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ChangeLog
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ChangeLog
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TODO
---------
Required Features:
-Add support for multiple files
Optional Features:
-Add exclusion lists for single sets of elements of phenotypes
-Add exclusion lists for single sets of elements of genotypes
Changes
-------------
-------------
21-10-2014
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Added check for rank of covariate matrix to avoid miss-calculations of
results when covariates are linearly dependent.
An error is given and the program is exited while
letting the user know that covariates need to change.
Added MPI functionality for clusters.
Screen output happens on process 0
and multiple output files are produced, one per process.
8-10-2014
--------------
Added naming checks/warning for element ids.
Changed calculation of Standard errors to numerically robust versions.
Reduced memcpy overhead of XR and XR XL factors.
Created efficient calculation with corrections of covariance matrices.
Covariants are displayed as results with -i only when the snp/XR is significant.
Added a better performing operation for the calculation of residuals.
Stable user usable version.
22-9-2014
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Fixed countless bugs as a cause of non normal problem dimensions.
Added several more dimension checks.
Removed some warnings and changed comiling commands.
Added over 150+ automated tests for validity checks.
Broke fake files tests (re-add?).
Multiple Non linear interactions added for single analysis.
Single Non linear interactions added for multiple analysis.
Stable user usable version.
10-9-2014
--------------
Fixed bug related to naming of results.
Changed file reading of XR from c to c++ for stability.
Added check of dimension required by OLS math.
Basis for non linear interaction added.
Stable user usable version.
9-9-2014
--------------
Fixed bug related to reusing the same instance of the solver. AIOwrapper is now recreated on every call.
Added Additive,Recessive, Dominant models.
Added option for Custom Models. Custom Additive Model uses custom factors.
Custom Linear Model uses custom models with beta coefficients for each column of the independent variable.
8-9-2014
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Removed individuals with covariates missing
Fixed SST Bug
Fixed Individuals Exclude list Bug
Added faster SST calculation
4-9-2014
--------------
First user usable version.
Several Bug-fixes.
Added parameters to control thresholds of significance.
Storing output as readable .txt and binary data.
Both .txt and binary have different parametrization thresholds.
Text-files should always store less results.
Thresholds for text-files cannot include more results than the ones for binary files.
Added bigger test files.
Added program to transform binary result files to text files with parametrized thresholds.
Added HPC functions for sum of squares calculations.