|
The primary analysis of the inter-egg correlations is accomplished with several
scripts written by Doug Mast.
This page documents the scripts and provides access to the actual code that
implements the intended analysis, allowing completely unambiguous interpretation.
The scripts may be used by anyone who wishes to perform similar or related
analyses.
README -- Doug's notes on what the files contain
These are the scripts used in my initial inter-egg correlation study. The
contents of each file are as follows:
pcint (Mathematica) --- script that computes correlation-coefficient
thresholds for each significance level.
readegg.m (Matlab) --- downloads ASCII data from noosphere with wget,
computes correlations for a single day, and
stores summarized results. called from Matlab by
readegg(month, day, year, controlflag), where
controlflag is 0 for synchronous, 1 for my original
control, and 2 (or anything else) for my second
control. the two controls use different random seeds.
parseegg.sed --- sed commands used within readegg.m to translate the
ASCII data from noosphere into Matlab-readable form.
readeggmult.m --- matlab script to call readegg.m for multiple days
summarizeegg.m --- matlab script to sum stored results for all days
(need to change a flag to do summary for control #2).
eggintsk.nb --- Mathematica notebook file that computes p-values for
the summarized results. (includes results)
FWIW, I used Matlab 5.2, Mathematica 3.0, GNU sed 3.02, and GNU wget 1.5.3,
all running on Linux/Intel.
All of the files are fairly ugly, and the integration is poor---I'd call
them "research quality" rather than "production quality" code. Feel free to
run these programs, ask questions, find bugs, make improvements, etc. etc.
Doug Mast (mast@sabine.acs.psu.edu)
State College, PA
April 22, 2000
readegg.m
function readegg(month,day,year,controlflag);
cd /home/work3/egg;
dateint=month*1e6+day*1e4+year;
% only download data for synchronous runs (always do synchronous runs
% before control runs!)
if(controlflag~=1)
eval(['!wget -O eggdata.raw
"http://teilhard.global-mind.org/cgi-bin/eggdatareq.p
l?month=' num2str(month) '&year=' num2str(year) '&day=' num2str(day)
'&stime=00:
00:00&etime=23:59:59&gzip=no&idate=no"']);
eval(['!sed -f parseegg.sed eggdata.raw > eggdata.cooked']);
end
load eggdata.cooked;
eggvec=eggdata(1,:) % vector with egg numbers for each data column
colstart=4; % first three data columns are bookkeeping info
colstop=size(eggdata,2);
n=colstop-colstart+1;
if(controlflag==1)
rand('state',dateint); % for reproducibility, seed Matlab's pseudo-RNG
% with date in integer form
else
rand('state',floor(dateint/277));
end
% rsig(X) is Pearson correlation coefficient for confidence level 10^(-X)
nsiglevel=8;
rsig(1)=0.1678015; rsig(2)=0.2996953;
rsig(3)=0.3911500; rsig(4)=0.4623388;
rsig(5)=0.5206954; rsig(6)=0.5699623;
rsig(7)=0.6123520; rsig(8)=0.6493093;
sigrec=zeros(colstop,colstop,nsiglevel+1); % store who correlates with whom
nsamp=60;
ntry=0;
for i=1:nsiglevel
nsig(i)=0;
end
numruns=24*3600/nsamp;
nsec=nsamp*numruns;
for irun=1:numruns
istart=(irun-1)*nsamp+2;
istop=istart+nsamp-1;
% for regular runs, correlate with signals at same time; for control runs,
% correlate with signals having random offsets
if (controlflag>=1)
jstart=round(rand(1)*(nsec-nsamp))+2;
jstop=jstart+nsamp-1;
else
jstart=istart;
jstop=istop;
end
for i=colstart:colstop
itmp=i-colstart+1;
isig=eggdata(istart:istop,i);
for j=colstart:i-1
jtmp=j-colstart+1;
jsig=eggdata(jstart:jstop,j);
if((max(isig)<200) & (max(jsig)<200))
rtmp=pearsonr(isig,jsig);
ntry=ntry+1;
sigrec(i,j,nsiglevel+1)=sigrec(i,j,nsiglevel+1)+1;
% sigrec(i,j,nsiglevel+1) = number
else % of tries for egg pair (i,j)
rtmp=0;
end
for isiglevel=nsiglevel:-1:1
if (rtmp > rsig(isiglevel))
nsig(isiglevel)=nsig(isiglevel)+1;
sigrec(i,j,isiglevel)=sigrec(i,j,isiglevel)+1;
end
end
end
end
ntry
nsig % view correlations as they accumulate
end
% write significance results to a file labeled by date and controlflag
filenameout=['results/results.' num2str(day) '-' num2str(month) '-'
num2str(year
) '.' num2str(controlflag) ];
fp=fopen(filenameout,'w');
fprintf(fp,'%d %d\n',dateint, nsamp);
fprintf(fp,'%d %d\n',controlflag, ntry);
for isiglevel=1:nsiglevel
fprintf(fp,'%d %g\n',nsig(isiglevel), nsig(isiglevel)/ntry);
end
fclose(fp);
% also write a file saying who correlated with whom
filenameout=['results/sigrec.' num2str(day) '-' num2str(month) '-'
num2str(year)
'.' num2str(controlflag)];
fp=fopen(filenameout,'w');
for i=colstart:n
for j=colstart:i-1
fprintf(fp,'\n%d %d %d ',eggvec(i),eggvec(j),sigrec(i,j,nsiglevel+1));
for isiglevel=1:nsiglevel
fprintf(fp,'%d ',sigrec(i,j,isiglevel));
end
end
end
fclose(fp);
readeggmult.m
year=1999;
monthlength=[31; 28; 31; 30; 31; 30; 31; 31; 30; 31; 30; 31];
for month=1:12
for day=1:monthlength(month)
readegg(month,day,year,0);
readegg(month,day,year,1);
readegg(month,day,year,2);
end
end
summarizeegg.m
clear;
cd /home/work3/egg;
year=1999;
monthstart=[1;1;1;1;1;1;1;1;1;1;1;1];
monthlength=[31; 28; 31; 30; 31; 30; 31; 31; 30; 31; 30; 31];
nsiglevel=8;
ntry=0;
ntrycontrol=0;
nsig=zeros(1,nsiglevel);
nsigcontrol=zeros(1,nsiglevel);
for month=1:2
for day=1:monthlength(month)
controlflag=0;
filenamein=['results/results.' num2str(day) '-' num2str(month) '-'
num2str(ye
ar) '.' num2str(controlflag)];
eval(['load ' filenamein]);
ntry=ntry+results(2,2);
for siglevel=1:nsiglevel
nsig(siglevel)=nsig(siglevel)+results(siglevel+2,1);
end
controlflag=1;
filenamein=['results/results.' num2str(day) '-' num2str(month) '-'
num2str(ye
ar) '.' num2str(controlflag) ];
eval(['load ' filenamein]);
ntrycontrol=ntrycontrol+results(2,2);
for siglevel=1:nsiglevel
nsigcontrol(siglevel)=nsigcontrol(siglevel)+results(siglevel+2,1);
end
end
end
ntry
nsig
ntrycontrol
nsigcontrol
syncresults=nsig/ntry.*[1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10]
controlresults=nsigcontrol/ntrycontrol.*[1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10]
parseegg.sed
1,8d
s/"gmtime"/ 888 /g
s/,,,,$/ 999 999 999 999 /g
s/,,,$/ 999 999 999 /g
s/,,$/ 999 999 /g
s/,$/ 999 /g
s/,,,,,/ 999 999 999 999 /g
s/,,,,/ 999 999 999 /g
s/,,,/ 999 999 /g
s/,,/ 999 /g
s/,/ /g
pcint
nu=n-2;
pr=1/Sqrt[Pi] Gamma[(nu+1)/2]/Gamma[nu/2] (1-x^2)^(0.5(nu-2));
pc[n_,r_]=Integrate[pr,{x,r,1}];
x8 = x /. N[FindRoot[10^8 pc[60,x]==1,{x,.64,.66}, MaxIterations -> 10000],7]
x7 = x /. N[FindRoot[10^7 pc[60,x]==1,{x,.61,.62}, MaxIterations -> 10000],7]
x6 = x /. N[FindRoot[10^6 pc[60,x]==1,{x,.56,.58}, MaxIterations -> 10000],7]
x5 = x /. N[FindRoot[10^5 pc[60,x]==1,{x,.520695,.520697}, MaxIterations -> 10000],7]
x4 = x /. N[FindRoot[10^4 pc[60,x]==1,{x,.46233,.46234}, MaxIterations -> 10000],7]
x3 = x /. N[FindRoot[10^3 pc[60,x]==1,{x,.3911504,.3911505}, MaxIterations -> 10000],7]
x2 = x /. N[FindRoot[10^2 pc[60,x]==1,{x,.2996952,.2996953}, MaxIterations -> 10000],7]
x1 = x /. N[FindRoot[10^1 pc[60,x]==1,{x,.1677,.1679}, MaxIterations -> 10000],7]
eggintsk.nb
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*)
(***********************************************************************
End of Mathematica Notebook file.
***********************************************************************)
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