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[Octave-cvsupdate] SF.net SVN: octave:[10742] trunk/octave-forge/extra/lssa
|
From: <be...@us...> - 2012-07-12 05:03:42
|
Revision: 10742
http://octave.svn.sourceforge.net/octave/?rev=10742&view=rev
Author: benjf5
Date: 2012-07-12 05:03:35 +0000 (Thu, 12 Jul 2012)
Log Message:
-----------
Fixed o18.csv (had the wrong data before) and added the beginning of a demonstration script.
Modified Paths:
--------------
trunk/octave-forge/extra/lssa/data/o18.csv
trunk/octave-forge/extra/lssa/lombcoeff.m
trunk/octave-forge/extra/lssa/lscomplex.m
trunk/octave-forge/extra/lssa/lsreal.m
Added Paths:
-----------
trunk/octave-forge/extra/lssa/SampleScriptWithVostokData
Added: trunk/octave-forge/extra/lssa/SampleScriptWithVostokData
===================================================================
--- trunk/octave-forge/extra/lssa/SampleScriptWithVostokData (rev 0)
+++ trunk/octave-forge/extra/lssa/SampleScriptWithVostokData 2012-07-12 05:03:35 UTC (rev 10742)
@@ -0,0 +1,53 @@
+## Copyright (C) 2012 Benjamin Lewis
+## Licensed under the GNU GPL v2
+
+## This is just a sample script to introduce the purpose and usage of
+## the Lomb-Scargle Least Squares method with experimental data, here
+## using the Vostok ice core data collected and measured by J.R. Petit
+## et. al. and published in Nature; also available from the NOAA's
+## Paleoclimatology pages here:
+## <http://www.ncdc.noaa.gov/paleo/icecore/antarctica/vostok/vostok_data.html>.
+
+co2 = csvread("./data/co2.csv")(2:end,2:end);
+ch4 = csvread("./data/ch4.csv")(2:end,2:end);
+o18 = csvread("./data/o18.csv")(2:end,2:end);
+deut = csvread("./data/deut.csv")(2:end,2:end);
+dust = csvread("./data/dust.csv")(2:end,2:end);
+## The limited ranges are to deal with artifacts from the extraction of
+## the R data, notably that it leaves an extra column on the front of 0s
+## and the first row is text that Octave refuses to process.
+
+## Columns in co2 are Depth, Ice Age, Gas Age, and CO2 Concentration.
+## Columns in ch4 are Depth, Ice Age, Gas Age, and CH4 Concentration.
+## Columns in o18 are Depth, Ice Age, Gas Age, and Atmospheric O18.
+## Columns in dust are Depth, Ice Age, Dust Concentration.
+## Columns in deut are Depth, Ice Age, D concentration, and DeltaTS.
+
+co2_fig = figure("visible","off","name","CO2");
+ch4_fig = figure("visible","off","name","CH4");
+o18_fig = figure("visible","off","name","O18");
+deut_fig = figure("visible","off","name","Deuterium");
+dust_fig = figure("visible","off","name","Dust");
+## Generates figures and attaches handles to them for easy access.
+
+## Now we need some data to display; I'll run a few functions.
+ls_complex_co2_ice_age = lscomplex(co2(:,2),co2(:,4),1,100,20);
+ls_complex_co2_gas_age = lscomplex(co2(:,3),co2(:,4),1,100,20);
+ls_real_co2_ice_age = lsreal(co2(:,2),co2(:,4),1,100,20);
+ls_real_co2_gas_age = lsreal(co2(:,3),co2(:,4),1,100,20);
+
+figure(co2_fig);
+subplot(4,2,1);
+plot(-(co2(:,2)),co2(:,4));
+title("Gas levels over ice age");
+subplot(4,2,2);
+plot(-(co2(:,3),co2(:,4));
+title("Gas levels over gas age");
+subplot(4,2,3);
+
+
+## to implement:
+## - displays of all the data and flaws in trying to model with just
+ ## using L-S data
+## - correlations of every data set with every other data set
+## - Comparing ls* results to periodogram results
\ No newline at end of file
Modified: trunk/octave-forge/extra/lssa/data/o18.csv
===================================================================
--- trunk/octave-forge/extra/lssa/data/o18.csv 2012-07-10 14:20:31 UTC (rev 10741)
+++ trunk/octave-forge/extra/lssa/data/o18.csv 2012-07-12 05:03:35 UTC (rev 10742)
@@ -1,523 +1,319 @@
-"","depth.corrected","Ice.age..GT4.","Dust.Conc..ppm."
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Modified: trunk/octave-forge/extra/lssa/lombcoeff.m
===================================================================
--- trunk/octave-forge/extra/lssa/lombcoeff.m 2012-07-10 14:20:31 UTC (rev 10741)
+++ trunk/octave-forge/extra/lssa/lombcoeff.m 2012-07-12 05:03:35 UTC (rev 10742)
@@ -22,19 +22,19 @@
## @seealso{lombnormcoeff}
## @end deftypefn
-%!shared t, x, o, maxfreq
+%!test
+%! shared t, x, o, maxfreq
%! maxfreq = 4 / ( 2 * pi );
%! t = linspace(0,8); x = ( 2.*sin(maxfreq.*t) + 3.*sin((3/4)*maxfreq.*t)
%! - 0.5 .* sin((1/4)*maxfreq.*t) - 0.2 .* cos(maxfreq .* t)
%! + cos((1/4)*maxfreq.*t)); o = [ maxfreq , 3 / 4 * maxfreq , 1 / 4 * maxfreq ];
-%! assert( lombcoeff(t,x,o(1)) = );
-%! assert( lombcoeff(t,x,o(2)) = );
-%! assert( lombcoeff(t,x,o(3)) = );
+%!assert( lombcoeff(t,x,o(1)),10788.9848389923,5e-10 );
+%!assert( lombcoeff(t,x,o(2)),12352.6413413457,5e-10 );
+%!assert( lombcoeff(t,x,o(3)),13673.4098969780,5e-10 );
function coeff = lombcoeff(T, X, o)
theta = atan2(sum(sin(2 .* o .* T )), sum(cos(2.*o.*T)))/ (2 * o );
- coeff = ( sum(X .* cos(o .* T - tau))**2)/(sum(cos(o.*T-tau).**2)) +
- ( sum(X .* sin(o .* T - tau))**2)/(sum(sin(o.*T-tau).**2));
+ coeff = ( sum(X .* cos(o .* T - theta))**2)/(sum(cos(o.*T-theta).**2)) + ( sum(X .* sin(o .* T - theta))**2)/(sum(sin(o.*T-theta).**2));
end function
Modified: trunk/octave-forge/extra/lssa/lscomplex.m
===================================================================
--- trunk/octave-forge/extra/lssa/lscomplex.m 2012-07-10 14:20:31 UTC (rev 10741)
+++ trunk/octave-forge/extra/lssa/lscomplex.m 2012-07-12 05:03:35 UTC (rev 10742)
@@ -26,7 +26,7 @@
%!test
%! shared t, x, o, maxfreq
%! maxfreq = 4 / ( 2 * pi ); t = [0:0.008:8]; x = ( 2.*sin(maxfreq.*t) + 3.*sin((3/4)*maxfreq.*t)- 0.5 .* sin((1/4)*maxfreq.*t) - 0.2 .* cos(maxfreq .* t) + cos((1/4)*maxfreq.*t)); o = [ maxfreq , 3 / 4 * maxfreq , 1 / 4 * maxfreq ];
-%! assert( lscomplex(t,x,maxfreq,2,2), [-0.40075 - 2.36687i , 1.22666 - 2.24390i , 1.93643 - 1.51554i , 2.12505 - 0.95410i ] );
+%! assert( lscomplex(t,x,maxfreq,2,2), [-0.400754376933531 - 2.366871097665244i, 1.226663545950135 - 2.243899314661490i, 1.936433327880238 - 1.515538553198501i, 2.125045509991203 - 0.954100898917708i ], 6e-14 );
Modified: trunk/octave-forge/extra/lssa/lsreal.m
===================================================================
--- trunk/octave-forge/extra/lssa/lsreal.m 2012-07-10 14:20:31 UTC (rev 10741)
+++ trunk/octave-forge/extra/lssa/lsreal.m 2012-07-12 05:03:35 UTC (rev 10742)
@@ -25,9 +25,10 @@
%!shared t, x, o, maxfreq
%! maxfreq = 4 / ( 2 * pi );
-%! t = linspace(0,8); x = ( 2.*sin(maxfreq.*t) + 3.*sin((3/4)*maxfreq.*t)
-%! - 0.5 .* sin((1/4)*maxfreq.*t) - 0.2 .* cos(maxfreq .* t)
-%! + cos((1/4)*maxfreq.*t)); o = [ maxfreq , 3 / 4 * maxfreq , 1 / 4 * maxfreq ];
+%! t = linspace(0,8);
+%! x = ( 2.*sin(maxfreq.*t) + 3.*sin((3/4)*maxfreq.*t) - 0.5 .* sin((1/4)*maxfreq.*t) - 0.2 .* cos(maxfreq .* t) + cos((1/4)*maxfreq.*t));
+%! assert(lsreal(t,x,maxfreq,2,2),[-1.68275915310663 + 4.70126183846743i, 1.93821553170889 + 4.95660209883437i, 4.38145452686697 + 2.14403733658600i, 5.27425332281147 - 0.73933440226597i],6e-14)
+%! #In the assert here, I've got an error bound large enough to catch individual system errors which would present no real issue.
function transform = lsreal( t, x, omegamax, ncoeff, noctave)
## the R function runs the following command:
@@ -38,7 +39,7 @@
## where rp = complex(noctave*ncoeff) so ... I can just store that as noctave*ncoeff and have no
## problems, I guess.
## Possibly throw an error if ncoeff <= 0.
- k = n = min(length(x),length(t)); ## THIS IS VECTOR-ONLY. I'd need to add another bit of code to
+ k = n = length(t); ## THIS IS VECTOR-ONLY. I'd need to add another bit of code to
## make it array-safe, and that's not knowing right now what else will be necessary.
transform = zeros(1,(noctave * ncoeff)); ## In the C code, this is rendered as a Complex, but Octave doesn't care.
od = 2 ^ ( - 1 / ncoeff ); ## this will cause a crash if ncoeff=0; prefer error & quit?
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