio.
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;; @param <df1> Degrees of freedom.
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;; @param <df2> Degrees of freedom.
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;; @return Probablity of F variance ratio for <df1>, <df2> degress of freedom.
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;; @syntax (stat:get-diagonal <X>)
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;; @param <X> An matrix filled with numbers.
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;; @return A list from the diagonal elements of <X>.
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;; @syntax (stat:lag <X> <n>)
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;; @param <X> A list of numbers.
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;; @param <n> Lag n.
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;; @return A differenced list of <X> with a lag of <n>.
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;; If the length of list <X> is <l> then the length of the resulting
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;; differenced list is <l - n>.
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;; @syntax (stat:mat-map <op> <A> <B>)
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;; @return Matrix map, e.g. '(stat:mat-map + A B)'.
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;; Used for adding and subtracting matrices.
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;; @syntax (stat:matrix <C1> .... <CN>)
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;; @param <C1> The first column list of values.
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;; @param <CN> The Nth column list of values.
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;; @return A matrix off <1> to <N> columns <C>.
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;; @syntax (stat:mean <X>)
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;; @param <X> A list of numbers.
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;; @return The mean of data in list <X>.
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;; @syntax (stat:moments <X>)
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;; @param <X> A list of numbers.
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;; @return Calculates all moments of list <X>.
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;; @syntax (stat:multiple-reg <X> <offY>)
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;; @param <X> A matrix of numbers.
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;; @param <offY> Zero based offset into <Y>.
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;; @return Multiple regression of vars in <X> onto <Y> at <offsetY>.
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;; @syntax (stat:power <TS>)
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;; @param <TS> A time series of numbers.
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;; @return The power spectrum of a time series
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;; @syntax (stat:regression <X> <Y>)
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;; @param <X> A list of numbers.
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;; @param <Y> A list of numbers.
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;; returns <(b0 b1)> coefficients of regression <Y = b0 + b1*X>.
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;; @syntax (stat:sdev <X>)
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;; @param <X> A list of numbers.
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;; @return Standard deviation of data in list <X>.
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;; @syntax (stat:smooth <X> <alpha>)
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;; @param <X> A list of numbers.
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;; @param <alpha> Smoothing coefficient <0 < alpha < 1>.
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;; @return Exponentially smoothed sequence in <X>.
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;; @syntax (stat:sum <X>)
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;; @param <X> A list of numbers,
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;; @return Sum of data in list <X>.
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;; @syntax (stat:sum-d2 <X>)
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;; @param <X> A list of numbers.
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;; @return Sum of squared diffs <(x - mean(X))^2> in list <X>.
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;; @syntax (stat:sum-d2xy <X> <Y>)
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;; @return Sum of squared differences <(x - y)^2> of elements in lists <X> and <Y>.
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;; @syntax (stat:sum-sq <X>)
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;; @param <X> A list of numbers.
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;; @return Sum of <x*x> data elements in list <X>.
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;; @syntax (stat:sum-xy <X> <Y>)
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;; @param <X> A list of numbers.
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;; @param <Y> A list of numbers.
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;; @return Sum of products <x*y> data elements in lists <X> and <Y>.
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;; @syntax (stat:var <X>)
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;; @param <X> A list of numbers.
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;; @return The variance of the data in list <X>.
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(context 'stat)
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;------------------- General uni and bi-variate statistics --------------------
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; sum of a data vector X
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(define (sum X)
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(apply add X))
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; mean of a data vector X
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(define (mean X)
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(div (sum X) (length X)))
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; variance of a data vector X
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(define (var X)
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(div (sum-d2 X) (sub (length X) 1)))
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; standard deviation of a data vector X
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(define (sdev X)
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(sqrt (var X)))
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; sum of squares of a data vector X
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(define (sum-sq X)
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(apply add (map mul X X)))
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; sum of the product of data vectors X*Y
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(define (sum-xy X Y)
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(apply add (map mul X Y)))
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; covariance of data vectors X Y
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(define (cov X Y)
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(sub (sum-xy X Y) (div (mul (sum X) (sum Y)) (length X))))
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; sum of sqared differenses of X to mean of X
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(define (sum-d2 X)
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(sub (sum-sq X) (div (mul (sum X) (sum X)) (length X))))
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; Pearson r, product moment correlation of data vectors X and Y
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(define (stat:corr X Y)
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(div (cov X Y) (sqrt (mul (sum-d2 X) (sum-d2 Y)))))
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; regression Yest = b0 + b1*X calculates intercept b0 and slope b1
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(define (regression X Y)
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(set 'b1 (div (cov X Y) (sum-d2 X)))
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(set 'b0 (sub (mean Y) (mul b1 (mean X))))
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(list b0 b1))
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; fitted line using regression Y on X
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(define (fit X Y, coeffs b0 b1)
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(set 'coeffs (regression X Y))
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(set 'b0 (first coeffs))
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(set 'b1 (last coeffs))
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(map (lambda (x) (add b0 (mul x b1))) X))
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; sum of squared differences of X and Y
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(define (sum-d2xy X Y)
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(apply add (map (lambda (x y) (mul (sub x y) (sub x y))) X Y)))
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; moments of a vector of numbers
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;
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(define (moments vector, n median mean avg-dev std-dev var skew kurtosis dev sum)
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(set 'n (length vector))
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(set 'sum (apply add vector))
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(set 'mean (div sum n))
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(set 'avg-dev 0 'std-dev 0 'var 0 'skew 0 'kurtosis 0)
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(set 'dev (map sub vector (dup mean n)))
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(set 'avg-dev (div (apply add (map abs dev)) n))
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(set 'var (div (apply add (map mul dev dev)) (- n 1)))
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(set 'skew (apply add (map mul dev dev dev)))
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(set 'kurtosis (apply add (map mul dev dev dev dev)))
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(set 'std-dev (sqrt var))
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(if (> var 0.0)
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(begin
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(set 'skew (div skew (mul n var std-dev)))
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(set 'kurtosis (sub (div kurtosis (mul n var var)) 3.0))))
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(sort vector)
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(set 'mid (/ n 2))
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(if (= 0 (% n 2))
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(set 'median (div (add (nth mid vector) (nth (- mid 1) vector)) 2))
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(set 'median (nth mid vector)))
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(list n median mean avg-dev std-dev var skew kurtosis)
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; (println (format "n: %d" n))
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; (println (format "median: %f" median))
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; (println (format "mean: %f" mean))
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; (println (format "average_deviation: %f" avg-dev))
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; (println (format "standard_deviation: %f" std-dev))
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; (println (format "variance: %f" var))
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; (println (format "skew: %f" skew))
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; (println (format "kurtosis: %f" kurtosis))
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)
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;-------------------------------- Time Series ----------------------------------
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; expontial smoothing with 0 < alpha <= 1
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(define (smooth lst alpha , previous slist)
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(set 'previous (first lst))
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(set 'slist '())
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(dolist (elmnt lst)
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(set 'previous (add (mul alpha elmnt) (mul (sub 1 alpha) previous)))
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(push previous slist))
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(reverse slist)) ; could be written shorter starting v.9.9.5
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; because push returns the modified list
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;
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; seasonal difference list with variable lag
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; the resulting list is lag shorterm than the original
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;
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(define (lag lst n , sLst)
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(set 'sLst lst)
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(dotimes (i n) (pop lst))
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(set 'sLst (slice sLst 0 (length lst)))
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(map sub lst sLst))
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;
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; cumulate of a list
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;
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(define (cumulate lst , sc cum)
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(set 'sc 0.0)
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(set 'cum '())
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(dolist (x lst)
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(push (inc sc x) cum))
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(reverse cum)) ; could be written shorter after 9.9.5
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; because push returns the list
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;
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; power spectrum
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;
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; takes a rows by 2 columns matrix with real part in the first and
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; imagenary part the in the second column. If all numbers are real
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; then the second column is just 0's.
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;
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; returns a matrix with two rows. First row contains power numbers
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; and second row contains the respective frequencies
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;
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(define (power ts , lenOrg fts n n2 ps mid frqs)
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; remember original length
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(set 'lenOrg (length ts))
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; do discrete fourier transform
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(set 'fts (transpose (fft ts)))
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; calc power spectrum
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(set 'n (length (transpose fts)))
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(set 'n2 (mul n n))
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(set 'ps (map (lambda (x y) (add (mul x x) (mul y y))) (nth 0 fts) (nth 1 fts)))
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(set 'ps (map (lambda (x) (mul (div x n2) 2)) ps))
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; the first and last are not multiplied by 2, divide them back
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; use deprecated nth-set in versions older than 9.9.02
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(setf (ps 0) (div (first ps) 2))
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(set 'mid (sub (div n 2) 1))
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(replace mid ps (div (nth mid ps) 2))
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; calc a vector with frequencies, adjusted for the new power-2 length
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; which came back from the FFT
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(set 'frqs (sequence 0 (- n 1)))
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(set 'frqs (map (lambda (x) (mul (div x n) lenOrg)) frqs))
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(transpose (matrix ps frqs)))
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;------------------------- multivariate statistics -----------------------------
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;
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; multiple regression of variables in X onto one of variables in X, Y
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; indicated by column offset offY
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;
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; X is N rows by k columns, the column at offset offY is Y
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;
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; returns a matrix with two rows:
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; first row is regression coefficients and multiple R: b0, b1, b2 ....., R
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; second row is sum of squares: regression-SQ, error-SQ, total-SQ
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; (the unused part of the second row is <tt>nil</tt> padded)
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;
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; the SQs can be used to calculate mean sqares for regression and error:
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;
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; regression-MSQ = regression-SQ / (k - 1)
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; error-MSQ = error-sq / (n - k - 1)
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;
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; F-ratio = regression-MSQ / error-MSQ
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; with k and (n - k - 1) df degreees of freedom
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;
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;
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;
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;
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(define (multiple-reg X offY , Y Ycoffs b b0 R2 Yest sqErr sqTotal sqReg sq d)
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(set 'covX (cov-matrix X))
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(set 'Y (extract-col X offY))
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; covX is the covariance matrix
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(pop covX offY)
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(set 'cvX (transpose covX))
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; the covariance matrix is reduced to cvX and the
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; extracted values put in Ycoffs
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(set 'Ycoffs (matrix (pop cvX offY)))
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; b contains the regression coefficients except for b0
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(set 'b (multiply (invert cvX) Ycoffs))
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; calculate multiple R2 as b'*b / sqTotal
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(set 'sqTotal (sum-d2 Y))
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(set 'R2 (div (first (first (multiply (transpose b) Ycoffs))) sqTotal))
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; estimate Y without b0
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(set 'Yest (multiply (reduce-col X offY) b))
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; calculate b0, d is the difference between Y and the Y estimate
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; b0 is the mean of differences between Y and Yest
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(set 'd (mat-map sub (matrix Y) Yest))
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(set 'b0 (mean (first (transpose d))))
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; estimate Y including b0
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(set 'Yest (mat-map add Yest (matrix (dup b0 (length Yest)))))
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; error sum of squares
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(set 'sqErr (sum-d2xy Y (first (transpose Yest))))
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; regression sum of squares
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(set 'sqReg (sub sqTotal sqErr))
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; make list b out of b0, b1, b2 ... sqrt(R2)
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(set 'b (append (list b0) (first (transpose b)) (list (sqrt R2))))
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; make list sq out of sqReg, sqErr and sqTotal
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(set 'sq (list sqReg sqErr sqTotal))
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; return matrix with two rows:
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(transpose (matrix b sq)))
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;
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; covariance matrix cov
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;
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; matrix x with N rows and k columns
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;
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;
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(define (cov-matrix X , XtX N I sumX sumX2)
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(set 'XtX (multiply (transpose X) X))
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(set 'N (length X))
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(set 'I (matrix (dup 1 N)))
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(set 'sumX (multiply (transpose X) I))
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(set 'sumX2 (multiply sumX (transpose sumX)))
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(set 'sumX2 (multiply sumX2 (diagonal (div 1 N) (length sumX2))))
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(mat-map sub XtX sumX2))
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;
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; correlation matrix
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;
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; matrix X with N rows and k columns
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;
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;
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(define (corr-matrix X , covX N d dd)
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(set 'covX (cov-matrix X))
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(set 'd (matrix (get-diagonal covX)))
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(set 'dd (multiply d (transpose d)))
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(set 'dd (map (lambda (z) (map sqrt z)) dd))
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(mat-map div covX dd))
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;
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; probablity of F variance ratio with degrees of freedom df1 df2
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;
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;
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(define (f-prob F df1 df2)
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(let (prob (mul 2 (betai (div df2 (add df2 (mul df1 F)))
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(mul 0.5 df2)
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(mul 0.5 df1))))
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(div (if (> prob 1) (sub 2 prob) prob) 2)))
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;----------------------------- utility functions -------------------------------
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;
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; make a matrix from 1 up to 16 lists
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;
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(define (matrix)
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(transpose (args)))
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;
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; make a diagonal matrix n by n and elmnt in the diagonal
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;
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;
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(define (diagonal elmnt n, m lst)
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(set 'm '())
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(dotimes (i n)
|
|
(set 'lst (dup 0 n))
|
|
; use deprecated nth-set in versions older than 9.9.02
|
|
(if (< (sys-info -2) 9902)
|
|
(nth-set (lst i) elmnt)
|
|
(setf (lst i) elmnt))
|
|
(push lst m))
|
|
(reverse m)) ; make shorter starting v.9.9.5
|
|
|
|
;
|
|
; get the diagonal from a square matrix
|
|
;
|
|
(define (get-diagonal X , d x)
|
|
(set 'd '())
|
|
(dotimes (idx (length X))
|
|
(push (nth idx (nth idx X)) d))
|
|
(reverse d))
|
|
|
|
;
|
|
; matrix map
|
|
;
|
|
; e.g.: (mat-map sub A B) ;; for matrix subtraction
|
|
;
|
|
(define (mat-map op A B)
|
|
(map (lambda (x y) (map op x y)) A B))
|
|
|
|
;
|
|
; reduce matrix by a column at offset
|
|
;
|
|
; returns the reduced matrix
|
|
;
|
|
(define (reduce-col matr off, X)
|
|
(set 'matr (transpose matr))
|
|
(pop matr off)
|
|
(transpose matr))
|
|
|
|
;
|
|
; extract a column from a matrix
|
|
;
|
|
; returns the extracted column
|
|
;
|
|
(define (extract-col matr off, X)
|
|
(pop (transpose matr) off))
|
|
|
|
;
|
|
; convert list to ascii lines terminated by CR-LF
|
|
; for storage in files usable by Gnuplot, R, Excel etc.
|
|
;
|
|
; example:
|
|
;
|
|
; (write-file "MyData.txt" (list2ascii mydata-list))
|
|
;
|
|
(define (list2ascii lst)
|
|
(append (join (map string lst) "\r\n") "\r\n"))
|
|
|
|
; eof
|
|
|
|
|