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1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 | # statistics.tcl --
#
# Package for basic statistical analysis
#
# version 0.1: initial implementation, january 2003
# version 0.1.1: added linear regres
# version 0.1.2: border case in stdev taken care of
# version 0.1.3: moved initialisation of CDF to first call, november 2004
# version 0.3: added test for normality (as implemented by Torsten Reincke), march 2006
# (also fixed an error in the export list)
# version 0.4: added the multivariate linear regression procedures by
# Eric Kemp-Benedict, february 2007
# version 0.5: added the population standard deviation and variance,
# as suggested by Dimitrios Zachariadis
# version 0.6: added pdf and cdf procedures for various distributions
# (provided by Eric Kemp-Benedict)
# version 0.7: added Kruskal-Wallis test (by Torsten Berg)
# version 0.8: added Wilcoxon test and Spearman rank correlation
# version 0.9: added kernel density estimation
# version 0.9.3: added histogram-alt, corrected test-normal
package require Tcl 8.4
package provide math::statistics 1.0
package require math
if {![llength [info commands ::lrepeat]]} {
# Forward portability, emulate lrepeat
proc ::lrepeat {n args} {
if {$n < 1} {
return -code error "must have a count of at least 1"
}
set res {}
while {$n} {
foreach x $args { lappend res $x }
incr n -1
}
return $res
}
}
# ::math::statistics --
# Namespace holding the procedures and variables
#
namespace eval ::math::statistics {
#
# Safer: change to short procedures
#
namespace export mean min max number var stdev pvar pstdev basic-stats corr \
histogram histogram-alt interval-mean-stdev t-test-mean quantiles \
test-normal lillieforsFit \
autocorr crosscorr filter map samplescount median \
test-2x2 print-2x2 control-xbar test_xbar \
control-Rchart test-Rchart \
test-Kruskal-Wallis analyse-Kruskal-Wallis group-rank \
test-Wilcoxon spearman-rank spearman-rank-extended \
test-Duckworth
#
# Error messages
#
variable NEGSTDEV {Zero or negative standard deviation}
variable TOOFEWDATA {Too few or invalid data}
variable OUTOFRANGE {Argument out of range}
#
# Coefficients involved
#
variable factorNormalPdf
set factorNormalPdf [expr {sqrt(8.0*atan(1.0))}]
# xbar/R-charts:
# Data from:
# Peter W.M. John:
# Statistical methods in engineering and quality assurance
# Wiley and Sons, 1990
#
variable control_factors {
A2 {1.880 1.093 0.729 0.577 0.483 0.419 0.419}
D3 {0.0 0.0 0.0 0.0 0.0 0.076 0.076}
D4 {3.267 2.574 2.282 2.114 2.004 1.924 1.924}
}
}
# mean, min, max, number, var, stdev, pvar, pstdev --
# Return the mean (minimum, maximum) value of a list of numbers
# or number of non-missing values
#
# Arguments:
# type Type of value to be returned
# values List of values to be examined
#
# Results:
# Value that was required
#
#
namespace eval ::math::statistics {
foreach type {mean min max number stdev var pstdev pvar} {
proc $type { values } "BasicStats $type \$values"
}
proc basic-stats { values } "BasicStats all \$values"
}
# BasicStats --
# Return the one or all of the basic statistical properties
#
# Arguments:
# type Type of value to be returned
# values List of values to be examined
#
# Results:
# Value that was required
#
proc ::math::statistics::BasicStats { type values } {
variable TOOFEWDATA
if { [lsearch {all mean min max number stdev var pstdev pvar} $type] < 0 } {
return -code error \
-errorcode ARG -errorinfo [list unknown type of statistic -- $type] \
[list unknown type of statistic -- $type]
}
set min {}
set max {}
set mean {}
set stdev {}
set var {}
set sum 0.0
set sumsq 0.0
set number 0
set first {}
foreach value $values {
if { $value == {} } {
continue
}
set value [expr {double($value)}]
if { $first == {} } {
set first $value
}
incr number
set sum [expr {$sum+$value}]
set sumsq [expr {$sumsq+($value-$first)*($value-$first)}]
if { $min == {} || $value < $min } {
set min $value
}
if { $max == {} || $value > $max } {
set max $value
}
}
if { $number > 0 } {
set mean [expr {$sum/$number}]
} else {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
if { $number > 1 } {
set var [expr {($sumsq-($mean-$first)*($sum-$number*$first))/double($number-1)}]
#
# Take care of a rare situation: uniform data might
# cause a tiny negative difference
#
if { $var < 0.0 } {
set var 0.0
}
set stdev [expr {sqrt($var)}]
}
set pvar [expr {($sumsq-($mean-$first)*($sum-$number*$first))/double($number)}]
#
# Take care of a rare situation: uniform data might
# cause a tiny negative difference
#
if { $pvar < 0.0 } {
set pvar 0.0
}
set pstdev [expr {sqrt($pvar)}]
set all [list $mean $min $max $number $stdev $var $pstdev $pvar]
#
# Return the appropriate value
#
set $type
}
# histogram --
# Return histogram information from a list of numbers
#
# Arguments:
# limits Upper limits for the buckets (in increasing order)
# values List of values to be examined
# weights List of weights, one per value (optional)
#
# Results:
# List of number of values in each bucket (length is one more than
# the number of limits)
#
#
proc ::math::statistics::histogram { limits values {weights {}} } {
if { [llength $limits] < 1 } {
return -code error -errorcode ARG -errorinfo {No limits given} {No limits given}
}
if { [llength $weights] > 0 && [llength $values] != [llength $weights] } {
return -code error -errorcode ARG -errorinfo {Number of weights be equal to number of values} {Weights and values differ in length}
}
set limits [lsort -real -increasing $limits]
for { set index 0 } { $index <= [llength $limits] } { incr index } {
set buckets($index) 0
}
set last [llength $limits]
# Will do integer arithmetic if unset
if {$weights eq ""} {
set weights [lrepeat [llength $values] 1]
}
foreach value $values weight $weights {
if { $value == {} } {
continue
}
set index 0
set found 0
foreach limit $limits {
if { $value <= $limit } {
set found 1
set buckets($index) [expr $buckets($index)+$weight]
break
}
incr index
}
if { $found == 0 } {
set buckets($last) [expr $buckets($last)+$weight]
}
}
set result {}
for { set index 0 } { $index <= $last } { incr index } {
lappend result $buckets($index)
}
return $result
}
# histogram-alt --
# Return histogram information from a list of numbers -
# intervals are open-ended at the lower bound instead of at the upper bound
#
# Arguments:
# limits Upper limits for the buckets (in increasing order)
# values List of values to be examined
# weights List of weights, one per value (optional)
#
# Results:
# List of number of values in each bucket (length is one more than
# the number of limits)
#
#
proc ::math::statistics::histogram-alt { limits values {weights {}} } {
if { [llength $limits] < 1 } {
return -code error -errorcode ARG -errorinfo {No limits given} {No limits given}
}
if { [llength $weights] > 0 && [llength $values] != [llength $weights] } {
return -code error -errorcode ARG -errorinfo {Number of weights be equal to number of values} {Weights and values differ in length}
}
set limits [lsort -real -increasing $limits]
for { set index 0 } { $index <= [llength $limits] } { incr index } {
set buckets($index) 0
}
set last [llength $limits]
# Will do integer arithmetic if unset
if {$weights eq ""} {
set weights [lrepeat [llength $values] 1]
}
foreach value $values weight $weights {
if { $value == {} } {
continue
}
set index 0
set found 0
foreach limit $limits {
if { $value < $limit } {
set found 1
set buckets($index) [expr $buckets($index)+$weight]
break
}
incr index
}
if { $found == 0 } {
set buckets($last) [expr $buckets($last)+$weight]
}
}
set result {}
for { set index 0 } { $index <= $last } { incr index } {
lappend result $buckets($index)
}
return $result
}
# corr --
# Return the correlation coefficient of two sets of data
#
# Arguments:
# data1 List with the first set of data
# data2 List with the second set of data
#
# Result:
# Correlation coefficient of the two
#
proc ::math::statistics::corr { data1 data2 } {
variable TOOFEWDATA
set number 0
set sum1 0.0
set sum2 0.0
set sumsq1 0.0
set sumsq2 0.0
set sumprod 0.0
foreach value1 $data1 value2 $data2 {
if { $value1 == {} || $value2 == {} } {
continue
}
set value1 [expr {double($value1)}]
set value2 [expr {double($value2)}]
set sum1 [expr {$sum1+$value1}]
set sum2 [expr {$sum2+$value2}]
set sumsq1 [expr {$sumsq1+$value1*$value1}]
set sumsq2 [expr {$sumsq2+$value2*$value2}]
set sumprod [expr {$sumprod+$value1*$value2}]
incr number
}
if { $number > 0 } {
set numerator [expr {$number*$sumprod-$sum1*$sum2}]
set denom1 [expr {sqrt($number*$sumsq1-$sum1*$sum1)}]
set denom2 [expr {sqrt($number*$sumsq2-$sum2*$sum2)}]
if { $denom1 != 0.0 && $denom2 != 0.0 } {
set corr_coeff [expr {$numerator/$denom1/$denom2}]
} elseif { $denom1 != 0.0 || $denom2 != 0.0 } {
set corr_coeff 0.0 ;# Uniform against non-uniform
} else {
set corr_coeff 1.0 ;# Both uniform
}
} else {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
return $corr_coeff
}
# lillieforsFit --
# Calculate the goodness of fit according to Lilliefors
# (goodness of fit to a normal distribution)
#
# Arguments:
# values List of values to be tested for normality
#
# Result:
# Value of the statistic D
#
proc ::math::statistics::lillieforsFit {values} {
#
# calculate the goodness of fit according to Lilliefors
# (goodness of fit to a normal distribution)
#
# values -> list of values to be tested for normality
# (these values are sampled counts)
#
# calculate standard deviation and mean of the sample:
set n [llength $values]
if { $n < 5 } {
return -code error "Insufficient number of data (at least five required)"
}
set sd [stdev $values]
set mean [mean $values]
# sort the sample for further processing:
set values [lsort -real $values]
# standardize the sample data (Z-scores):
foreach x $values {
lappend stdData [expr {($x - $mean)/double($sd)}]
}
# compute the value of the distribution function at every sampled point:
foreach x $stdData {
lappend expData [pnorm $x]
}
# compute D+:
set i 0
foreach x $expData {
incr i
lappend dplus [expr {$i/double($n)-$x}]
}
set dplus [lindex [lsort -real $dplus] end]
# compute D-:
set i 0
foreach x $expData {
incr i
lappend dminus [expr {$x-($i-1)/double($n)}]
}
set dminus [lindex [lsort -real $dminus] end]
# Calculate the test statistic D
# by finding the maximal vertical difference
# between the sample and the expectation:
#
set D [expr {$dplus > $dminus ? $dplus : $dminus}]
# We now use the modified statistic Z,
# because D is only reliable
# if the p-value is smaller than 0.1
return [expr {$D * (sqrt($n) - 0.01 + 0.831/sqrt($n))}]
}
# pnorm --
# Calculate the cumulative distribution function (cdf)
# for the standard normal distribution like in the statistical
# software 'R' (mean=0 and sd=1)
#
# Arguments:
# x Value fro which the cdf should be calculated
#
# Result:
# Value of the statistic D
#
proc ::math::statistics::pnorm {x} {
#
# cumulative distribution function (cdf)
# for the standard normal distribution like in the statistical software 'R'
# (mean=0 and sd=1)
#
# x -> value for which the cdf should be calculated
#
set sum [expr {double($x)}]
set oldSum 0.0
set i 1
set denom 1.0
while {$sum != $oldSum} {
set oldSum $sum
incr i 2
set denom [expr {$denom*$i}]
#puts "$i - $denom"
set sum [expr {$oldSum + pow($x,$i)/$denom}]
}
return [expr {0.5 + $sum * exp(-0.5 * $x*$x - 0.91893853320467274178)}]
}
# pnorm_quicker --
# Calculate the cumulative distribution function (cdf)
# for the standard normal distribution - quicker alternative
# (less accurate)
#
# Arguments:
# x Value for which the cdf should be calculated
#
# Result:
# Value of the statistic D
#
proc ::math::statistics::pnorm_quicker {x} {
set n [expr {abs($x)}]
set n [expr {1.0 + $n*(0.04986735 + $n*(0.02114101 + $n*(0.00327763 \
+ $n*(0.0000380036 + $n*(0.0000488906 + $n*0.000005383)))))}]
set n [expr {1.0/pow($n,16)}]
#
if {$x >= 0} {
return [expr {1 - $n/2.0}]
} else {
return [expr {$n/2.0}]
}
}
# test-normal --
# Test for normality (using method Lilliefors)
#
# Arguments:
# data Values that need to be tested
# significance Level at which the discrepancy from normality is tested
#
# Result:
# 1 if the Lilliefors statistic D is larger than the critical level
#
# Note:
# There was a mistake in the implementation before 0.9.3: confidence (wrong word)
# instead of significance. To keep compatibility with earlier versions, both
# significance and 1-significance are accepted.
#
proc ::math::statistics::test-normal {data significance} {
set D [lillieforsFit $data]
if { $significance > 0.5 } {
set significance [expr {1.0-$significance}] ;# Convert the erroneous levels pre 0.9.3
}
set Dcrit --
if { abs($significance-0.20) < 0.0001 } {
set Dcrit 0.741
}
if { abs($significance-0.15) < 0.0001 } {
set Dcrit 0.775
}
if { abs($significance-0.10) < 0.0001 } {
set Dcrit 0.819
}
if { abs($significance-0.05) < 0.0001 } {
set Dcrit 0.895
}
if { abs($significance-0.01) < 0.0001 } {
set Dcrit 1.035
}
if { $Dcrit != "--" } {
return [expr {$D > $Dcrit ? 1 : 0 }]
} else {
return -code error "Significancce level must be one of: 0.20, 0.15, 0.10, 0.05 or 0.01"
}
}
# t-test-mean --
# Test whether the mean value of a sample is in accordance with the
# estimated normal distribution with a certain probability
# (Student's t test)
#
# Arguments:
# data List of raw data values (small sample)
# est_mean Estimated mean of the distribution
# est_stdev Estimated stdev of the distribution
# alpha Probability level (0.95 or 0.99 for instance)
#
# Result:
# 1 if the test is positive, 0 otherwise. If there are too few data,
# returns an empty string
#
proc ::math::statistics::t-test-mean { data est_mean est_stdev alpha } {
variable NEGSTDEV
variable TOOFEWDATA
if { $est_stdev <= 0.0 } {
return -code error -errorcode ARG -errorinfo $NEGSTDEV $NEGSTDEV
}
set allstats [BasicStats all $data]
set alpha2 [expr {(1.0+$alpha)/2.0}]
set sample_mean [lindex $allstats 0]
set sample_number [lindex $allstats 3]
if { $sample_number > 1 } {
set tzero [expr {abs($sample_mean-$est_mean)/$est_stdev * \
sqrt($sample_number-1)}]
set degrees [expr {$sample_number-1}]
set prob [cdf-students-t $degrees $tzero]
return [expr {$prob<$alpha2}]
} else {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
}
# interval-mean-stdev --
# Return the interval containing the mean value and one
# containing the standard deviation with a certain
# level of confidence (assuming a normal distribution)
#
# Arguments:
# data List of raw data values
# confidence Confidence level (0.95 or 0.99 for instance)
#
# Result:
# List having the following elements: lower and upper bounds of
# mean, lower and upper bounds of stdev
#
#
proc ::math::statistics::interval-mean-stdev { data confidence } {
variable TOOFEWDATA
set allstats [BasicStats all $data]
set conf2 [expr {(1.0+$confidence)/2.0}]
set mean [lindex $allstats 0]
set number [lindex $allstats 3]
set stdev [lindex $allstats 4]
if { $number > 1 } {
set degrees [expr {$number-1}]
set student_t [expr {sqrt([Inverse-cdf-toms322 1 $degrees $conf2])}]
set mean_lower [expr {$mean-$student_t*$stdev/sqrt($number)}]
set mean_upper [expr {$mean+$student_t*$stdev/sqrt($number)}]
set stdev_lower {}
set stdev_upper {}
return [list $mean_lower $mean_upper $stdev_lower $stdev_upper]
} else {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
}
# quantiles --
# Return the quantiles for a given set of data or histogram
#
# Arguments:
# (two arguments)
# data List of raw data values
# confidence Confidence level (0.95 or 0.99 for instance)
# (three arguments)
# limits List of upper limits from histogram
# counts List of counts for for each interval in histogram
# confidence Confidence level (0.95 or 0.99 for instance)
#
# Result:
# List of quantiles
#
proc ::math::statistics::quantiles { arg1 arg2 {arg3 {}} } {
variable TOOFEWDATA
if { [catch {
if { $arg3 == {} } {
set result \
[::math::statistics::QuantilesRawData $arg1 $arg2]
} else {
set result \
[::math::statistics::QuantilesHistogram $arg1 $arg2 $arg3]
}
} msg] } {
return -code error -errorcode $msg $msg
}
return $result
}
# QuantilesRawData --
# Return the quantiles based on raw data
#
# Arguments:
# data List of raw data values
# confidence Confidence level (0.95 or 0.99 for instance)
#
# Result:
# List of quantiles
#
proc ::math::statistics::QuantilesRawData { data confidence } {
variable TOOFEWDATA
variable OUTOFRANGE
if { [llength $confidence] <= 0 } {
return -code error -errorcode ARG "$TOOFEWDATA - quantiles"
}
if { [llength $data] <= 0 } {
return -code error -errorcode ARG "$TOOFEWDATA - raw data"
}
foreach cond $confidence {
if { $cond <= 0.0 || $cond >= 1.0 } {
return -code error -errorcode ARG "$OUTOFRANGE - quantiles"
}
}
#
# Sort the data first
#
set sorted_data [lsort -real -increasing $data]
#
# Determine the list element lower or equal to the quantile
# and return the corresponding value
#
set result {}
set number_data [llength $sorted_data]
foreach cond $confidence {
set elem [expr {round($number_data*$cond)-1}]
if { $elem < 0 } {
set elem 0
}
lappend result [lindex $sorted_data $elem]
}
return $result
}
# QuantilesHistogram --
# Return the quantiles based on histogram information only
#
# Arguments:
# limits Upper limits for histogram intervals
# counts Counts for each interval
# confidence Confidence level (0.95 or 0.99 for instance)
#
# Result:
# List of quantiles
#
proc ::math::statistics::QuantilesHistogram { limits counts confidence } {
variable TOOFEWDATA
variable OUTOFRANGE
if { [llength $confidence] <= 0 } {
return -code error -errorcode ARG "$TOOFEWDATA - quantiles"
}
if { [llength $confidence] <= 0 } {
return -code error -errorcode ARG "$TOOFEWDATA - histogram limits"
}
if { [llength $counts] <= [llength $limits] } {
return -code error -errorcode ARG "$TOOFEWDATA - histogram counts"
}
foreach cond $confidence {
if { $cond <= 0.0 || $cond >= 1.0 } {
return -code error -errorcode ARG "$OUTOFRANGE - quantiles"
}
}
#
# Accumulate the histogram counts first
#
set sum 0
set accumulated_counts {}
foreach count $counts {
set sum [expr {$sum+$count}]
lappend accumulated_counts $sum
}
set total_counts $sum
#
# Determine the list element lower or equal to the quantile
# and return the corresponding value (use interpolation if
# possible)
#
set result {}
foreach cond $confidence {
set found 0
set bound [expr {round($total_counts*$cond)}]
set lower_limit {}
set lower_count 0
foreach acc_count $accumulated_counts limit $limits {
if { $acc_count >= $bound } {
set found 1
break
}
set lower_limit $limit
set lower_count $acc_count
}
if { $lower_limit == {} || $limit == {} || $found == 0 } {
set quant $limit
if { $limit == {} } {
set quant $lower_limit
}
} else {
set quant [expr {$limit+($lower_limit-$limit) *
($acc_count-$bound)/($acc_count-$lower_count)}]
}
lappend result $quant
}
return $result
}
# autocorr --
# Return the autocorrelation function (assuming equidistance between
# samples)
#
# Arguments:
# data Raw data for which the autocorrelation must be determined
#
# Result:
# List of autocorrelation values (about 1/2 the number of raw data)
#
proc ::math::statistics::autocorr { data } {
variable TOOFEWDATA
if { [llength $data] <= 1 } {
return -code error -errorcode ARG "$TOOFEWDATA"
}
return [crosscorr $data $data]
}
# crosscorr --
# Return the cross-correlation function (assuming equidistance
# between samples)
#
# Arguments:
# data1 First set of raw data
# data2 Second set of raw data
#
# Result:
# List of cross-correlation values (about 1/2 the number of raw data)
#
# Note:
# The number of data pairs is not kept constant - because tests
# showed rather awkward results when it was kept constant.
#
proc ::math::statistics::crosscorr { data1 data2 } {
variable TOOFEWDATA
if { [llength $data1] <= 1 || [llength $data2] <= 1 } {
return -code error -errorcode ARG "$TOOFEWDATA"
}
#
# First determine the number of data pairs
#
set number1 [llength $data1]
set number2 [llength $data2]
set basic_stat1 [basic-stats $data1]
set basic_stat2 [basic-stats $data2]
set vmean1 [lindex $basic_stat1 0]
set vmean2 [lindex $basic_stat2 0]
set vvar1 [lindex $basic_stat1 end]
set vvar2 [lindex $basic_stat2 end]
set number_pairs $number1
if { $number1 > $number2 } {
set number_pairs $number2
}
set number_values $number_pairs
set number_delays [expr {$number_values/2.0}]
set scale [expr {sqrt($vvar1*$vvar2)}]
set result {}
for { set delay 0 } { $delay < $number_delays } { incr delay } {
set sumcross 0.0
set no_cross 0
for { set idx 0 } { $idx < $number_values } { incr idx } {
set value1 [lindex $data1 $idx]
set value2 [lindex $data2 [expr {$idx+$delay}]]
if { $value1 != {} && $value2 != {} } {
set sumcross \
[expr {$sumcross+($value1-$vmean1)*($value2-$vmean2)}]
incr no_cross
}
}
lappend result [expr {$sumcross/($no_cross*$scale)}]
incr number_values -1
}
return $result
}
# mean-histogram-limits
# Determine reasonable limits based on mean and standard deviation
# for a histogram
#
# Arguments:
# mean Mean of the data
# stdev Standard deviation
# number Number of limits to generate (defaults to 8)
#
# Result:
# List of limits
#
proc ::math::statistics::mean-histogram-limits { mean stdev {number 8} } {
variable NEGSTDEV
if { $stdev <= 0.0 } {
return -code error -errorcode ARG "$NEGSTDEV"
}
if { $number < 1 } {
return -code error -errorcode ARG "Number of limits must be positive"
}
#
# Always: between mean-3.0*stdev and mean+3.0*stdev
# number = 2: -0.25, 0.25
# number = 3: -0.25, 0, 0.25
# number = 4: -1, -0.25, 0.25, 1
# number = 5: -1, -0.25, 0, 0.25, 1
# number = 6: -2, -1, -0.25, 0.25, 1, 2
# number = 7: -2, -1, -0.25, 0, 0.25, 1, 2
# number = 8: -3, -2, -1, -0.25, 0.25, 1, 2, 3
#
switch -- $number {
"1" { set limits {0.0} }
"2" { set limits {-0.25 0.25} }
"3" { set limits {-0.25 0.0 0.25} }
"4" { set limits {-1.0 -0.25 0.25 1.0} }
"5" { set limits {-1.0 -0.25 0.0 0.25 1.0} }
"6" { set limits {-2.0 -1.0 -0.25 0.25 1.0 2.0} }
"7" { set limits {-2.0 -1.0 -0.25 0.0 0.25 1.0 2.0} }
"8" { set limits {-3.0 -2.0 -1.0 -0.25 0.25 1.0 2.0 3.0} }
"9" { set limits {-3.0 -2.0 -1.0 -0.25 0.0 0.25 1.0 2.0 3.0} }
default {
set dlim [expr {6.0/double($number-1)}]
for {set i 0} {$i <$number} {incr i} {
lappend limits [expr {$dlim*($i-($number-1)/2.0)}]
}
}
}
set result {}
foreach limit $limits {
lappend result [expr {$mean+$limit*$stdev}]
}
return $result
}
# minmax-histogram-limits
# Determine reasonable limits based on minimum and maximum bounds
# for a histogram
#
# Arguments:
# min Estimated minimum
# max Estimated maximum
# number Number of limits to generate (defaults to 8)
#
# Result:
# List of limits
#
proc ::math::statistics::minmax-histogram-limits { min max {number 8} } {
variable NEGSTDEV
if { $number < 1 } {
return -code error -errorcode ARG "Number of limits must be positive"
}
if { $min >= $max } {
return -code error -errorcode ARG "Minimum must be lower than maximum"
}
set result {}
set dlim [expr {($max-$min)/double($number-1)}]
for {set i 0} {$i <$number} {incr i} {
lappend result [expr {$min+$dlim*$i}]
}
return $result
}
# linear-model
# Determine the coefficients for a linear regression between
# two series of data (the model: Y = A + B*X)
#
# Arguments:
# xdata Series of independent (X) data
# ydata Series of dependent (Y) data
# intercept Whether to use an intercept or not (optional)
#
# Result:
# List of the following items:
# - (Estimate of) Intercept A
# - (Estimate of) Slope B
# - Standard deviation of Y relative to fit
# - Correlation coefficient R2
# - Number of degrees of freedom df
# - Standard error of the intercept A
# - Significance level of A
# - Standard error of the slope B
# - Significance level of B
#
#
proc ::math::statistics::linear-model { xdata ydata {intercept 1} } {
variable TOOFEWDATA
if { [llength $xdata] < 3 } {
return -code error -errorcode ARG "$TOOFEWDATA: not enough independent data"
}
if { [llength $ydata] < 3 } {
return -code error -errorcode ARG "$TOOFEWDATA: not enough dependent data"
}
if { [llength $xdata] != [llength $ydata] } {
return -code error -errorcode ARG "$TOOFEWDATA: number of dependent data differs from number of independent data"
}
set sumx 0.0
set sumy 0.0
set sumx2 0.0
set sumy2 0.0
set sumxy 0.0
set df 0
foreach x $xdata y $ydata {
if { $x != "" && $y != "" } {
set sumx [expr {$sumx+$x}]
set sumy [expr {$sumy+$y}]
set sumx2 [expr {$sumx2+$x*$x}]
set sumy2 [expr {$sumy2+$y*$y}]
set sumxy [expr {$sumxy+$x*$y}]
incr df
}
}
if { $df <= 2 } {
return -code error -errorcode ARG "$TOOFEWDATA: too few valid data"
}
if { $sumx2 == 0.0 } {
return -code error -errorcode ARG "$TOOFEWDATA: independent values are all the same"
}
#
# Calculate the intermediate quantities
#
set sx [expr {$sumx2-$sumx*$sumx/$df}]
set sy [expr {$sumy2-$sumy*$sumy/$df}]
set sxy [expr {$sumxy-$sumx*$sumy/$df}]
#
# Calculate the coefficients
#
if { $intercept } {
set B [expr {$sxy/$sx}]
set A [expr {($sumy-$B*$sumx)/$df}]
} else {
set B [expr {$sumxy/$sumx2}]
set A 0.0
}
#
# Calculate the error estimates
#
set stdevY 0.0
set varY 0.0
if { $intercept } {
set ve [expr {$sy-$B*$sxy}]
if { $ve >= 0.0 } {
set varY [expr {$ve/($df-2)}]
}
} else {
set ve [expr {$sumy2-$B*$sumxy}]
if { $ve >= 0.0 } {
set varY [expr {$ve/($df-1)}]
}
}
set seY [expr {sqrt($varY)}]
if { $intercept } {
set R2 [expr {$sxy*$sxy/($sx*$sy)}]
set seA [expr {$seY*sqrt(1.0/$df+$sumx*$sumx/($sx*$df*$df))}]
set seB [expr {sqrt($varY/$sx)}]
set tA {}
set tB {}
if { $seA != 0.0 } {
set tA [expr {$A/$seA*sqrt($df-2)}]
}
if { $seB != 0.0 } {
set tB [expr {$B/$seB*sqrt($df-2)}]
}
} else {
set R2 [expr {$sumxy*$sumxy/($sumx2*$sumy2)}]
set seA {}
set tA {}
set tB {}
set seB [expr {sqrt($varY/$sumx2)}]
if { $seB != 0.0 } {
set tB [expr {$B/$seB*sqrt($df-1)}]
}
}
#
# Return the list of parameters
#
return [list $A $B $seY $R2 $df $seA $tA $seB $tB]
}
# linear-residuals
# Determine the difference between actual data and predicted from
# the linear model
#
# Arguments:
# xdata Series of independent (X) data
# ydata Series of dependent (Y) data
# intercept Whether to use an intercept or not (optional)
#
# Result:
# List of differences
#
proc ::math::statistics::linear-residuals { xdata ydata {intercept 1} } {
variable TOOFEWDATA
if { [llength $xdata] < 3 } {
return -code error -errorcode ARG "$TOOFEWDATA: no independent data"
}
if { [llength $ydata] < 3 } {
return -code error -errorcode ARG "$TOOFEWDATA: no dependent data"
}
if { [llength $xdata] != [llength $ydata] } {
return -code error -errorcode ARG "$TOOFEWDATA: number of dependent data differs from number of independent data"
}
foreach {A B} [linear-model $xdata $ydata $intercept] {break}
set result {}
foreach x $xdata y $ydata {
set residue [expr {$y-$A-$B*$x}]
lappend result $residue
}
return $result
}
# median
# Determine the median from a list of data
#
# Arguments:
# data (Unsorted) list of data
#
# Result:
# Median (either the middle value or the mean of two values in the
# middle)
#
# Note:
# Adapted from the Wiki page "Stats", code provided by JPS
#
proc ::math::statistics::median { data } {
set org_data $data
set data {}
foreach value $org_data {
if { $value != {} } {
lappend data $value
}
}
set len [llength $data]
set data [lsort -real $data]
if { $len % 2 } {
lindex $data [expr {($len-1)/2}]
} else {
expr {([lindex $data [expr {($len / 2) - 1}]] \
+ [lindex $data [expr {$len / 2}]]) / 2.0}
}
}
# test-2x2 --
# Compute the chi-square statistic for a 2x2 table
#
# Arguments:
# a Element upper-left
# b Element upper-right
# c Element lower-left
# d Element lower-right
# Return value:
# Chi-square
# Note:
# There is only one degree of freedom - this is important
# when comparing the value to the tabulated values
# of chi-square
#
proc ::math::statistics::test-2x2 { a b c d } {
set ab [expr {$a+$b}]
set ac [expr {$a+$c}]
set bd [expr {$b+$d}]
set cd [expr {$c+$d}]
set N [expr {$a+$b+$c+$d}]
set det [expr {$a*$d-$b*$c}]
set result [expr {double($N*$det*$det)/double($ab*$cd*$ac*$bd)}]
}
# print-2x2 --
# Print a 2x2 table
#
# Arguments:
# a Element upper-left
# b Element upper-right
# c Element lower-left
# d Element lower-right
# Return value:
# Printed version with marginals
#
proc ::math::statistics::print-2x2 { a b c d } {
set ab [expr {$a+$b}]
set ac [expr {$a+$c}]
set bd [expr {$b+$d}]
set cd [expr {$c+$d}]
set N [expr {$a+$b+$c+$d}]
set chisq [test-2x2 $a $b $c $d]
set line [string repeat - 10]
set result [format "%10d%10d | %10d\n" $a $b $ab]
append result [format "%10d%10d | %10d\n" $c $d $cd]
append result [format "%10s%10s + %10s\n" $line $line $line]
append result [format "%10d%10d | %10d\n" $ac $bd $N]
append result "Chisquare = $chisq\n"
append result "Difference is significant?\n"
append result " at 95%: [expr {$chisq<3.84146? "no":"yes"}]\n"
append result " at 99%: [expr {$chisq<6.63490? "no":"yes"}]"
}
# control-xbar --
# Determine the control lines for an x-bar chart
#
# Arguments:
# data List of observed values (at least 20*nsamples)
# nsamples Number of data per subsamples (default: 4)
# Return value:
# List of: mean, lower limit, upper limit, number of data per
# subsample. Can be used in the test-xbar procedure
#
proc ::math::statistics::control-xbar { data {nsamples 4} } {
variable TOOFEWDATA
variable control_factors
#
# Check the number of data
#
if { $nsamples <= 1 } {
return -code error -errorcode DATA -errorinfo $OUTOFRANGE \
"Number of data per subsample must be at least 2"
}
if { [llength $data] < 20*$nsamples } {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
set nogroups [expr {[llength $data]/$nsamples}]
set mrange 0.0
set xmeans 0.0
for { set i 0 } { $i < $nogroups } { incr i } {
set subsample [lrange $data [expr {$i*$nsamples}] [expr {$i*$nsamples+$nsamples-1}]]
set xmean 0.0
set xmin [lindex $subsample 0]
set xmax $xmin
foreach d $subsample {
set xmean [expr {$xmean+$d}]
set xmin [expr {$xmin<$d? $xmin : $d}]
set xmax [expr {$xmax>$d? $xmax : $d}]
}
set xmean [expr {$xmean/double($nsamples)}]
set xmeans [expr {$xmeans+$xmean}]
set mrange [expr {$mrange+($xmax-$xmin)}]
}
#
# Determine the control lines
#
set xmeans [expr {$xmeans/double($nogroups)}]
set mrange [expr {$mrange/double($nogroups)}]
set A2 [lindex [lindex $control_factors 1] $nsamples]
if { $A2 == "" } { set A2 [lindex [lindex $control_factors 1] end] }
return [list $xmeans [expr {$xmeans-$A2*$mrange}] \
[expr {$xmeans+$A2*$mrange}] $nsamples]
}
# test-xbar --
# Determine if any data points lie outside the x-bar control limits
#
# Arguments:
# control List returned by control-xbar with control data
# data List of observed values
# Return value:
# Indices of any subsamples that violate the control limits
#
proc ::math::statistics::test-xbar { control data } {
foreach {xmean xlower xupper nsamples} $control {break}
if { [llength $data] < 1 } {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
set nogroups [expr {[llength $data]/$nsamples}]
if { $nogroups <= 0 } {
set nogroup 1
set nsamples [llength $data]
}
set result {}
for { set i 0 } { $i < $nogroups } { incr i } {
set subsample [lrange $data [expr {$i*$nsamples}] [expr {$i*$nsamples+$nsamples-1}]]
set xmean 0.0
foreach d $subsample {
set xmean [expr {$xmean+$d}]
}
set xmean [expr {$xmean/double($nsamples)}]
if { $xmean < $xlower } { lappend result $i }
if { $xmean > $xupper } { lappend result $i }
}
return $result
}
# control-Rchart --
# Determine the control lines for an R chart
#
# Arguments:
# data List of observed values (at least 20*nsamples)
# nsamples Number of data per subsamples (default: 4)
# Return value:
# List of: mean range, lower limit, upper limit, number of data per
# subsample. Can be used in the test-Rchart procedure
#
proc ::math::statistics::control-Rchart { data {nsamples 4} } {
variable TOOFEWDATA
variable control_factors
#
# Check the number of data
#
if { $nsamples <= 1 } {
return -code error -errorcode DATA -errorinfo $OUTOFRANGE \
"Number of data per subsample must be at least 2"
}
if { [llength $data] < 20*$nsamples } {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
set nogroups [expr {[llength $data]/$nsamples}]
set mrange 0.0
for { set i 0 } { $i < $nogroups } { incr i } {
set subsample [lrange $data [expr {$i*$nsamples}] [expr {$i*$nsamples+$nsamples-1}]]
set xmin [lindex $subsample 0]
set xmax $xmin
foreach d $subsample {
set xmin [expr {$xmin<$d? $xmin : $d}]
set xmax [expr {$xmax>$d? $xmax : $d}]
}
set mrange [expr {$mrange+($xmax-$xmin)}]
}
#
# Determine the control lines
#
set mrange [expr {$mrange/double($nogroups)}]
set D3 [lindex [lindex $control_factors 3] $nsamples]
set D4 [lindex [lindex $control_factors 5] $nsamples]
if { $D3 == "" } { set D3 [lindex [lindex $control_factors 3] end] }
if { $D4 == "" } { set D4 [lindex [lindex $control_factors 5] end] }
return [list $mrange [expr {$D3*$mrange}] \
[expr {$D4*$mrange}] $nsamples]
}
# test-Rchart --
# Determine if any data points lie outside the R-chart control limits
#
# Arguments:
# control List returned by control-xbar with control data
# data List of observed values
# Return value:
# Indices of any subsamples that violate the control limits
#
proc ::math::statistics::test-Rchart { control data } {
foreach {rmean rlower rupper nsamples} $control {break}
#
# Check the number of data
#
if { [llength $data] < 1 } {
return -code error -errorcode DATA -errorinfo $TOOFEWDATA $TOOFEWDATA
}
set nogroups [expr {[llength $data]/$nsamples}]
set result {}
for { set i 0 } { $i < $nogroups } { incr i } {
set subsample [lrange $data [expr {$i*$nsamples}] [expr {$i*$nsamples+$nsamples-1}]]
set xmin [lindex $subsample 0]
set xmax $xmin
foreach d $subsample {
set xmin [expr {$xmin<$d? $xmin : $d}]
set xmax [expr {$xmax>$d? $xmax : $d}]
}
set range [expr {$xmax-$xmin}]
if { $range < $rlower } { lappend result $i }
if { $range > $rupper } { lappend result $i }
}
return $result
}
# test-Duckworth --
# Determine if two data sets have the same median according to the Tukey-Duckworth test
#
# Arguments:
# list1 Values in the first data set
# list2 Values in the second data set
# significance Significance level (either 0.05, 0.01 or 0.001)
#
# Returns:
# 0 if the medians are unequal, 1 if they are equal, -1 if the test can not
# be conducted (the smallest value must be in a different set than the greatest value)
#
proc ::math::statistics::test-Duckworth {list1 list2 significance} {
set sorted1 [lsort -real $list1]
set sorted2 [lsort -real -decreasing $list2]
set lowest1 [lindex $sorted1 0]
set lowest2 [lindex $sorted2 end]
set greatest1 [lindex $sorted1 end]
set greatest2 [lindex $sorted2 0]
if { $lowest1 <= $lowest2 && $greatest1 >= $greatest2 } {
return -1
}
if { $lowest1 >= $lowest2 && $greatest1 <= $greatest2 } {
return -1
}
#
# Determine how many elements of set 1 are lower than the lowest of set 2
# Ditto for the number of elements of set 2 greater than the greatest of set 1
# (Or vice versa)
#
if { $lowest1 < $lowest2 } {
set lowest $lowest2
set greatest $greatest1
} else {
set lowest $lowest1
set greatest $greatest2
set sorted1 [lsort -real $list2]
set sorted2 [lsort -real -decreasing $list1]
#lassign [list $sorted1 $sorted2] sorted2 sorted1
}
set count1 0
set count2 0
foreach v1 $sorted1 {
if { $v1 >= $lowest } {
break
}
incr count1
}
foreach v2 $sorted2 {
if { $v2 <= $greatest } {
break
}
incr count2
}
#
# Determine the statistic D, possibly with correction
#
set n1 [llength $list1]
set n2 [llength $list2]
set correction 0
if { 3 + 4*$n1/3 <= $n2 && $n2 <= 2*$n1 } {
set correction -1
}
if { 3 + 4*$n2/3 <= $n1 && $n1 <= 2*$n2 } {
set correction -1
}
set D [expr {$count1 + $count2 + $correction}]
switch -- [string trim $significance 0] {
".05" {
return [expr {$D >= 7? 0 : 1}]
}
".01" {
return [expr {$D >= 10? 0 : 1}]
}
".001" {
return [expr {$D >= 13? 0 : 1}]
}
default {
return -code error "Significance level must be 0.05, 0.01 or 0.001"
}
}
}
#
# Load the auxiliary scripts
#
source [file join [file dirname [info script]] pdf_stat.tcl]
source [file join [file dirname [info script]] plotstat.tcl]
source [file join [file dirname [info script]] liststat.tcl]
source [file join [file dirname [info script]] mvlinreg.tcl]
source [file join [file dirname [info script]] kruskal.tcl]
source [file join [file dirname [info script]] wilcoxon.tcl]
source [file join [file dirname [info script]] stat_kernel.tcl]
#
# Define the tables
#
namespace eval ::math::statistics {
variable student_t_table
# set student_t_table [::math::interpolation::defineTable student_t
# {X 80% 90% 95% 98% 99%}
# {X 0.80 0.90 0.95 0.98 0.99
# 1 3.078 6.314 12.706 31.821 63.657
# 2 1.886 2.920 4.303 6.965 9.925
# 3 1.638 2.353 3.182 4.541 5.841
# 5 1.476 2.015 2.571 3.365 4.032
# 10 1.372 1.812 2.228 2.764 3.169
# 15 1.341 1.753 2.131 2.602 2.947
# 20 1.325 1.725 2.086 2.528 2.845
# 30 1.310 1.697 2.042 2.457 2.750
# 60 1.296 1.671 2.000 2.390 2.660
# 1.0e9 1.282 1.645 1.960 2.326 2.576 }]
# PM
#set chi_squared_table [::math::interpolation::defineTable chi_square
# ...
}
#
# Simple test code
#
if { [info exists ::argv0] && ([file tail [info script]] == [file tail $::argv0]) } {
console show
puts [interp aliases]
set values {1 1 1 1 {}}
puts [::math::statistics::basic-stats $values]
set values {1 2 3 4}
puts [::math::statistics::basic-stats $values]
set values {1 -1 1 -2}
puts [::math::statistics::basic-stats $values]
puts [::math::statistics::mean $values]
puts [::math::statistics::min $values]
puts [::math::statistics::max $values]
puts [::math::statistics::number $values]
puts [::math::statistics::stdev $values]
puts [::math::statistics::var $values]
set novals 100
#set maxvals 100001
set maxvals 1001
while { $novals < $maxvals } {
set values {}
for { set i 0 } { $i < $novals } { incr i } {
lappend values [expr {rand()}]
}
puts [::math::statistics::basic-stats $values]
puts [::math::statistics::histogram {0.0 0.2 0.4 0.6 0.8 1.0} $values]
set novals [expr {$novals*10}]
}
puts "Normal distribution:"
puts "X=0: [::math::statistics::pdf-normal 0.0 1.0 0.0]"
puts "X=1: [::math::statistics::pdf-normal 0.0 1.0 1.0]"
puts "X=-1: [::math::statistics::pdf-normal 0.0 1.0 -1.0]"
set data1 {0.0 1.0 3.0 4.0 100.0 -23.0}
set data2 {1.0 2.0 4.0 5.0 101.0 -22.0}
set data3 {0.0 2.0 6.0 8.0 200.0 -46.0}
set data4 {2.0 6.0 8.0 200.0 -46.0 1.0}
set data5 {100.0 99.0 90.0 93.0 5.0 123.0}
puts "Correlation data1 and data1: [::math::statistics::corr $data1 $data1]"
puts "Correlation data1 and data2: [::math::statistics::corr $data1 $data2]"
puts "Correlation data1 and data3: [::math::statistics::corr $data1 $data3]"
puts "Correlation data1 and data4: [::math::statistics::corr $data1 $data4]"
puts "Correlation data1 and data5: [::math::statistics::corr $data1 $data5]"
# set data {1.0 2.0 2.3 4.0 3.4 1.2 0.6 5.6}
# puts [::math::statistics::basicStats $data]
# puts [::math::statistics::interval-mean-stdev $data 0.90]
# puts [::math::statistics::interval-mean-stdev $data 0.95]
# puts [::math::statistics::interval-mean-stdev $data 0.99]
# puts "\nTest mean values:"
# puts [::math::statistics::test-mean $data 2.0 0.1 0.90]
# puts [::math::statistics::test-mean $data 2.0 0.5 0.90]
# puts [::math::statistics::test-mean $data 2.0 1.0 0.90]
# puts [::math::statistics::test-mean $data 2.0 2.0 0.90]
set rc [catch {
set m [::math::statistics::mean {}]
} msg ] ; # {}
puts "Result: $rc $msg"
puts "\nTest quantiles:"
set data {1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0}
set quantiles {0.11 0.21 0.51 0.91 0.99}
set limits {2.1 4.1 6.1 8.1}
puts [::math::statistics::quantiles $data $quantiles]
set histogram [::math::statistics::histogram $limits $data]
puts [::math::statistics::quantiles $limits $histogram $quantiles]
puts "\nTest autocorrelation:"
set data {1.0 -1.0 1.0 -1.0 1.0 -1.0 1.0 -1.0 1.0}
puts [::math::statistics::autocorr $data]
set data {1.0 -1.1 2.0 -0.6 3.0 -4.0 0.5 0.9 -1.0}
puts [::math::statistics::autocorr $data]
puts "\nTest histogram limits:"
puts [::math::statistics::mean-histogram-limits 1.0 1.0]
puts [::math::statistics::mean-histogram-limits 1.0 1.0 4]
puts [::math::statistics::minmax-histogram-limits 1.0 10.0 10]
}
#
# Test xbar/R-chart procedures
#
if { 0 } {
set data {}
for { set i 0 } { $i < 500 } { incr i } {
lappend data [expr {rand()}]
}
set limits [::math::statistics::control-xbar $data]
puts $limits
puts "Outliers? [::math::statistics::test-xbar $limits $data]"
set newdata {1.0 1.0 1.0 1.0 0.5 0.5 0.5 0.5 10.0 10.0 10.0 10.0}
puts "Outliers? [::math::statistics::test-xbar $limits $newdata] -- 0 2"
set limits [::math::statistics::control-Rchart $data]
puts $limits
puts "Outliers? [::math::statistics::test-Rchart $limits $data]"
set newdata {0.0 1.0 2.0 1.0 0.4 0.5 0.6 0.5 10.0 0.0 10.0 10.0}
puts "Outliers? [::math::statistics::test-Rchart $limits $newdata] -- 0 2"
}
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