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Perl script.pl
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# quorumSubsample 4.3 by John Alroy
# see end of file for version history
# location of input and output data files
$PATH = "./";
# if multiple files are listed, subsampled diversity for each one will
# be reported both jointly and separately
@FILES = ("filename.extension");
$TRIALS = 1000;
# options CR, UW, or O2W (default SQS)
$METHOD = "SQS";
# taxonomic rank (required, options genus or species)
$RANK = "genus";
if ( $RANK !~ /^(genus|species)$/ ) {
print "\nExiting because RANK must be 'species' or 'genus'\n\n";
exit;
}
# time scale (options stages, subepochs, FR2, Peters, a file with numbers,
# or a number; default is 11 Myr bins)
$SCALE = "filename.extension";
# a number in Ma is required if SCALE is numerical
$MAXMA = "";
if ( $METHOD eq "SQS" || ! $METHOD ) {
$QUORUM = 0.4;
} elsif ( $METHOD eq "CR" ) {
$QUOTA = 1000;
} elsif ( $METHOD eq "UW" ) {
$QUOTA = 100;
} elsif ( $METHOD eq "O2W" ) {
$QUOTA = 10000;
}
# draw all occurrences and count genera seen at the quorum level(s)
# (option no, default yes)
$EXACT = "yes";
# subsample abundance data (only works for CR and SQS; default no)
$ABUND = "no";
# draw entire collections (option no, default yes)
$BYCOLLECTION = "yes";
# definition of singletons (option one reference and not recommended,
# default one occurrence)
$SINGLETONS = "";
# exclude most common (dominant) genus (option yes, default no)
$EXCLUDE = "no";
# exclude taxa in most diverse collection from singleton count
# (option yes, default no)
$BIGGEST = "no";
# draw all collections in a reference before going to the next one (optional
# and recommended)
$SEQUENTIAL = "yes";
# fixed number of collections drawn per reference (default no limit,
# but recommended)
$COLLSPERREF = 3;
# minimum number of references per bin (default none, and not recommended)
$REFQUOTA = 0;
# disperse sampling among references with a throwback algorithm (optional
# and not recommended)
$DISPERSE = "no";
# assign collections spanning multiple bins to the ones including more than
# half of their age estimate limits (default no; options yes or a fraction)
$DEORPHAN = "no";
if ( $DEORPHAN > 0 && $DEORPHAN < 0.5 || $DEORPHAN > 1 ) {
print "\nExiting because DEORPHAN must be 'yes' or a number between 0.5 and 1.0\n\n";
exit;
}
if ( $DEORPHAN =~ /y/i ) {
$DEORPHAN = 0.5;
}
# use interpolated boundary estimates in PaleoDB download file (default no,
# but recommended)
$INTERPOLATE = "";
# print data for bins sometimes under quota (default no)
$USEFAILED = "";
# print data only for bins in the range of those that meet the subsampling
# target (default no)
$TRIM = "";
# number of collections a bin must include to be analyzed
$MINCOLLBYBIN = 1;
# intervals must include as many collections as the maximum drawn
# (default no, and not recommended)
$MATCHMAX = "";
if ( $SCALE !~ /[^0-9]/ && $MAXMA == 0 ) {
print "\nExiting because MAXMA has not been set\n\n";
exit;
}
if ( $EXACT !~ /n/i && $SINGLETONS =~ /r/i ) {
print "\nWarning: SINGLETONS is forced to equal 'occurrences' if you choose the EXACT option\n";
}
if ( $EXACT !~ /n/i && $DISPERSE =~ /y/i ) {
print "\nWarning: DISPERSE doesn't work if you choose the EXACT option\n";
}
my ($nbin,%lookup,@binlist,@base,@top,$numeric);
if ( ! $SCALE ) {
%BINS = ("Cambrian" => 4, "Ordovician" => 5, "Silurian" => 2, "Devonian" => 5, "Carboniferous" => 5, "Permian" => 4, "Triassic" => 4, "Jurassic" => 6, "Cretaceous" => 8, "Cenozoic" => 6);
for my $p ( "Cambrian", "Ordovician", "Silurian", "Devonian", "Carboniferous", "Permian", "Triassic", "Jurassic", "Cretaceous", "Cenozoic" ) {
for my $b ( 1..$BINS{$p} ) {
$nbin++;
$lookup{$p." ".$b} = $nbin;
my $i = $p;
if ( $i =~ /^C/ ) {
$i =~ s/Cambrian/Cm/;
$i =~ s/Carboniferous/C/;
$i =~ s/Cretaceous/K/;
$i =~ s/Cenozoic/Cz/;
} else {
$i =~ s/(.).*/$1/;
}
$binlist[$nbin] = $i.$b;
}
}
} elsif ( $SCALE !~ /stages|epochs|fr2|peters/i && $SCALE =~ /[A-Za-z].*[^0-9]/ ) {
open IN,"<./$SCALE";
while (<IN>) {
$nbin++;
}
close IN;
# assumes there is no header, columns are tab-delimited, the first
# column gives the base of the bin in Ma, and the second gives the
# bin name
my $id = $nbin;
open IN,"<./$SCALE";
while (<IN>) {
s/\n//;
my @words = split /\t/,$_;
$base[$id] = sprintf "%.3f",$words[0];
$top[$id-1] = $base[$id];
if ( $words[1] ) {
$binlist[$id] = $words[1];
} else {
$binlist[$id] = $nbin;
}
$id--;
}
close IN;
# rename the scale to allow tests for numeric values later
$SCALE = "custom";
} elsif ( $SCALE =~ /stages|epochs|fr2|peters/i ) {
if ( $SCALE =~ /stages/ ) {
open IN,"<./Gradstein_stages";
} elsif ( $SCALE =~ /epochs/ ) {
open IN,"<./Gradstein_subepochs";
} elsif ( $SCALE =~ /fr2/i ) {
open IN,"<./FR2_bins";
} elsif ( $SCALE =~ /peters/ ) {
open IN,"<./Peters_stages";
}
while (<IN>) {
s/\n//;
s/"//g;
$nbin++;
$lookup{$_} = $nbin;
$binlist[$nbin] = $_;
}
close IN;
# intervals are in reverse order
my @temp = @binlist;
for my $i ( 0..$#binlist ) {
$binlist[$i] = $temp[$nbin - $i + 1];
}
for my $b ( keys %lookup ) {
$lookup{$b} = $nbin - $lookup{$b} + 1;
}
} elsif ( $SCALE > 0 ) {
$numeric = 1;
$nbin = int( $MAXMA / $SCALE );
for my $i ( 1..$nbin ) {
$base[$nbin - $i + 1] = $i * $SCALE;
$top[$nbin - $i + 1] = ( $i - 1 ) * $SCALE;
$binlist[$nbin - $i + 1] = $i;
}
}
if ( ! @binlist ) {
print "\nExiting the scale '$SCALE' seems to be misformatted\n\n";
exit;
}
my (@shortnames,%maxma,%minma,$fref,%incoll,$totalcolls,$lastcoll,$totaloccs,$binnedcolls,%bincolls,%binoccs,%binabund,%bybin,%bybinref,%collfromref,%id,%idname,%allseen,%abund,%raw);
for my $file ( @FILES ) {
my $shortname = $file;
$shortname =~ s/\.(txt|csv|tab)//;
push @shortnames , $shortname;
if ( ! open IN,"<$PATH/$file" ) {
print "\nExiting because $file couldn't be found\n\n";
exit;
}
$_ = <IN>;
s/\n//;
my @f = split /,/,$_;
# coll no is column 0
my ($fgen,$fsp,$fabund,$fbin,$fbin2,$fmax,$fmin,$fextant);
for my $i ( 0..$#f ) {
if ( $f[$i] =~ /occurrence(|s).genus_name/ ) {
$fgen = $i;
} elsif ( $f[$i] =~ /occurrence(|s).species_reso/ ) {
$fspreso = $i;
} elsif ( $f[$i] =~ /occurrence(|s).species_name/ ) {
$fsp = $i;
} elsif ( $f[$i] =~ /occurrence(|s).abund_value/ ) {
$fabund = $i;
} elsif ( $f[$i] eq "stage" && ( $SCALE =~ /stages/i || $SCALE > 0 ) && $SCALE !~ /fr2|peters/i ) {
$fbin = $i;
} elsif ( $f[$i] eq "subepoch" && $SCALE =~ /epochs/i ) {
$fbin = $i;
} elsif ( $f[$i] eq "epoch" && $SCALE =~ /epochs/i ) {
$fbin2 = $i;
} elsif ( $f[$i] eq "FR2_bin" && $SCALE =~ /fr2/i ) {
$fbin = $i;
} elsif ( $f[$i] eq "Peters.interval" && $SCALE =~ /peters/i ) {
$fbin = $i;
} elsif ( $f[$i] eq "10_my_bin" && $SCALE !~ /stages|epochs|fr2|peters/i && $SCALE =~ /[^0-9]/ ) {
$fbin = $i;
} elsif ( $f[$i] eq "interpolated_base" && $INTERPOLATE =~ /y/i ) {
$fmax = $i;
} elsif ( $f[$i] eq "interpolated_top" && $INTERPOLATE =~ /y/i ) {
$fmin = $i;
} elsif ( $f[$i] =~ /(interval_base|ma_max|max_ma)$/ && $INTERPOLATE !~ /y/i ) {
$fmax = $i;
} elsif ( $f[$i] =~ /(interval_top|ma_min|min_ma)$/ && $INTERPOLATE !~ /y/i ) {
$fmin = $i;
} elsif ( $f[$i] =~ /collection(|s).reference_no/ ) {
$fref = $i;
} elsif ( $f[$i] eq $RANK."_extant" ) {
$fextant = $i;
}
}
if ( $RANK =~ /sp/i && ! $fsp ) {
print "\nExiting because $file doesn't have a species name field\n\n";
exit;
} elsif ( ( $SCALE > 0 || $SCALE eq "custom" ) && ! $fmax ) {
print "\nExiting because $file doesn't have a maximum estimate field\n\n";
exit;
} elsif ( ( $SCALE > 0 || $SCALE eq "custom" ) && ! $fmin ) {
print "\nExiting because $file doesn't have a minimum age estimate field\n\n";
exit;
} elsif ( $SCALE == 0 && $SCALE ne "custom" && ! $fbin ) {
print "\nExiting because $file doesn't have the right time scale field\n\n";
exit;
} elsif ( $fref == 0 && ( $COLLSPERREF > 0 || $REFQUOTA > 0 || $SEQUENTIAL =~ /y/i ) ) {
print "\nExiting because $file doesn't have a collection reference number field\n\n";
exit;
}
while (<IN>) {
s/\n//;
# a comma followed by a space is assumed to be embedded junk
$_ =~ s/, / /g;
my @f = split /,/,$_;
$f[$fbin] =~ s/"//g;
my $within = $lookup{$f[$fbin]};
if ( ! $within && $lookup{$f[$fbin2]} ) {
$within = $lookup{$f[$fbin2]};
}
if ( $SCALE > 0 || $SCALE eq "custom" ) {
my $range = $f[$fmax] - $f[$fmin];
$within = "";
for my $b ( 1..$nbin ) {
if ( $f[$fmax] eq "" ) {
last;
}
my ($upper,$lower) = ($f[$fmin],$f[$fmax]);
if ( $top[$b] > $f[$fmin] ) {
$upper = $top[$b];
}
if ( $base[$b] < $f[$fmax] ) {
$lower = $base[$b];
}
if ( $top[$b] <= $f[$fmin] && $base[$b] >= $f[$fmax] ) {
$within = $b;
last;
} elsif ( $DEORPHAN >= 0.5 && $lower - $upper >= $range * $DEORPHAN ) {
$within = $b;
last;
}
}
if ( $within ne "" ) {
if ( $f[$fbin] > 0 && $fbin > 0 ) {
$stageIn{$within}{$f[$fbin]}++;
}
}
} elsif ( $within && $f[$fmax] > 0 ) {
if ( $f[$fmax] > $maxma{$within} ) {
$maxma{$within} = $f[$fmax];
}
if ( $f[$fmin] > 0 && ( $f[$fmin] < $minma{$within} || $minma{$within} == 0 ) ) {
$minma{$within} = $f[$fmin];
}
}
$totaloccs++;
my $thiscoll = $f[0];
if ( $thiscoll != $lastcoll ) {
$totalcolls++;
}
# forces by-occurrence sampling
if ( $BYCOLLECTION =~ /n/i ) {
$f[0] = $totaloccs;
}
if ( $within > 0 && ( $ABUND !~ /y/i || $f[$abund] > 0 ) ) {
my $name = $f[$fgen];
if ( $RANK =~ /^s/i ) {
# knocks out sp. spp. indet. most informals
if ( $f[$fsp] =~ /[^a-z]/ || $f[$fspreso] =~ /inf/ ) {
next;
}
$name .= " ".$f[$fsp];
}
if ( $thiscoll != $lastcoll ) {
$bincolls{$within}++;
$binnedcolls++;
}
$incoll{$f[0]}++;
if ( $incoll{$f[0]} == 1 ) {
push @{$bybin{$within}} , $f[0];
push @{$bybinref{$within}{$f[$fref]}} , $f[0];
$collfromref{$f[0]} = $f[$fref];
}
if ( ! $id{$name} ) {
$ngen++;
$id{$name} = $ngen;
$idname{$ngen} = $name;
$infile{$ngen} = $shortname;
}
push @{$list{$f[0]}} , $id{$name};
$binoccs{$within}++;
if ( $ABUND =~ /y/i ) {
$abund{$f[0]}{$id{$name}} = $f[$fabund];
$binabund{$within} += $f[$fabund];
}
if ( ! $allseen{$name}{$within} ) {
$raw{$within}++;
$allseen{$name}{$within}++;
if ( ! $first{$name} || $within < $first{$name} ) {
$first{$name} = $within;
}
if ( ! $last{$name} || $within > $last{$name} ) {
$last{$name} = $within;
}
$extant{$name} = $f[$fextant];
}
}
$lastcoll = $thiscoll;
}
close IN;
}
print "\n";
if ( ! $fref ) {
print "Warning: because the file doesn't include reference numbers, Good's u will be\n based on taxa found in one collection instead of one reference\n\n";
}
print "full data set: $totalcolls collections and $totaloccs occurrences\n";
my $temp = 0;
$temp += $binoccs{$_} foreach keys %binoccs;
printf "binned data set: $binnedcolls collections and %d occurrences\n",$temp;
my (%refs,%refseen);
for my $bin ( reverse 1..$nbin ) {
my @byrefs = keys %{$bybinref{$bin}};
$refs{$bin} = $#byrefs + 1;
$refseen{$_}++ foreach keys %{$bybinref{$bin}};
}
if ( $fref > 0 ) {
my @temp = keys %refseen;
printf "binned data derive from %d references\n",$#temp+1;
}
my (%rawrt,%rawbc,%rawsingle,%gap,%notgap,%rawone,%rawtwo,%rawthree,%rawpart);
my $totalextant;
for my $g ( keys %first ) {
if ( $extant{$g} =~ /y/i ) {
$last{$g} = $nbin + 1; # bug fix
$allseen{$g}{$nbin+1}++; # new line
$totalextant++;
}
if ( $first{$g} == $last{$g} ) {
$rawsingle{$first{$g}}++;
}
for my $bin ( $first{$g}..$last{$g} ) {
$rawrt{$bin}++;
if ( $bin != $first{$g} ) {
$rawbc{$bin}++;
}
if ( $bin != $first{$g} && $bin != $last{$g} ) {
if ( ! $allseen{$g}{$bin} ) {
$gap{$bin}++;
} else {
$notgap{$bin}++;
}
}
if ( ! $allseen{$g}{$bin-1} && $allseen{$g}{$bin} && ! $allseen{$g}{$bin+1} ) {
$rawone{$bin}++;
} elsif ( $allseen{$g}{$bin-1} && $allseen{$g}{$bin} ) {
$rawtwo{$bin}++;
}
if ( $allseen{$g}{$bin-1} && $allseen{$g}{$bin} && $allseen{$g}{$bin+1} ) {
$rawthree{$bin}++;
} elsif ( $allseen{$g}{$bin-1} && ! $allseen{$g}{$bin} && $allseen{$g}{$bin+1} ) {
$rawpart{$bin}++;
}
# forward gap fillers
if ( $allseen{$g}{$bin-1} && $allseen{$g}{$bin} && ! $allseen{$g}{$bin+1} && $allseen{$g}{$bin+2} ) {
$rawXXOX{$bin}++;
} elsif ( $allseen{$g}{$bin-1} && ! $allseen{$g}{$bin} && ! $allseen{$g}{$bin+1} && $allseen{$g}{$bin+2} ) {
$rawXOOX{$bin}++;
}
# backward gap fillers
if ( $allseen{$g}{$bin-2} && ! $allseen{$g}{$bin-1} && $allseen{$g}{$bin} && $allseen{$g}{$bin+1} ) {
$rawXXOXb{$bin}++;
} elsif ( $allseen{$g}{$bin-2} && ! $allseen{$g}{$bin-1} && ! $allseen{$g}{$bin} && $allseen{$g}{$bin+1} ) {
$rawXOOXb{$bin}++;
}
}
}
$ranks = ( $RANK =~ /^s/i ) ? "species" : "genera";
if ( $totalextant > 0 ) {
print "$totalextant of the $ngen binned $ranks are extant\n\n";
} else {
print "none of the $ngen binned $ranks are extant\n\n";
}
my (%everdrawn,%everseen,%failed,%lastfailed,%collsused,%collsdrawn,%occsdrawn,%singledrawn,%subone,%subtwo,%maxgdrawn,%freq1,%freq2,%freq3,%freqmax,%ccurve,%atq,%bpdbybin);
$|=1;
print "trials: ";
for my $t ( 1..$TRIALS ) {
print "\rtrials: $t ";
my (%seen,%lastused,%usedintrial,%trialcolls,%genera);
for my $bin ( reverse 1..$nbin ) {
if ( $bincolls{$bin} >= $MINCOLLBYBIN && ( ! $failed{$bin} || $USEFAILED =~ /y/i ) ) {
my (@colls,%inref,%drawn,%drawnfromref);
my %collsinref = ();
for my $r ( keys %{$bybinref{$bin}} ) {
my $n = $#{$bybinref{$bin}{$r}} + 1;
$collsinref{$_} = $n foreach @{$bybinref{$bin}{$r}};
}
if ( ( $REFQUOTA > 0 || $SEQUENTIAL =~ /y/i ) && $refs{$bin} >= $REFQUOTA ) {
my @byrefs = keys %{$bybinref{$bin}};
my @subrefs = ();
my $myquota;
if ( $REFQUOTA > 0 ) {
$myquota = $REFQUOTA;
} else {
$myquota = $refs{$bin};
}
while ( $#subrefs + 1 < $myquota && $#byrefs > -1 ) {
my $i = int( rand( $#byrefs + 1 ) );
push @subrefs , $byrefs[$i];
splice @byrefs , $i , 1;
}
for my $s ( @subrefs ) {
my @temp = @{$bybinref{$bin}{$s}};
if ( $COLLSPERREF > 0 && scalar(@temp) >= $COLLSPERREF ) {
for my $i ( 1..$COLLSPERREF ) {
my $x = int( rand( $#temp + 1 ) );
push @colls , $temp[$x];
splice @temp , $x , 1;
}
} else {
push @colls , @temp;
}
for my $c ( @{$bybinref{$bin}{$s}} ) {
$inref{$_}{$s}++ foreach @{$list{$c}};
}
}
} elsif ( $COLLSPERREF > 0 ) {
for my $r ( keys %{$bybinref{$bin}} ) {
my @temp = @{$bybinref{$bin}{$r}};
if ( $COLLSPERREF > 0 && scalar(@temp) >= $COLLSPERREF ) {
for my $i ( 1..$COLLSPERREF ) {
my $x = int( rand( $#temp + 1 ) );
push @colls , $temp[$x];
splice @temp , $x , 1;
}
} else {
push @colls , @temp;
}
}
} else {
@colls = @{$bybin{$bin}};
for my $r ( keys %{$bybinref{$bin}} ) {
for my $c ( @{$bybinref{$bin}{$r}} ) {
$inref{$_}{$r}++ foreach @{$list{$c}};
}
}
}
# these variables need to be recomputed during
# every trial because of the REFQUOTA algorithm
@{$trialcolls{$bin}} = @colls;
my $nocc = 0;
my $ncoll = $#colls + 1;
my %freq = ();
for my $c ( @colls ) {
if ( $ABUND =~ /y/i ) {
$nocc += $abund{$c}{$_} foreach @{$list{$c}};
$freq{$_} += $abund{$c}{$_} foreach @{$list{$c}};
} else {
$nocc += $#{$list{$c}} + 1;
$freq{$_}++ foreach @{$list{$c}};
}
}
my ($maxocc,$maxc,$maxg) = (0,0,"");
for my $g ( keys %freq ) {
if ( $freq{$g} == 1 ) {
$freq1{$bin}[$t]++;
} elsif ( $freq{$g} == 2 ) {
$freq2{$bin}[$t]++;
} elsif ( $freq{$g} == 3 ) {
$freq3{$bin}[$t]++;
}
}
# classical rarefaction of occurrences
if ( $METHOD eq "CR" ) {
my @occs = ();
for my $c ( @colls ) {
if ( $ABUND =~ /y/i ) {
for my $g ( @{$list{$c}} ) {
for my $i ( 1..int($abund{$c}{$g}) ) {
push @occs , $g;
}
}
} else {
push @occs , $_ foreach @{$list{$c}};
}
}
if ( $#occs + 1 >= $QUOTA ) {
for $q ( 1..$QUOTA ) {
my $i = int( rand( $#occs + 1 ) );
my $g = $occs[$i];
splice @occs , $i , 1;
$drawn{$g}++;
$everdrawn{$idname{$g}}{$bin}++;
$occsdrawn{$bin}[$t]++;
my @temp = keys %drawn;
$ccurve{$bin}{$q} += $#temp + 1;
$atq{$bin}{$q}++;
}
} else {
$failed{$bin}++;
$lastfailed{$bin} = $t;
%drawn = ();
}
push @{$genera{$bin}} , $_ foreach keys %drawn;
# unweighted list subsampling
} elsif ( $METHOD eq "UW" ) {
for $q ( 1..$QUOTA ) {
if ( $#colls == -1 ) {
$failed{$bin}++;
$lastfailed{$bin} = $t;
%drawn = ();
last;
}
my $c = int( rand( $#colls + 1 ) );
$drawn{$_}++ foreach @{$list{$colls[$c]}};
$everdrawn{$idname{$_}}{$bin}++ foreach @{$list{$colls[$c]}};
$collsdrawn{$bin}[$t]++;
$occsdrawn{$bin}[$t] += $#{$list{$colls[$c]}};
splice @colls , $c , 1;
my @temp = keys %drawn;
$ccurve{$bin}{$q} += $#temp + 1;
$atq{$bin}{$q}++;
}
push @{$genera{$bin}} , $_ foreach keys %drawn;
# occurrences squared-weighted list subsampling
} elsif ( $METHOD eq "O2W" ) {
my $sumo2 = 0;
while ( $sumo2 < $QUOTA ) {
if ( $#colls == -1 ) {
$failed{$bin}++;
$lastfailed{$bin} = $t;
%drawn = ();
last;
}
my $c = int( rand( $#colls + 1 ) );
my $o2 = ( $#{$list{$colls[$c]}} + 1 )**2;
if ( $o2 + $sumo2 > $QUOTA && $o2 + $sumo2 - $QUOTA > $QUOTA - $sumo2 ) {
last;
}
$drawn{$_}++ foreach @{$list{$colls[$c]}};
$everdrawn{$idname{$_}}{$bin}++ foreach @{$list{$colls[$c]}};
$collsdrawn{$bin}[$t]++;
$occsdrawn{$bin}[$t] += $#{$list{$colls[$c]}};
$sumo2 += $o2;
splice @colls , $c , 1;
}
push @{$genera{$bin}} , $_ foreach keys %drawn;
# default is SQS
} else {
# SQS requires at least two collections
if ( $bincolls{$bin} < 2 ) {
next;
}
my ($notDominant,$singletons,$doubletons,$bpd) = (0,0,0,0);
my ($maxocc,$maxc,$maxg) = (0,0,"");
for my $c ( @colls ) {
if ( $#{$list{$c}} + 1 > $maxocc ) {
$maxocc = $#{$list{$c}} + 1;
$maxc = $c;
}
}
# treat singletons appearing in the largest collection
# as non-singletons
my %inmax = ();
if ( $BIGGEST =~ /y/i ) {
for my $g ( @{$list{$maxc}} ) {
$inmax{$g}++;
}
}
# count singletons and doubletons and identify dominant
delete $freq{''};
my %thisfreq;
for my $g ( keys %freq ) {
$notDominant++;
my @refs = keys %{$inref{$g}};
$thisfreq{$g} = $#refs + 1;
if ( $SINGLETONS !~ /ref/i ) {
$thisfreq{$g} = $freq{$g};
}
if ( $thisfreq{$g} > 1 || $inmax{$g} > 0 ) {
if ( $thisfreq{$g} == 2 ) {
$doubletons++;
}
if ( $freq{$g} / $nocc > $bpd ) {
$bpd = $freq{$g} / $nocc;
$maxg = $g;
}
} else {
$singletons++;
}
}
# include most common (dominant) taxon
if ( $EXCLUDE !~ /y/i ) {
$maxg = "";
} else {
$notDominant--;
if ( $thisfreq{$maxg} == 2 ) {
$doubletons--;
}
}
$freqmax{$bin} = $freq{$maxg};
$bpdbybin{$bin} += $bpd;
# exact SQS algorithm that requires sampling all
# occurrences and counting taxa at quorum level(s)
if ( $EXACT !~ /n/i ) {
my (@temp,@pool,%freqnow,%firstseen,%hitat,@drawnfrom,$lastfrom,$collsnow,$occsnow,$maxnow,$allnow,$singlenow,@fromnow,@subnow,$u,$lastu,$occsdrawn);
# if SEQUENTIAL is true the collections are
# already in random order (and clustered by
# reference)
# if not, randomize them here
if ( $SEQUENTIAL !~ /y/i ) {
my @temp;
while ( @colls ) {
my $x = int( rand( $#colls + 1 ) );
push @temp, ( splice @colls , $x , 1 );
}
@colls = @temp;
}
# randomize occurrences within collections
# one way or another
for my $c ( @colls ) {
my @temp = @{$list{$c}};
while ( @temp ) {
my $x = int( rand( $#temp + 1 ) );
push @pool , splice( @temp , $x , 1 );
push @drawnfrom , $c;
}
}
while ( @pool ) {
my $g = shift @pool;
my $from = shift @drawnfrom;
if ( $from != $lastfrom ) {
$lastfrom = $from;
$collsnow++;
}
$freqnow{$g}++;
$occsnow++;
if ( $g eq $maxg ) {
$maxnow++;
}
push @{$hitat{$g}} , $occsnow;
if ( $freqnow{$g} == 1 ) {
$allnow++;
if ( ( $inmax{$g} == 0 || $freq{$g} > 1 ) && $g ne $maxg ) {
$singlenow++;
}
$firstseen{$g} = $occsnow;
} elsif ( $freqnow{$g} == 2 && ( $inmax{$g} == 0 || $freq{$g} > 1 ) && $g ne $maxg ) {
$singlenow--;
}
$u = 0;
if ( $occsnow > $maxnow ) {
$u = 1 - $singlenow / ( $occsnow - $maxnow );
}
if ( $TRIALS <= 100 ) {
push @{$uyielding[$bin][$allnow]} , $u;
$didyield[$bin][$allnow]{$t}++;
}
if ( $allnow > $maxyielding ) {
$maxyielding = $allnow;
}
# record current diversity
# the last draw couldn't have been a singleton,
# so diversity couldn't have changed
# record each sample size at which the quorum
# is exceeded
if ( $u >= $QUORUM && $lastu < $QUORUM ) {
push @fromnow , $collsnow;
push @subnow , $occsnow;
}
$lastu = $u;
}
# identify taxa that were drawn before or at
# the median occurrence count yielding a quorum
if ( @subnow ) {
my ($i,$j) = ( int ( $#subnow / 2 ),int( ( $#subnow + 1 ) / 2 ) );
$occsdrawn{$bin}[$t] = ( $subnow[$i] + $subnow[$j] ) / 2;
$collsdrawn{$bin}[$t] = ( $fromnow[$i] + $fromnow[$j] ) / 2;
my $o = int( $occsdrawn{$bin}[$t] );
for my $g ( keys %firstseen ) {
if ( $firstseen{$g} <= $o ) {
# compute the number of times each taxon was
# drawn in order to identify the dominant in
# the subsample
my @temp = @{$hitat{$g}};
while ( $temp[$#temp] > $o ) {
pop @temp;
}
$drawn{$g} = $#temp + 1;
$everdrawn{$idname{$g}}{$bin} += $#temp + 1;
}
}
} else {
$failed{$bin}++;
$lastfailed{$bin} = $t;
$maxbybin{$bin} -= $maxsum;
$bpdbybin{$bin} -= $bpd;
if ( $USEFAILED =~ /y/i ) {
%drawn = %freqnow;
} else {
$occsdrawn{$bin}[$t] = -1;
}
}
}
# inexact SQS algorithm employing estimated frequencies
# NOTE: Good's u sensu stricto isn't used here at all
# because the correction factor is subtracted from the
# frequencies instead of multiplied by them, and the
# equation's numerator and denominator are both
# different; the former involves the doubleton counts
# and the latter is the number of genera and not of
# occurrences
else {
my $correction;
if ( $notDominant > 0 ) {
$correction = ( $singletons + $doubletons / 2 ) / $notDominant;
} else {
$failed{$bin}++;
$lastfailed{$bin} = $t;
}
my %prop = ();
my $maxsum = 0;
if ( $nocc > $freq{$maxg} ) {
$prop{$_} = ( $freq{$_} - $correction ) / ( $nocc - $freq{$maxg} ) foreach keys %freq;
delete $prop{$maxg};
$maxsum += $prop{$_} foreach keys %prop;
}
$maxbybin{$bin} += $maxsum;
my ($sumprop,$stopped) = (0,0);
while ( $sumprop < $QUORUM ) {
if ( $#colls == -1 || $nocc - $freq{$maxg} < 1 ) {
$failed{$bin}++;
$lastfailed{$bin} = $t;
$maxbybin{$bin} -= $maxsum;
$bpdbybin{$bin} -= $bpd;
last;
}
my $c = -1;
# draw collections with a probability inversely
# proportional to the number of collections
# per reference
if ( $DISPERSE =~ /y/i && $SEQUENTIAL !~ /y/i ) {
while ( $c == -1 ) {
$c = int( rand( $#colls + 1 ) );
if ( rand() > 1 / $collsinref{$colls[$c]} ) {
$c = -1;
}
}
}
# draw all collections in a given reference
# before going to the next one
# the collections were grouped by reference
# earlier in the reference randomization
# section, so simply draw them in order
elsif ( $SEQUENTIAL =~ /y/i ) {
$c = 0;
}
# conventional algorithm ignoring references
else {
$c = int( rand( $#colls + 1 ) );
}
my $fromcoll = 0;
for my $g ( @{$list{$colls[$c]}} ) {
if ( ! $drawn{$g} && $g ne $maxg ) {
$sumprop += $prop{$g};
if ( $sumprop >= $QUORUM ) {
$stopped++;
}
}
$drawn{$g}++;
$everdrawn{$idname{$g}}{$bin}++;
$drawnfromref{$g}{$collfromref{$colls[$c]}}++;
# random throwback algorithm
if ( rand() > $prop{$g} && $sumprop >= $QUORUM ) {
$sumprop -= $prop{$g};
$everdrawn{$idname{$g}}{$bin} -= $drawn{$g};
delete $drawn{$g};
delete $drawnfromref{$g};
} else {
if ( $ABUND =~ /y/i ) {
$occsdrawn{$bin}[$t] += $abund{$colls[$c]}{$g};
} else {
$occsdrawn{$bin}[$t]++;
}
$fromcoll++;
}
if ( $stopped > 0 ) {
last;
}
}
if ( $fromcoll > 0 ) {
$collsdrawn{$bin}[$t]++;
}
if ( $stopped > 0 ) {
last;
}
splice @colls , $c , 1;
}
}
for my $g ( keys %drawn ) {
push @{$genera{$bin}} , $g;
my @refs = keys %{$drawnfromref{$g}};
my $thisfreq = $#refs + 1;
if ( $SINGLETONS !~ /ref/i ) {
$thisfreq = $drawn{$g};
}
if ( $thisfreq == 1 && $g ne $maxg && ( $inmax{$g} == 0 || $freq{$g} > 1 ) ) {
$singledrawn{$bin}[$t] += $drawn{$g};
}
if ( $drawn{$g} == 1 ) {
$subone{$bin}[$t]++;
} elsif ( $drawn{$g} == 2 ) {
$subtwo{$bin}[$t]++;
}
}
$maxgdrawn{$bin}[$t] = $drawn{$maxg};
}
}
}
# compute tallies for this trial
my (%first,%last);
for my $g ( keys %extant ) {
if ( $extant{$g} =~ /y/i ) {
$last{$id{$g}} = $nbin + 1;
$seen{$nbin+1}{$id{$g}}++;
}
}
for my $bin ( reverse 1..$nbin ) {
if ( $bincolls{$bin} >= $MINCOLLBYBIN && ( $lastfailed{$bin} != $t || ! $failed{$bin} || $USEFAILED =~ /y/i ) ) {
for my $c ( @{$trialcolls{$bin}} ) {
$collsused{$bin}++;
for my $g ( @{$list{$c}} ) {
if ( $lastused{$g} != $bin ) {
$genused{$bin}++;
$usedintrial{$bin}++;
$lastused{$g} = $bin;
}
}
}
for my $g ( @{$genera{$bin}} ) {
if ( $g > 0 && ! $seen{$bin}{$g} ) {
$sib{$bin}[$t]++;
$byfile{$bin}{$infile{$g}}++;
$first{$g} = $bin;
if ( $last{$g} eq "" ) {
$last{$g} = $bin;
}
}
if ( $g > 0 && ! $seen{$bin}{$g} && $lastfailed{$bin+1} != $t && $lastfailed{$bin+2} != $t ) {
if ( $seen{$bin+1}{$g} ) {
$two{$bin+1}[$t]++;
}
if ( $seen{$bin+1}{$g} && $seen{$bin+2}{$g} ) {
$three{$bin+1}[$t]++;
$sumthree++;
$binsumthree{$bin+1}++;
} elsif ( ! $seen{$bin+1}{$g} && $seen{$bin+2}{$g} ) {
$part{$bin+1}[$t]++;
$sumpart++;
$binsumpart{$bin+1}++;
}
# forward gap fillers
if ( $seen{$bin+1}{$g} && ! $seen{$bin+2}{$g} && $seen{$bin+3}{$g} ) {
$XXOX{$bin+1}[$t]++;
} elsif ( ! $seen{$bin+1}{$g} && ! $seen{$bin+2}{$g} && $seen{$bin+3}{$g} ) {
$XOOX{$bin+1}[$t]++;
}
# backward gap fillers
if ( ! $seen{$bin+1}{$g} && $seen{$bin+2}{$g} && $seen{$bin+3}{$g} ) {
$XXOXb{$bin+2}[$t]++;
} elsif ( ! $seen{$bin+1}{$g} && ! $seen{$bin+2}{$g} && $seen{$bin+3}{$g} ) {
$XOOXb{$bin+2}[$t]++;
}
}
$seen{$bin}{$g}++;
$everseen{$idname{$g}}{$bin}++;
}
for my $g ( keys %{$seen{$bin+1}} ) {
if ( ! $seen{$bin}{$g} && ! $seen{$bin+2}{$g} ) {
$one{$bin+1}[$t]++;
}
}
} else {
$collsdrawn{$bin}[$t] = -1;
$occsdrawn{$bin}[$t] = -1;
$freq1{$bin}[$t] = -1;
$freq2{$bin}[$t] = -1;
$freq3{$bin}[$t] = -1;
$sib{$bin}[$t] = -1;
$one{$bin+1}[$t] = -1;
$two{$bin+1}[$t] = -1;
$three{$bin+1}[$t] = -1;
$sumthree -= $binsumthree{$bin+1};
$part{$bin+1}[$t] = -1;
$sumpart -= $binsumpart{$bin+1};
($XXOX{$bin+1}[$t],$XOOX{$bin+1}[$t],$XXOXb{$bin+1}[$t],$XOOXb{$bin+1}[$t]) = (-1,-1,-1,-1);
($rt{$bin}[$t],$bc{$bin}[$t],$single{$bin}[$t]) = (-1,-1,-1);
$singledrawn{$bin}[$t] = -1;
$subone{$bin}[$t] = -1;
$subtwo{$bin}[$t] = -1;
$maxgdrawn{$bin}[$t] = -1;
}
if ( $lastfailed{$bin} == $t ) {
my %freq;
for my $c ( @{$bybin{$bin}} ) {
$freq{$_}++ foreach @{$list{$c}};
}
}
}
for my $g ( keys %first ) {
for my $bin ( $first{$g}..$last{$g} ) {
$rt{$bin}[$t]++;
}
if ( $first{$g} == $last{$g} ) {
$single{$first{$g}}[$t]++;
} else {
for my $bin ( $first{$g}+1..$last{$g} ) {
$bc{$bin}[$t]++;
}
}
}
}
print "\n";
my ($firstbin,$lastbin) = ($nbin,1);
if ( $TRIM =~ /y/i ) {
($firstbin,$lastbin) = ("","");
for $b ( reverse 1..$nbin ) {
if ( $bincolls{$b} >= $MINCOLLBYBIN && ( $failed{$b} < $TRIALS || $USEFAILED =~ /y/i ) ) {
if ( ! $firstbin ) {
$firstbin = $lastbin;
}
$lastbin = $b;
}
}
if ( ! $firstbin ) {
$firstbin = $lastbin;
}
}
if ( $METHOD =~ /CR|UW/ ) {