@@ -20,7 +20,10 @@ my $builder = Test::Run::Builder->new(
},
requires => {
'Carp' => 0,
+ 'List::MoreUtils' => 0,
+ 'List::Util' => 0,
'POSIX' => 0,
+ 'perl' => '5.006',
'strict' => 0,
'vars' => 0,
'warnings' => 0,
@@ -1,5 +1,17 @@
Revision history for Perl extension Statistics::Descriptive.
+3.0607 2014-02-01
+ - Fix the List::MoreUtils prereqs.
+ - http://www.cpantesters.org/cpan/report/365b752c-8adf-11e3-bd14-e3bee4621ba3
+ - Thanks to Chris Williams (BINGOS) for the CPAN Testers Report.
+
+3.0606 2014-01-31
+ - Implement the median_absolute_deviation method.
+ - https://bitbucket.org/shlomif/perl-statistics-descriptive/pull-request/5/median-absolute-deviation-method/diff
+ - Thanks to Kang-min Liu.
+ - Minimal version of perl set to 5.6.0 (CPANTS).
+ - Add standalone LICENSE file (CPANTS).
+
3.0605 2013-05-21
- Add t/style-trailing-space.t .
- Add t/cpan-changes.t .
@@ -0,0 +1,396 @@
+Terms of Perl itself
+
+a) the GNU General Public License as published by the Free
+ Software Foundation; either version 1, or (at your option) any
+ later version, or
+b) the "Artistic License"
+
+----------------------------------------------------------------------------
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+
+The End
+
@@ -1,6 +1,8 @@
Build.PL
Changes
+LICENSE
MANIFEST
+META.json
META.yml
Makefile.PL
README
@@ -12,14 +14,15 @@ lib/Statistics/Descriptive/Smoother.pm
lib/Statistics/Descriptive/Smoother/Exponential.pm
lib/Statistics/Descriptive/Smoother/Weightedexponential.pm
rejects/descr.t
-scripts/tag-release.pl
scripts/bump-version-number.pl
-t/lib/Utils.pm
+scripts/tag-release.pl
t/00-load.t
t/cpan-changes.t
t/descr.t
t/descr_smooth_methods.t
t/freq_distribution-1-rt-34999.t
+t/lib/Utils.pm
+t/median_absolute_deviation.t
t/mode.t
t/outliers.t
t/pod-coverage.t
@@ -29,4 +32,3 @@ t/smoother.t
t/smoother_exponential.t
t/smoother_weightedexponential.t
t/style-trailing-space.t
-META.json
@@ -4,7 +4,7 @@
"Shlomi Fish <shlomif@iglu.org.il>"
],
"dynamic_config" : 1,
- "generated_by" : "Module::Build version 0.3901, CPAN::Meta::Converter version 2.120921",
+ "generated_by" : "Module::Build version 0.4007, CPAN::Meta::Converter version 2.132830",
"keywords" : [
"average",
"distribution",
@@ -39,7 +39,10 @@
"runtime" : {
"requires" : {
"Carp" : "0",
+ "List::MoreUtils" : "0",
+ "List::Util" : "0",
"POSIX" : "0",
+ "perl" : "5.006",
"strict" : "0",
"vars" : "0",
"warnings" : "0"
@@ -49,27 +52,27 @@
"provides" : {
"Statistics::Descriptive" : {
"file" : "lib/Statistics/Descriptive.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
},
"Statistics::Descriptive::Full" : {
"file" : "lib/Statistics/Descriptive.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
},
"Statistics::Descriptive::Smoother" : {
"file" : "lib/Statistics/Descriptive/Smoother.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
},
"Statistics::Descriptive::Smoother::Exponential" : {
"file" : "lib/Statistics/Descriptive/Smoother/Exponential.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
},
"Statistics::Descriptive::Smoother::Weightedexponential" : {
"file" : "lib/Statistics/Descriptive/Smoother/Weightedexponential.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
},
"Statistics::Descriptive::Sparse" : {
"file" : "lib/Statistics/Descriptive.pm",
- "version" : "3.0605"
+ "version" : "3.0607"
}
},
"release_status" : "stable",
@@ -82,5 +85,5 @@
"url" : "https://bitbucket.org/shlomif/perl-statistics-descriptive"
}
},
- "version" : "3.0605"
+ "version" : "3.0607"
}
@@ -9,7 +9,7 @@ build_requires:
configure_requires:
Module::Build: 0.36
dynamic_config: 1
-generated_by: 'Module::Build version 0.3901, CPAN::Meta::Converter version 2.120921'
+generated_by: 'Module::Build version 0.4007, CPAN::Meta::Converter version 2.132830'
keywords:
- average
- distribution
@@ -27,25 +27,28 @@ name: Statistics-Descriptive
provides:
Statistics::Descriptive:
file: lib/Statistics/Descriptive.pm
- version: 3.0605
+ version: 3.0607
Statistics::Descriptive::Full:
file: lib/Statistics/Descriptive.pm
- version: 3.0605
+ version: 3.0607
Statistics::Descriptive::Smoother:
file: lib/Statistics/Descriptive/Smoother.pm
- version: 3.0605
+ version: 3.0607
Statistics::Descriptive::Smoother::Exponential:
file: lib/Statistics/Descriptive/Smoother/Exponential.pm
- version: 3.0605
+ version: 3.0607
Statistics::Descriptive::Smoother::Weightedexponential:
file: lib/Statistics/Descriptive/Smoother/Weightedexponential.pm
- version: 3.0605
+ version: 3.0607
Statistics::Descriptive::Sparse:
file: lib/Statistics/Descriptive.pm
- version: 3.0605
+ version: 3.0607
requires:
Carp: 0
+ List::MoreUtils: 0
+ List::Util: 0
POSIX: 0
+ perl: 5.006
strict: 0
vars: 0
warnings: 0
@@ -53,4 +56,4 @@ resources:
homepage: http://web-cpan.berlios.de/modules/Statistics-Descriptive/
license: http://dev.perl.org/licenses/
repository: https://bitbucket.org/shlomif/perl-statistics-descriptive
-version: 3.0605
+version: 3.0607
@@ -1,4 +1,5 @@
-# Note: this file was auto-generated by Module::Build::Compat version 0.39_01
+# Note: this file was auto-generated by Module::Build::Compat version 0.4007
+require 5.006;
use ExtUtils::MakeMaker;
WriteMakefile
(
@@ -7,6 +8,8 @@ WriteMakefile
'PREREQ_PM' => {
'Benchmark' => 0,
'Carp' => 0,
+ 'List::MoreUtils' => 0,
+ 'List::Util' => 0,
'POSIX' => 0,
'Test::More' => 0,
'lib' => 0,
@@ -4,7 +4,7 @@ use warnings;
use base 'Statistics::Descriptive::Smoother';
-our $VERSION = '3.0605';
+our $VERSION = '3.0607';
sub _new {
my ($class, $args) = @_;
@@ -5,7 +5,7 @@ use warnings;
use Carp;
use base 'Statistics::Descriptive::Smoother';
-our $VERSION = '3.0605';
+our $VERSION = '3.0607';
sub _new {
my ($class, $args) = @_;
@@ -5,7 +5,7 @@ use warnings;
use Carp;
-our $VERSION = '3.0605';
+our $VERSION = '3.0607';
sub instantiate {
my ($class, $args) = @_;
@@ -5,12 +5,11 @@ use warnings;
##This module draws heavily from perltoot v0.4 from Tom Christiansen.
-require 5.00404; ##Yes, this is underhanded, but makes support for me easier
- ##Not only that, but it's the latest "safe" version of
- ##Perl5. 01-03 weren't bug free.
+use 5.006;
+
use vars (qw($VERSION $Tolerance $Min_samples_number));
-$VERSION = '3.0605';
+$VERSION = '3.0607';
$Tolerance = 0.0;
$Min_samples_number = 4;
@@ -19,7 +18,7 @@ package Statistics::Descriptive::Sparse;
use vars qw($VERSION);
-$VERSION = '3.0605';
+$VERSION = '3.0607';
use vars qw(%fields);
use Carp;
@@ -113,75 +112,76 @@ sub _is_permitted
}
sub add_data {
- my $self = shift; ##Myself
- my $oldmean;
- my ($min,$mindex,$max,$maxdex,$sum,$sumsq,$count);
- my $aref;
-
- if (ref $_[0] eq 'ARRAY') {
- $aref = $_[0];
- }
- else {
- $aref = \@_;
- }
+ my $self = shift; ##Myself
+ my $oldmean;
+ my ($min,$mindex,$max,$maxdex,$sum,$sumsq,$count);
+ my $aref;
- ##If we were given no data, we do nothing.
- return 1 if (!@{ $aref });
+ if (ref $_[0] eq 'ARRAY') {
+ $aref = $_[0];
+ }
+ else {
+ $aref = \@_;
+ }
- ##Take care of appending to an existing data set
+ ##If we were given no data, we do nothing.
+ return 1 if (!@{ $aref });
- if (!defined($min = $self->min()))
- {
- $min = $aref->[$mindex = 0];
- }
- else
- {
- $mindex = $self->mindex();
- }
+ ##Take care of appending to an existing data set
- if (!defined($max = $self->max()))
- {
- $max = $aref->[$maxdex = 0];
- }
- else
- {
- $maxdex = $self->maxdex();
- }
+ if (!defined($min = $self->min()))
+ {
+ $min = $aref->[$mindex = 0];
+ }
+ else
+ {
+ $mindex = $self->mindex();
+ }
- $sum = $self->sum();
- $sumsq = $self->sumsq();
- $count = $self->count();
-
- ##Calculate new mean, sumsq, min and max;
- foreach ( @{ $aref } ) {
- $sum += $_;
- $sumsq += $_**2;
- $count++;
- if ($_ >= $max) {
- $max = $_;
- $maxdex = $count-1;
+ if (!defined($max = $self->max()))
+ {
+ $max = $aref->[$maxdex = 0];
}
- if ($_ <= $min) {
- $min = $_;
- $mindex = $count-1;
+ else
+ {
+ $maxdex = $self->maxdex();
}
- }
- $self->min($min);
- $self->mindex($mindex);
- $self->max($max);
- $self->maxdex($maxdex);
- $self->sample_range($max - $min);
- $self->sum($sum);
- $self->sumsq($sumsq);
- $self->mean($sum / $count);
- $self->count($count);
- ##indicator the value is not cached. Variance isn't commonly enough
- ##used to recompute every single data add.
- $self->_variance(undef);
- return 1;
+ $sum = $self->sum();
+ $sumsq = $self->sumsq();
+ $count = $self->count();
+
+ ##Calculate new mean, sumsq, min and max;
+ foreach ( @{ $aref } ) {
+ $sum += $_;
+ $sumsq += $_**2;
+ $count++;
+ if ($_ >= $max) {
+ $max = $_;
+ $maxdex = $count-1;
+ }
+ if ($_ <= $min) {
+ $min = $_;
+ $mindex = $count-1;
+ }
+ }
+
+ $self->min($min);
+ $self->mindex($mindex);
+ $self->max($max);
+ $self->maxdex($maxdex);
+ $self->sample_range($max - $min);
+ $self->sum($sum);
+ $self->sumsq($sumsq);
+ $self->mean($sum / $count);
+ $self->count($count);
+ ##indicator the value is not cached. Variance isn't commonly enough
+ ##used to recompute every single data add.
+ $self->_variance(undef);
+ return 1;
}
+
sub standard_deviation {
my $self = shift; ##Myself
return undef if (!$self->count());
@@ -190,35 +190,34 @@ sub standard_deviation {
##Return variance; if needed, compute and cache it.
sub variance {
- my $self = shift; ##Myself
+ my $self = shift; ##Myself
- return undef if (!$self->count());
+ my $count = $self->count();
- my $div = @_ ? 0 : 1;
- my $count = $self->count();
- if ($count < 1 + $div) {
- return 0;
- }
+ return undef if !$count;
- if (!defined($self->_variance())) {
- my $variance = ($self->sumsq()- $count * $self->mean()**2);
+ return 0 if $count == 1;
- # Sometimes due to rounding errors we get a number below 0.
- # This makes sure this is handled as gracefully as possible.
- #
- # See:
- #
- # https://rt.cpan.org/Public/Bug/Display.html?id=46026
- if ($variance < 0)
- {
- $variance = 0;
- }
+ if (!defined($self->_variance())) {
+ my $variance = ($self->sumsq()- $count * $self->mean()**2);
- $variance /= $count - $div;
+ # Sometimes due to rounding errors we get a number below 0.
+ # This makes sure this is handled as gracefully as possible.
+ #
+ # See:
+ #
+ # https://rt.cpan.org/Public/Bug/Display.html?id=46026
- $self->_variance($variance);
- }
- return $self->_variance();
+ $variance = $variance < 0 ? 0 : $variance / ($count - 1);
+
+ $self->_variance($variance);
+
+ # Return now to avoid re-entering this sub
+ # (and therefore save time when many objects are used).
+ return $variance;
+ }
+
+ return $self->_variance();
}
##Clear a stat. More efficient than destroying an object and calling
@@ -228,7 +227,7 @@ sub clear {
my $key;
return if (!$self->count());
- while (my($field, $value) = each %fields) {
+ while (my($field, $value) = each %fields) { # could use a slice assignment here
$self->{$field} = $value;
}
}
@@ -239,7 +238,7 @@ package Statistics::Descriptive::Full;
use vars qw($VERSION);
-$VERSION = '3.0605';
+$VERSION = '3.0607';
use Carp;
use POSIX ();
@@ -249,6 +248,9 @@ use vars qw(@ISA $a $b %fields);
@ISA = qw(Statistics::Descriptive::Sparse);
+use List::MoreUtils ();
+use List::Util ();
+
##Create a list of fields not to remove when data is updated
%fields = (
_permitted => undef, ##Place holder for the inherited key hash
@@ -261,7 +263,7 @@ use vars qw(@ISA $a $b %fields);
__PACKAGE__->_make_private_accessors(
[qw(data samples frequency geometric_mean harmonic_mean
least_squares_fit median mode
- skewness kurtosis
+ skewness kurtosis median_absolute_deviation
)
]
);
@@ -305,15 +307,18 @@ sub _delete_all_cached_keys
{
my $self = shift;
+ my %keys = %{ $self };
+
+ # Remove reserved keys for this class from the deletion list
+ delete @keys{keys %{$self->_reserved}};
+ delete @keys{keys %{$self->_permitted}};
+ delete $keys{_trimmed_mean_cache};
+
KEYS_LOOP:
- foreach my $key (keys %{ $self }) { # Check each key in the object
- # If it's a reserved key for this class, keep it
- if ($self->_is_reserved($key) || $self->_is_permitted($key))
- {
- next KEYS_LOOP;
- }
- delete $self->{$key}; # Delete the out of date cached key
+ foreach my $key (keys %keys) { # Check each key in the object
+ delete $self->{$key}; # Delete any out of date cached key
}
+ $self->{_trimmed_mean_cache} = {}; # just reset this one
return;
}
@@ -334,25 +339,76 @@ sub clear {
}
sub add_data {
- my $self = shift;
- my $aref;
+ my $self = shift; ##Myself
- if (ref $_[0] eq 'ARRAY') {
- $aref = $_[0];
- }
- else {
- $aref = \@_;
- }
- $self->SUPER::add_data($aref); ##Perform base statistics on the data
- push @{ $self->_data() }, @{ $aref };
- ##Clear the presorted flag
- $self->presorted(0);
+ my $aref;
+
+ if (ref $_[0] eq 'ARRAY') {
+ $aref = $_[0];
+ }
+ else {
+ $aref = \@_;
+ }
- $self->_delete_all_cached_keys();
+ ##If we were given no data, we do nothing.
+ return 1 if (!@{ $aref });
- return 1;
+ my $oldmean;
+ my ($min, $max, $sum, $sumsq);
+ my $count = $self->count;
+
+ # $count is modified lower down, but we need this flag after that
+ my $has_existing_data = $count;
+
+ # Take care of appending to an existing data set
+ if ($has_existing_data) {
+ $min = $self->min();
+ $max = $self->max();
+ $sum = $self->sum();
+ $sumsq = $self->sumsq();
+ }
+ else {
+ $min = $aref->[0];
+ $max = $aref->[0];
+ $sum = 0;
+ $sumsq = 0;
+ }
+
+ # need to allow for already having data
+ $sum += List::Util::sum (@$aref);
+ $sumsq += List::Util::sum (map {$_ ** 2} @$aref);
+ $max = List::Util::max ($max, @$aref);
+ $min = List::Util::min ($min, @$aref);
+ $count += scalar @$aref;
+ my $mean = $sum / $count;
+
+ $self->min($min);
+ $self->max($max);
+ $self->sample_range($max - $min);
+ $self->sum($sum);
+ $self->sumsq($sumsq);
+ $self->mean($mean);
+ $self->count($count);
+
+ ##Variance isn't commonly enough
+ ##used to recompute every single data add, so just clear its cache.
+ $self->_variance(undef);
+
+ push @{ $self->_data() }, @{ $aref };
+
+ # no need to clear keys if we are a newly populated object,
+ # and profiling shows it takes a long time when creating
+ # and populating many stats objects
+ if ($has_existing_data) {
+ ##Clear the presorted flag
+ $self->presorted(0);
+ $self->_delete_all_cached_keys();
+ }
+
+ return 1;
}
+
sub add_data_with_samples {
my ($self,$aref_values) = @_;
@@ -446,6 +502,46 @@ sub get_smoothed_data {
$self->{_smoother}->get_smoothed_data();
}
+sub maxdex {
+ my $self = shift;
+
+ return undef if !$self->count;
+ my $maxdex;
+
+ if ($self->presorted) {
+ $maxdex = $self->count - 1;
+ }
+ else {
+ my $max = $self->max;
+ $maxdex = List::MoreUtils::first_index {$_ == $max} $self->get_data;
+ }
+
+ $self->{maxdex} = $maxdex;
+
+ return $maxdex;
+}
+
+sub mindex {
+ my $self = shift;
+
+ return undef if !$self->count;
+ #my $maxdex = $self->{maxdex};
+ #return $maxdex if defined $maxdex;
+ my $mindex;
+
+ if ($self->presorted) {
+ $mindex = 0;
+ }
+ else {
+ my $min = $self->min;
+ $mindex = List::MoreUtils::first_index {$_ == $min} $self->get_data;
+ }
+
+ $self->{mindex} = $mindex;
+
+ return $mindex;
+}
+
sub sort_data {
my $self = shift;
@@ -454,9 +550,9 @@ sub sort_data {
##Sort the data in descending order
$self->_data([ sort {$a <=> $b} @{$self->_data()} ]);
$self->presorted(1);
- ##Fix the maxima and minima indices
- $self->mindex(0);
- $self->maxdex($#{$self->_data()});
+ ##Fix the maxima and minima indices - no, this is unnecessary now we have methods
+ #$self->mindex(0);
+ #$self->maxdex($#{$self->_data()});
}
return 1;
@@ -920,6 +1016,20 @@ sub least_squares_fit {
return @{ $self->_least_squares_fit() };
}
+sub median_absolute_deviation {
+ my ($self) = @_;
+
+ if (!defined($self->_median_absolute_deviation()))
+ {
+ my $stat = $self->new;
+ $stat->add_data(map { abs($_ - $self->median) } $self->get_data);
+ $self->_median_absolute_deviation($stat->median);
+ }
+
+ return $self->_median_absolute_deviation();
+}
+
+
1;
package Statistics::Descriptive;
@@ -3,7 +3,7 @@
use strict;
use warnings;
-use Test::More tests => 54;
+use Test::More tests => 61;
use lib 't/lib';
use Utils qw/is_between compare_hash_by_ranges/;
@@ -452,3 +452,71 @@ use Statistics::Descriptive;
);
}
+
+# Tests for mindex and maxdex on unsorted data,
+# including when new data are added which should not change the values
+{
+ my $stats_class = 'Statistics::Descriptive::Full';
+ my $stat1 = $stats_class->new();
+
+ my @data1 = (20, 1 .. 3, 100, 1..5);
+ my @data2 = (25, 30);
+
+ my $e_maxdex = 4;
+ my $e_mindex = 1;
+
+ $stat1->add_data(@data1); # initialise
+
+ # TEST*2
+ is ($stat1->mindex, $e_mindex, "initial mindex is correct");
+ is ($stat1->maxdex, $e_maxdex, "initial maxdex is correct");
+
+ # TEST*2
+ $stat1->add_data(@data2); # add new data
+ is ($stat1->mindex, $e_mindex, "mindex is correct after new data added");
+ is ($stat1->maxdex, $e_maxdex, "maxdex is correct after new data added");
+
+ # TEST*2
+ $stat1->median; # trigger a sort
+ $e_maxdex = scalar @data1 + scalar @data2 - 1;
+ is ($stat1->mindex, 0, "mindex is correct after sorting");
+ is ($stat1->maxdex, $e_maxdex, "maxdex is correct after sorting");
+
+}
+
+
+# what happens when we add new data?
+# Recycle the same data so mean, sd etc remain the same
+{
+ my $stats_class = 'Statistics::Descriptive::Full';
+ my $stat1 = $stats_class->new();
+ my $stat2 = $stats_class->new();
+
+ my @data1 = (1 .. 9, 100);
+ my @data2 = (100 .. 110);
+
+ # sample of methods
+ my @methods = qw /mean standard_deviation count skewness kurtosis median/;
+
+ $stat1->add_data(@data1); # initialise
+ foreach my $meth (@methods) { # run some methods
+ $stat1->$meth;
+ }
+ $stat1->add_data(@data2); # add new data
+ foreach my $meth (@methods) { # re-run some methods
+ $stat1->$meth;
+ }
+
+ $stat2->add_data(@data1, @data2); # initialise with all data
+ foreach my $meth (@methods) { # run some methods
+ $stat2->$meth;
+ }
+
+ # TEST
+ is_deeply (
+ $stat1,
+ $stat2,
+ 'stats consistent after adding new data',
+ );
+
+}
@@ -0,0 +1,26 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use Test::More tests => 2;
+
+use Statistics::Descriptive;
+
+{
+ my $stat = Statistics::Descriptive::Full->new();
+
+ $stat->add_data( 1, 1, 1, 2, 2, 2, 2, 4, 7 );
+
+ my $mad = $stat->median_absolute_deviation();
+
+ # TEST
+ ok (defined($mad),
+ "median_absolute_deviation is not undefined"
+ );
+
+ # TEST
+ is($mad, 1,
+ "median_absolute_deviation is correct"
+ );
+}