Author: bugman
Date: Tue Jan 20 14:07:07 2015
New Revision: 27239
URL: http://svn.gna.org/viewcvs/relax?rev=27239&view=rev
Log:
Merged revisions 27200-27230 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27200 | tlinnet | 2015-01-16 23:19:25 +0100 (Fri, 16 Jan 2015) | 3 lines
Added save state for testing implementation of error analysis.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27201 | tlinnet | 2015-01-16 23:19:44 +0100 (Fri, 16 Jan 2015) | 4 lines
Start of implementation of systemtest
Relax_disp.test_task_7882_monte_carlo_std_residual, to test doing Monte-Carlo
simulations with errors drawn from a
Gauss distribution with a width corresponding to the standard devition of
the sum of squares of residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27202 | tlinnet | 2015-01-16 23:19:47 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented target function for relaxation dispersion, which calculate the
sum of squares of residuals and the standard deviation of these.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27203 | tlinnet | 2015-01-16 23:19:50 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented storing of sum of squares and the standard deviation of these
for relaxation dispersion, when doing a point calculation.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27204 | tlinnet | 2015-01-16 23:19:51 +0100 (Fri, 16 Jan 2015) | 3 lines
Stored the sums of squares of the residuals "sos" and standard deviation of
this "sos_std" per spin after optimisation.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27205 | tlinnet | 2015-01-16 23:19:54 +0100 (Fri, 16 Jan 2015) | 3 lines
Added to systemtest Relax_disp.test_task_7882_monte_carlo_std_residual()
that spin.sos and spin.sos_std is stored after grid search.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27206 | tlinnet | 2015-01-16 23:19:56 +0100 (Fri, 16 Jan 2015) | 3 lines
Extracted "sos" and "sos_std" after grid search.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27207 | tlinnet | 2015-01-16 23:19:58 +0100 (Fri, 16 Jan 2015) | 3 lines
In systemtest Relax_disp.test_task_7882_monte_carlo_std_residual() inserted
sanity checks of calculation of degrees of freedom.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27208 | tlinnet | 2015-01-16 23:20:01 +0100 (Fri, 16 Jan 2015) | 5 lines
Speed-up of systemtest Relax_disp.test_task_7882_monte_carlo_std_residual()
by copying pipe instead of reading results 3 times.
Tested creation of Monte-Carlo data, where errors are generated with width
of standard deviation or residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27209 | tlinnet | 2015-01-16 23:20:04 +0100 (Fri, 16 Jan 2015) | 3 lines
Extended user function monte_carlo.create_data() to accept
'method="sum_squares"', to create Monte-Carlo data.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27210 | tlinnet | 2015-01-16 23:20:06 +0100 (Fri, 16 Jan 2015) | 3 lines
Extended backend in pipe_control.error_analysis.monte_carlo_create_data()
to return errors as the standard deviation of the sum of squares of the
residual.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27211 | tlinnet | 2015-01-16 23:20:08 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented the api_base method of return_error_sum_squares(), as raising
an error if not defined for the api for the pipe_type.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27212 | tlinnet | 2015-01-16 23:20:11 +0100 (Fri, 16 Jan 2015) | 3 lines
Implemented in the relaxation dispersion API, the function to return errors
as the standard deviation of sums squared residuals.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27213 | tlinnet | 2015-01-16 23:20:13 +0100 (Fri, 16 Jan 2015) | 3 lines
Added 'sos' and 'sos_std' as parameter object in relaxation dispersion.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27214 | tlinnet | 2015-01-17 14:16:50 +0100 (Sat, 17 Jan 2015) | 17 lines
Reverted range of commits r27213:r27202 as this was a bad implementation.
To get the distribution, one should look at the sum of squares.
But this should be from the weighted sum of squares, which is stored as
chi2.
The API provides a method of model_statistics(), to get:
k - number of parameters.
n - number of data points.
chi2 - the chi-squared value.
Then reduced chi2 can be computed. chi2_red = chi2/(n-k)
And the error distribution be drawn from this.
The command used was:
svn merge -r27213:r27201 .
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27215 | tlinnet | 2015-01-17 17:25:12 +0100 (Sat, 17 Jan 2015) | 3 lines
Simplification of systemtest
Relax_disp.test_task_7882_monte_carlo_std_residual, to just test the creation
of Monte-Carlo data where errors are drawn from the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27216 | tlinnet | 2015-01-17 17:25:15 +0100 (Sat, 17 Jan 2015) | 3 lines
Extension of the userfunction monte_carlo.create_data, to draw errors from
the reduced chi2 gauss distribution as found by best fit.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27217 | tlinnet | 2015-01-17 17:25:16 +0100 (Sat, 17 Jan 2015) | 3 lines
Adding to back-end of pipe_control.error_analysis(), to modify datapoint as
error drawn from the reduced chi2 gauss distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27218 | tlinnet | 2015-01-17 17:25:18 +0100 (Sat, 17 Jan 2015) | 3 lines
Adding empty API method to return errors from the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27219 | tlinnet | 2015-01-17 17:25:20 +0100 (Sat, 17 Jan 2015) | 3 lines
Added API function in relaxation dispersion to return error structure from
the reduced chi2 distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27220 | tlinnet | 2015-01-18 17:32:37 +0100 (Sun, 18 Jan 2015) | 8 lines
Temporary test of making a confidence interval as described in fitting
guide.
This is systemtest Relax_disp.x_test_task_7882_kex_conf, which is not
activated by default.
Running the test, interestingely shows, there is a possibility for a lower
global kex.
But the value only differ from kex=1826 to kex=1813.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27221 | tlinnet | 2015-01-19 13:48:41 +0100 (Mon, 19 Jan 2015) | 8 lines
Change to systemtest Relax_disp.x_test_task_7882_kex_conf()
This is just a temporary systemtest, to check for local minima.
This is method in regression book of Graphpad:
http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf
Page: 109-111.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27222 | tlinnet | 2015-01-19 13:48:44 +0100 (Mon, 19 Jan 2015) | 3 lines
Raising an error, if the R2eff model is used, and drawing errors from the
fit.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27223 | tlinnet | 2015-01-19 13:48:46 +0100 (Mon, 19 Jan 2015) | 3 lines
To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), adding
test for raise of errors, if the R2eff model is selected.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.
........
r27224 | tlinnet | 2015-01-20 12:02:01 +0100 (Tue, 20 Jan 2015) | 5 lines
Added test of argument "distribution" in
Ãpipe_control.error_analysis.monte_carlo_create_data().
This is to make sure that a wrong argument is not passed into the function.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27225 | tlinnet | 2015-01-20 12:02:10 +0100 (Tue, 20 Jan 2015) | 5 lines
Extended the user function 'monte_carlo.create_data', to allow for the
defition of the STD to use in gauss distribution.
This is for creation of Monte-Carlo simulations, where one has perhaps
gained information about the expected errors of the datapoints, which is not
measured.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27226 | tlinnet | 2015-01-20 12:02:12 +0100 (Tue, 20 Jan 2015) | 5 lines
In backend pipe_control.error_analysis.monte_carlo_create_data() added the
argument 'fixed_error' to allow for fixed input of error to the gauss
distribution.
Inserted a range of checks, to make sure function behaves as expected.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27227 | tlinnet | 2015-01-20 12:02:14 +0100 (Tue, 20 Jan 2015) | 3 lines
Added to pipe_control.error_analysis.monte_carlo_create_data() the creation
of datapoints for a fixed distribution.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27228 | tlinnet | 2015-01-20 12:02:16 +0100 (Tue, 20 Jan 2015) | 4 lines
To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), added
tests for creation of Monte-Carlo data
by different methods.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27229 | tlinnet | 2015-01-20 12:41:21 +0100 (Tue, 20 Jan 2015) | 4 lines
In pipe_control.error_analysis.monte_carlo_create_data(), if data is of
list type or ndarray, then modify the datapoint according to the fixed error
if
the distribution is set to 'fixed'.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
r27230 | tlinnet | 2015-01-20 12:41:23 +0100 (Tue, 20 Jan 2015) | 5 lines
Expanded the STD acronym, to the meaning of Standard deviation.
This is in the user function 'monte_carlo.create_data'.
Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation,
where errors are generated with width of standard deviation or residuals.):
Implement Monte-Carlo simulation, where errors are generated with width of
standard deviation or residuals.
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/error_testing/task_7882.bz2
- copied unchanged from r27230,
trunk/test_suite/shared_data/dispersion/error_testing/task_7882.bz2
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/pipe_control/error_analysis.py
branches/frame_order_cleanup/specific_analyses/api_base.py
branches/frame_order_cleanup/specific_analyses/relax_disp/api.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/user_functions/monte_carlo.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/pipe_control/error_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/error_analysis.py?rev=27239&r1=27238&r2=27239&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/api_base.py?rev=27239&r1=27238&r2=27239&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/api.py?rev=27239&r1=27238&r2=27239&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=27239&r1=27238&r2=27239&view=diff
Modified: branches/frame_order_cleanup/user_functions/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/monte_carlo.py?rev=27239&r1=27238&r2=27239&view=diff
r27239 - in /branches/frame_order_cleanup: ./ pipe_control/ specific_analyses/ specific_analyses/relax_disp/ test_suite/shar...