Re: Code Problem

The first reason is because this loop is never entered:

while( $mutrate - 0.01 > $DBL_EPSILON ){
[download]

So the ends without ever executing your print statement.

The reason the loop is never entered is because this condition: $mutrate - 0.01 > $DBL_EPSILON is always false.

You are setting $DBL_EPSILON to $e = 1:

my $DBL_EPSILON = $e =1; $e /= 2 while $e /2 +1 > 1;
[download]

Which means that unless $mutrate is greater than 1.1 when you reach the loop; you're never going to enter the loop and thus never going to print anything.

I can only guess what value you actually wanted to set $DBL_EPSILON to, so I won't try.

Also, this: if ($matrix[$i][$j] =~ /[^0.00]/){ isn't doing what you want it to either.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

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Re^2: Code Problem by madM (Beadle) on Aug 10, 2013 at 11:46 UTC
Hi! Thanks.. i made some corrections now and the loop is getting started but i dont get the results i expect. I´m actually trying to translate this Darwin code: Any suggestions? Thanks a lot again! PAM1 := MutationMatrix: lnPAM1 := ln(MutationMatrix): k := 1: RateMutation := sum(Freq[i] * (1 - PAM1[i,i]), i= 1..20): iter := 0: # The following loop goes until the difference reach the computer's # precision. while abs(RateMutation - 0.01) > DBL_EPSILON do iter := iter + 1; k:= k * RateMutation * 100: lnPAM1 := lnPAM1 / (RateMutation * 100): PAM1 := exp(lnPAM1): RateMutation := sum(Freq[i] * (1 - PAM1[i,i]), i= 1..20); printf('After %d iteration(s), k=%f, RateMutation=%f ', iter, k, RateMutation); od: [download] And the outcome i expect is this: `After 1 iteration(s), k=44.530219, RateMutation=0.014324 After 2 iteration(s), k=63.785069, RateMutation=0.010027 After 3 iteration(s), k=63.959878, RateMutation=0.010000 After 4 iteration(s), k=63.960985, RateMutation=0.010000 After 5 iteration(s), k=63.960992, RateMutation=0.010000 After 6 iteration(s), k=63.960992, RateMutation=0.010000 After 7 iteration(s), k=63.960992, RateMutation=0.010000 After 8 iteration(s), k=63.960992, RateMutation=0.010000` [download] my @matrix =( [0.54, 0.03, 0.03, 0.03, 0.08, 0.04, 0.05, 0.05, 0.02, 0.02, 0.03, 0.0 +4, 0.03, 0.01, 0.06, 0.11, 0.06, 0.01, 0.01,0.06], [0.02, 0.57, 0.03, 0.01, 0.02, 0.06, 0.03, 0.01, 0.04, 0.01, 0.01, 0.1 +1, 0.02, 0.01, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01], [0.01, 0.02, 0.48, 0.06, 0.01, 0.03, 0.03, 0.03, 0.05, 0.01, 0.01, 0.0 +3, 0.01, 0.00, 0.01, 0.04, 0.03, 0.00, 0.02, 0.01], [0.02, 0.01, 0.09, 0.57, 0.01, 0.04, 0.11, 0.02, 0.03, 0.00, 0.00, 0.0 +3, 0.01, 0.00, 0.02, 0.04, 0.02, 0.00, 0.01, 0.00], [0.01, 0.00, 0.00, 0.00, 0.57, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.0 +0, 0.00, 0.01, 0.00, 0.01, 0.01, 0.01, 0.01, 0.01], [0.02, 0.04, 0.03, 0.02, 0.01, 0.42, 0.05, 0.01, 0.04, 0.01, 0.01, 0.0 +5, 0.02, 0.00, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01], [0.04, 0.04, 0.05, 0.13, 0.01, 0.11, 0.52, 0.02, 0.03, 0.01, 0.01, 0.0 +7, 0.01, 0.00, 0.02, 0.04, 0.04, 0.01, 0.01, 0.01], [0.05, 0.02, 0.05, 0.03, 0.02, 0.02, 0.02, 0.77, 0.02, 0.00, 0.00, 0.0 +2, 0.01, 0.00, 0.01, 0.04, 0.01, 0.01, 0.00, 0.01], [0.01, 0.01, 0.02, 0.01, 0.01, 0.02, 0.01, 0.00, 0.54, 0.00, 0.00, 0.0 +1, 0.01, 0.02, 0.01, 0.01, 0.01, 0.02, 0.04, 0.00], [0.02, 0.01, 0.01, 0.00, 0.03, 0.01, 0.01, 0.00, 0.01, 0.50, 0.10, 0.0 +1, 0.09, 0.04, 0.01, 0.01, 0.03, 0.02, 0.01, 0.18], [0.03, 0.02, 0.01, 0.01, 0.03, 0.03, 0.01, 0.00, 0.02, 0.13, 0.60, 0.0 +2, 0.19, 0.09, 0.02, 0.02, 0.02, 0.02, 0.03, 0.08], [0.03, 0.14, 0.06, 0.03, 0.01, 0.09, 0.06, 0.02, 0.05, 0.01, 0.01, 0.5 +0, 0.02, 0.01, 0.02, 0.04, 0.03, 0.01, 0.01, 0.01], [0.01, 0.01, 0.00, 0.00, 0.01, 0.02, 0.00, 0.00, 0.01, 0.03, 0.05, 0.0 +1, 0.42, 0.02, 0.00, 0.01, 0.01, 0.01, 0.01, 0.02], [0.01, 0.01, 0.00, 0.00, 0.02, 0.01, 0.00, 0.00, 0.03, 0.02, 0.04, 0.0 +0, 0.04, 0.61, 0.00, 0.01, 0.01, 0.07, 0.14, 0.01], [0.03, 0.01, 0.01, 0.01, 0.00, 0.01, 0.01, 0.01, 0.02, 0.00, 0.01, 0.0 +1, 0.01, 0.00, 0.72, 0.03, 0.01, 0.00, 0.00, 0.01], [0.07, 0.03, 0.06, 0.04, 0.05, 0.04, 0.03, 0.03, 0.02, 0.01, 0.01, 0.0 +4, 0.02, 0.01, 0.04, 0.43, 0.09, 0.02, 0.01, 0.01], [0.04, 0.02, 0.04, 0.02, 0.04, 0.03, 0.03, 0.01, 0.02, 0.02, 0.02, 0.0 +3, 0.03, 0.01, 0.02, 0.09, 0.52, 0.01, 0.01, 0.04], [0.00, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.0 +0, 0.00, 0.02, 0.00, 0.00, 0.00, 0.71, 0.02, 0.00], [0.00, 0.01, 0.01, 0.00, 0.01, 0.01, 0.00, 0.00, 0.05, 0.01, 0.01, 0.0 +1, 0.01, 0.10, 0.00, 0.01, 0.01, 0.06, 0.61, 0.01], [0.05, 0.01, 0.01, 0.01, 0.07, 0.02, 0.02, 0.01, 0.01, 0.20, 0.07, 0.0 +1, 0.06, 0.03, 0.01, 0.02, 0.06, 0.02, 0.02, 0.51]); my @frequency = ([0.08477395, 0.05103334, 0.03837665, 0.05740129, 0.01 +256165, 0.03471746, 0.06883297, 0.07907659, 0.02077239, 0.06813598, 0.08906677, 0.06501537 +, 0.02318017, 0.03823936, 0.04036729, 0.05668318, 0.05721648, 0.00871765 +, 0.02785317, 0.07797831]); my $mutrate=0; my $matrix2={}; my $e; $e=1;$e/=2 while $e/2+1>1; my @PAM1= @matrix; my @lnPAM1=(); LINE: for (my $i=0; $i<20; $i++){ for (my $j=0; $j<20; $j++){ if ($matrix[$i][$j] > 0){ $lnPAM1[$i][$j] = log $matrix[$i][$j]; }else{ next LINE; } } } for (my $i=0; $i<20; $i++){ $mutrate += $frequency[0][$i](1-$matrix[$i][$i]); } my $k=1; my $iter = 0; while (($mutrate-0.01) > $e){ $iter++; $k= $k $mutrate * 100; for (my $i=0; $i<20; $i++){ for (my $j=0; $j<20; $j++){ $lnPAM1[$i][$j] = $lnPAM1[$i][$j]/($mutrate * 100); $PAM1[$i][$j]=exp($lnPAM1[$i][$j]); $mutrate += $frequency[0][$i]*(1-$PAM1[$i][$i]); } } print " iteration: $iter, k: $k, MutationRate:$mutrate\n"; } [download]	[reply] [d/l] [select]
Re^3: Code Problem by BrowserUk (Patriarch) on Aug 10, 2013 at 13:18 UTC
Where does Freq[] come from in the Darwin code? With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply]
Re^4: Code Problem by madM (Beadle) on Aug 10, 2013 at 13:35 UTC
I calculated it before but here´s the darwin code for that `Freq := CreateArray(1..20,0): Tot := sum(sum(CountMatrix)): for i to 20 do Freq[i] := sum(CountMatrix[i])/Tot: od: print(Freq); [0.08477395, 0.05103334, 0.03837665, 0.05740129, 0.01256165, 0.0347174 +6, 0.06883297, 0.07907659, 0.02077239, 0.06813598, 0.08906677, 0.06501537 +, 0.02318017, 0.03823936, 0.04036729, 0.05668318, 0.05721648, 0.00871765 +, 0.02785317, 0.07797831] PercentageMutation := 100 * sum(Freq[i] * (1 - MutationMatrix[i,i]),i= +1..20); PercentageMutation := 44.5302` [download] And the Mutationmatrix is the matrix i wrote in the Perl Code	[reply] [d/l]
Re^5: Code Problem by BrowserUk (Patriarch) on Aug 10, 2013 at 13:45 UTC