Optimize tidyCovariates() for new Andromeda when data are large (Issue308) - #309
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@schuemie that is a nice performance gain, thanks. @anthonysena I don't see a problem with this PR, what do you think? |
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Looks great thanks @schuemie for identifying and fixing this issue! |
anthonysena
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* fix setting of continous covariates in case of multiple settings and add a test * update test * Optimizing tidyCovariates for large data. Fixes #308 (#309) Co-authored-by: ginberg <ginberg@gmail.com> Co-authored-by: Admin_mschuemi <Admin_mschuemi@its.jnj.com> * cran submission file * add params to getDBCovariateData (#312) * #292 add function to replace cohort schema and table * #292 add params * add test * doc * v3.11.0 * update news --------- Co-authored-by: Martijn Schuemie <schuemie@ohdsi.org> Co-authored-by: Admin_mschuemi <Admin_mschuemi@its.jnj.com>
ginberg
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* fix setting of continous covariates in case of multiple settings and add a test * update test * Optimizing tidyCovariates for large data. Fixes #308 (#309) Co-authored-by: ginberg <ginberg@gmail.com> Co-authored-by: Admin_mschuemi <Admin_mschuemi@its.jnj.com> * cran submission file * add params to getDBCovariateData (#312) * #292 add function to replace cohort schema and table * #292 add params * add test * doc * v3.11.0 * update news * Making removal of redundant covariates reproducible (with unit test). Fixes #315 (#316) Co-authored-by: Admin_mschuemi <Admin_mschuemi@its.jnj.com> * version update * prepare release * CRAN file --------- Co-authored-by: Martijn Schuemie <schuemie@ohdsi.org> Co-authored-by: Admin_mschuemi <Admin_mschuemi@its.jnj.com>
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As mentioned in #308, I found
tidyCovariates()to be extremely slow when data are very large (>= 8GB uncompressed). The simple adjustment in this PR leads to a >100 fold increase in speed in my example case. In general the change seems like a good idea.