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RFC: Any and all comments welcome on style/technique in new module to calculate G statistic

by hilitai (Monk)
on Jul 29, 2007 at 23:13 UTC ( #629450=perlmeditation: print w/replies, xml ) Need Help??

I've written a module to fill a need I can't seem to satisfy from CPAN. It takes a table of frequency data and calculates a G statistic for it, which can be used to determine if the frequency distribution significantly differs from an expected distribution. I'm thinking of submitting it to CPAN, but I've never done that before, and I'd like to get commentary on it before I embark on that process.

It's about 500 lines long. Thanks to anyone who takes the trouble to look at it.

#!/usr/bin/perl -w =head1 NAME Gstat - calculate G-statistic for tabular data =head1 SYNOPSIS use Gstat; $gt = Gstat->new($datafile); $degreesOfFreedom = $gt->getDF(); $gstat = $gt->getG(); $gt->setExpected($expectedvalues); $uncorrectedG = $gt->getRawG(); =head1 DESCRIPTION C<Gstat> is a class that calculates the G-statistic for goodness of fit for frequency data. It can be used on simple frequency distributions (1-way tables) or for analyses of independence (2-way tables). Note that C<Gstat> will B<not>, by itself, perform the significance test for you -- it just provides the G-statistic that can then be compared with the chi-square distribution to determine significance. =head1 OVERVIEW and EXAMPLES A goodness of fit test attempts to determine if an observed frequency distribution differs significantly from a hypothesized frequency distribution. From C<Gstat>'s point of view, these tests come in two flavors: 1-way tests (where a single frequency distribution is tested against an expected distribution) and 2-way tests (where a matrix of observed values is tested for independence -- that is, the lack of interaction effects among the two axes being measured). A simple example might help here. You've grown 160 plants from seed produced by a single parent plant. You observe that among the offspring plants, some have spiny leaves, some have hairy leaves, and some have smooth leaves. What is the likelihood that the distribution of this trait follows the expected values for simple Mendelian inheritance? Observed values: Spiny Hairy Smooth 95 53 12 Expected values (for a 9:3:3:1 ratio): 90 60 10 If the observed and expected values are put into two files, C<Gstat> can create a G-statistic object that will calculate the likelihood that the observed distribution is significantly different from the distribution that would be expected by simple inheritance. (The value of G for this comparison is approximately 1.495, with 2 degrees of freedom; the observed results are not significantly different from expected at the .05 -- or even .1 level.) 2-way tests will usually not need a table of expected values, as the expected values are generated from the observed value sums. However, one can be loaded for 2-way tables as well. To determine if the calculated G statistic indicates a statistically significant result, you will need to look up the values in a chi-square distribution on your own, or make use of the C<Statistics::Distributions> module: use Gstat; use Statistics::Distributions; ... my $gt = Gstat->new($data); my $df = $gt->getDF(); my $g = $gt->getG(); my $sig = '.05'; my $chis=Statistics::Distributions::chisqrdistr ($df,$sv); if ($g > $chis) { print "$g: Sig. at the $sv level. ($chis cutoff)\n" } By default, C<Gstat> returns a G statistic that has been modified by William's correction (Williams 1976). This correction reduces the value of G for smaller sample sizes, and has progressively less effect as the sample size increases. The raw, uncorrected G statistic is also available. Calculation methods based on Sokal, R.R., and F.J. Rohlf, Biometry. 1981. W.H. Freeman and Company, San Francisco. Williams, D.A. 1976. Improved likelihood ratio test for complete contingency tables. Biometrika, 63:33 - 37. =cut package Gstat; use strict; use vars qw($VERSION); $VERSION = '0.01'; my $self; =head1 Public Methods =head2 Constructor $g = Gstat->new($datafile); $g = new Gstat($datafile); I<datafile> is a file containing whitespace-delimited data counts, arranged into rows and columns. There must be B<no> non-numeric characters, B<no> empty cells, and B<no> zero counts. =cut sub new { my $type = shift; my $basefile = shift; if (! $basefile) { _error('1', ["Must pass in a filename for a file containing the data.", "Ex: \$g = new Gstat(\$datafile);"]); } $self = {}; _initialize($basefile); bless($self, $type); $self; } =head2 getG $float = $g->getG(); Returns the corrected G-statistic for the current observed and expected frequency counts. =cut sub getG { my $self = shift; $self->{'logsum'} = _sumCellOp(); $self->{'G'} = getRawG($self) / _williamsC(); $self->{'G'}; } =head2 getRawG $float = $g->getRawG(); Returns the uncorrected G-statistic for the current observed and expected frequency counts. This value can be misleadingly large for small sample sizes (n < 200). =cut sub getRawG { my $self = shift; $self->{'logsum'} = _sumCellOp(); $self->{'G'} = 2 * $self->{'logsum'}; 2 * $self->{'logsum'}; } =head2 setExpected $g->setExpected($expectedValues); If testing with a specific hypothesized distribution, the expected frequency values for that distribution, given the total sample size, must be input to C<Gstat>. The expected frequencies must be in a file with the same format constraints as the initial I<datafile>. =cut sub setExpected { my $self = shift; my $expFile = shift; my @expect; if (! open(EXP, "$expFile")) { _error('2', ["System error: cannot open '$expFile' for reading: $!."]); } while (<EXP>) { s/^\s*//; s/\s*$//; if ($_) { my @row = split(/\s+/); foreach my $cell (@row) { _checkNumValidity($cell); push(@expect, $cell); } } } close EXP; $self->{'expected'} = \@expect; } =head2 getDF $integer = $g->getDF(); Returns the current degrees of freedom for this distribution, which is calculated automatically from the observed data (I<rows> - 1 for 1-way tests, (I<rows> - 1) * (I<cols> - 1) for 2-way tests). =cut sub getDF { my $self = shift; $self->{'df'}; } =head2 setDF $g->setDF($integer); Sets the degrees of freedom for this distribution. Sometimes this value needs to be modified beyond the standard rules used by C<Gstat>; C<setDF> makes this possible. =cut sub setDF { my $self = shift; $self->{'df'} = shift; } =head2 getRow $rowref = $g->getRow(rownum); Returns a row from the array of observed data. Row numbering is zero-based. =cut sub getRow { my $self = shift; my $idx = shift; my @row = (); my $skip = $self->{'ncols'}; my $offset = ($idx + 1) * $skip; my $final = $offset + $skip; for my $cell ($offset .. $final - 1) { push(@row, $self->{'observed'}->[$cell]); } \@row; } =head2 getCol $colref = $g->getCol(colnum); Returns a column for the array of observed data. Column numbering is zero-based. =cut sub getCol { my $self = shift; my $idx = shift; my @col = (); my $skip = $self->{'ncols'}; my $max = $skip * $self->{'nrows'}; for (my $cell = $idx+1; $cell < $max; $cell += $skip) { push(@col,$self->{'observed'}->[$cell]); } \@col; } =head2 rowSum $integer = $g->rowSum($index); Returns the sum of the requested row. =cut sub rowSum { my $self = shift; my $idx = shift; $self->{'rowsums'}->[$idx]; } =head2 colSum $integer = $g->colSum($index); Returns the sum of the requested column. =cut sub colSum { my $self = shift; my $idx = shift; $self->{'colsums'}->[$idx]; } =head2 getRowNum $integer = $g->getRowNum(); Returns the number of rows in the data table. =cut sub getRowNum { my $self = shift; $self->{'nrows'}; } =head2 getColNum $integer = $g->getColNum(); Returns the number of columns in the data table. =cut sub getColNum { my $self = shift; $self->{'ncols'}; } =head2 getSumTotal $integer = $g->getSumTotal(); Returns the total number of observations. =cut sub getSumTotal { my $self = shift; $self->{'sumtotal'}; } # private methods sub _initialize { my $basefile = shift; if (! open(IN, "$basefile")) { _error('2', ["System error: cannot open '$basefile' for reading: $!."] +); } my @datastruct = (); my @rowsums = (); my @sumcols = (); my ($ncols, $nrows, $checkcol, $sumtotal, @row); $self->{'basefile'} = $basefile; $self->{'colsums'} = (); while (<IN>) { s/^\s*//; s/\s*$//; if ($_) { my @row = split(/\s+/); $ncols = scalar @row; if ($nrows) { if ($ncols != $checkcol) { _error(4, ["Data Table error: missing data in table."]); } } my $i = 0; foreach my $cell (@row) { push(@datastruct, $cell); $sumtotal += $cell; $self->{'colsums'}->[$i] += $cell; $i++; } $nrows++; push(@rowsums, _rowsum(\@row)); } $checkcol = $ncols; } close IN; _checkData(\@datastruct); $self->{'observed'} = \@datastruct; $self->{'rowsums'} = \@rowsums; $self->{'nrows'} = $nrows; $self->{'ncols'} = $ncols; $self->{'sumtotal'} = $sumtotal; # tabletype: 0 = 2-way, 1 = single column, 2 = single row if (($ncols == 1) || ($nrows == 1)) { if ($ncols == 1) { $self->{'df'} = $nrows - 1; $self->{'tabletype'} = 1; } if ($nrows == 1) { $self->{'df'} = $ncols - 1; $self->{'tabletype'} = 2; } } else { $self->{'df'} = ($nrows - 1) * ($ncols - 1); $self->{'tabletype'} = 0; } $self->{'expected'}= _expected(\@datastruct); } sub _williamsC { my $sumtotal = $self->{'sumtotal'}; my $rowsums = $self->{'rowsums'}; my $colsums = $self->{'colsums'}; if ($self->{'tabletype'} == 1) { $self->{'q'} = 1 + ($self->{'nrows'} + 1) / (6 * $sumtotal); } elsif ($self->{'tabletype'} == 2) { $self->{'q'} = 1 + ($self->{'ncols'} + 1) / (6 * $sumtotal); } else { my $recipRows = 0; my $recipCols = 0; foreach my $rval (@{$rowsums}) { $recipRows += (1 / $rval); } foreach my $cval (@{$colsums}) { $recipCols += (1 / $cval); } my $denom = 6 * $sumtotal * $self->{'df'}; my $num = ($sumtotal * $recipRows - 1) * ($sumtotal * $recipCols - 1) +; $self->{'q'} = 1 + $num / $denom; } } sub _expected { my $data = shift; my @expected = (); my $rows = $self->{'nrows'}; my $cols = $self->{'ncols'}; my $sumtotal = $self->{'sumtotal'}; for my $row (0 .. $rows-1) { my $marginalRow = $self->{'rowsums'}->[$row] / $sumtotal; my @a; for my $col (0 .. $cols-1) { my $marginalCol = $self->{'colsums'}->[$col] / $sumtotal; + push(@expected, ($marginalRow * $marginalCol * $sumtotal)) +; } } \@expected; } sub _sumCellOp { my $logsum = 0; my $ncells = $self->{'nrows'} * $self->{'ncols'}; my $o = $self->{'observed'}; my $e = $self->{'expected'}; for my $cell (0 .. $ncells-1) { $logsum += $o->[$cell] * log($o->[$cell] / $e->[$cell]); } $logsum; } sub _rowsum { my $row = shift; my $total = 0; foreach my $val (@{$row}) { $total += $val; } return $total; } sub _checkData { my $data = shift; foreach my $val (@{$data}) { _checkNumValidity($val); } } sub _checkNumValidity { my $value = shift; my $eString = "Invalid data."; if ($value !~ /^-?\d+\.?\d*$/) { _error(3, ["$eString Value '$value' is not a number."]); } if ($value == 0) { _error(4, ["$eString Found a zero frequency value. Can't continue."]); } } sub _error { my ($code, $message) = @_; my ($package, $filename, $line) = caller(1); print STDERR " Error: in $package: file $filename, line $line\n\n" +; print STDERR " Error: ", join("\n ",@{$message}), "\n\n"; print STDERR "This is the stack trace:\n"; exit $code; } 1;
  • Comment on RFC: Any and all comments welcome on style/technique in new module to calculate G statistic
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Re: RFC: Any and all comments welcome on style/technique in new module to calculate G statistic (::Gtest)
by tye (Sage) on Jul 30, 2007 at 06:05 UTC

    Just a quick note (I hope to have time to look further, but certainly not tonight nor tomorrow).

    Please don't make up a brand new top-level name in the Perl module heirarchy. I see you used Statistics::Distributions, so you should be familar with some of the many, many modules to be found undef Statistics:: (search CPAN for statistics and see how many hits are properly named under this root name).

    Doing a quick search to learn about "G statistics", it appears that a more canonical name is a G-test so I suggest you name your module Statistics::Gtest (unfortunately, hyphen isn't an appropriate character in a module name).

    I don't think it makes sense to define the primary interface based on reading a file to get the matrix of data. If I have the data in a 2-dimensional Perl array, why should I have to write that out to a file in order to perform a G-test on it? I can see offering an option to read a data file in order to produce the 2-dimensional Perl array.

    s/^\s*//; s/\s*$//; if ($_) { my @row = split(/\s+/);

    You can replace all of that with:

    if( /\S/ ) { my @row= split ' ', $_;

    (Note that I don't like making the $_ argument to split implicit.)

    Thanks for writing this and for asking for a review. Looks well-written and useful.

    - tye        

      i agree, interface shouldn't be primarily file-based. you might get an idea or two from my recently released module, Statistics::Benford.
Re: RFC: Any and all comments welcome on style/technique in new module to calculate G statistic
by liverpole (Monsignor) on Jul 30, 2007 at 02:44 UTC
    Hi hilitai,

    Your module is very readable; nice job!

    I particularly like your use of pod, intermixed with the code in such a way that each subroutine is documented by the corresponding pod block.  (It may be a more common technique than I'm aware, but I haven't seen it before).

    Here are a couple of minor suggestions, all related to open:

    1. You might consider using lexically-scoped filehandles, via FileHandle or IO::File.  Using IN runs the risk of stomping on a globally-defined IN from somewhere else (eg. the calling program).  (Same with EXP).
    2. You don't need quotation marks around $basefile in open(IN, "$basefile").  (Same with $expFile).
    3. Why not use the 3-argument form of open?

    s''(q.S:$/9=(T1';s;(..)(..);$..=substr+crypt($1,$2),2,3;eg;print$..$/
      Using IN runs the risk of stomping on a globally-defined IN from somewhere else (eg. the calling program).

      Only if the calling program does something stupid like:

      open( Gstat::IN, ...
      I particularly like your use of pod, intermixed with the code in such a way that each subroutine is documented by the corresponding pod block.

      While that works for strictly linear reading of code, the lack of visual distictiveness of POD (especially when POD includes code snippets, which most good POD does) make that style problematic for many other styles of reading code. It isn't all that bad in this particular case but that is mostly due to the fact that the pod for most of the functions is nearly minimal. When the documentation becomes more extensive (which usually happens with good modules), it will become quite painful to find the code amid the POD, at least for people like me who usually read code more holistically than strictly linearly. I also find that it interferes with updating and especially organizing the POD.

      Why not use the 3-argument form of open?

      Or, if you don't want to make your code not work for people who for some reason may be stuck with an old version of Perl, at least be specific about the fact that you want to read the files (which provides the most important benefits of 3-argument open):

      open( EXP, "< $expFile" )

      Not that I disagree with any of your suggestions (just with your encouragement of intermixing POD and code).

      - tye        

        I noticed the problem with the intermixed POD as soon as I put it in the PerlMonks text box. It's very easy to distinguish POD when you're looking at it with a syntax-highlighting text editor, but in plain black and white, it's much more difficult. This is a drawback to POD I hadn't thought about before, which is too bad, because I find keeping the documentation with the method/function to be very handy. Javadoc commenting gets around this problem by putting comment chars. on every line of the documentation comment; it's a pity that POD doesn't do the same. At least, I can't think of any non-cumbersome way to do this.

        Well, now I know why just about everybody else puts their POD at the beginning or end of the module.

        Thanks for the comments re: open(). Now that I think about it, the module should handle data passed in as arrayrefs. as well as text files; I'll have to think about this a little more. (And yes, top-level "Gstat::" won't fly.)

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