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MTS-merino pipeline code review #2
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Substantial revision of the drc module to create more robust DRC fits that use both the drc and dr4pl packages, constrain slope to be decreasing by default. Module now chooses the best among multiple fits. Docker in the drc module has also been updates to install the drc module. Changes to be committed: modified: docker_base/install_packages.R modified: drc/Dockerfile modified: drc/build_docker.sh modified: drc/docker_run.sh modified: drc/drc_compound.R new file: drc/install_packages.R modified: drc/src/drc_functions.R
updated documentation explaining the fitting procedure to better reflect the new drc module
Fit with UL close to 1 and decreasing slope for MTS type screens, UL is between 0 and 1 and slope is unconstrained for CPS screens
Implemented suggestions by Mustafa for readability and performance: to use a list and bind rather than adding rows, to use ifelse instead of if {} else{}, etc.
passes Riemann AUC for all compounds. Changed threshold for R^2 to 0. Also will provide R^2 of rejected fits for testing.
some columns were being modified based on hard-coded indexes which would cause issues in the future. Fixed this.
table will display rows where auc is NA but riemann auc is still present.
so that riemann aucs get displayed
drop rows without fits where auc is na from downstream analysis. (rows with auc=na are created by the new drc module)
fixed error when trying to drop columns from a DRC table that didn't exist. changed case_when syntax to help it run properly on aws
added print messages and messages to save intermediate files for debugging error that cannot be reproduced locally.
Removed code inserted for debugging error since it was resolved
upon failure, convergence should be FALSE not NA
updating s3 paths for annotations and features for local running
updated changelog to reflect the use of new analysis QC metrics in recent screens
Change to dockerfile
Cps export
updated drc readme to be consistent with current procedure
feat: merging files in a stream processed to reduce memory requirements
Performance improvement to merging CSV
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