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Plot ROC & PRC curves #34

Merged
merged 62 commits into from
Jan 21, 2023
Merged

Plot ROC & PRC curves #34

merged 62 commits into from
Jan 21, 2023

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Jan 10, 2023 •
edited

Issues

Change(s) made

  • New rules to calculate sensitivity, specificity, & recall and then plot ROC & PRC curves.

Checklist

(Strikethrough any points that are not applicable.)

  • Update the docs if there are any API changes (README.md, config/README.md, & quick-start.md).
  • Re-run the pipeline on an HPC and update the example report.
  • The checks succeed on your most recent commit. This is always required before the PR can be merged.

@kelly-sovacool
PGet predictions per model
4f3e46d
@kelly-sovacool
Add placeholder for roc curves plot
7c9f4ed
@kelly-sovacool
use purrr::map_dfr() for simplicity
5275ccf
@kelly-sovacool
Fix feature importance order
43aa3ae
@kelly-sovacool
Mutate benchmarks for simpler combining
d8fa5e2
@kelly-sovacool
Move rules for example report to separate module
cf490e9
@kelly-sovacool
Update DAG & rulegraph
688de47
@kelly-sovacool
Add roc plot to report
dd68317
@kelly-sovacool
[WIP] example code from https://github.com/SchlossLab/Barron_IBD-CDI_…
b5d3200 
…mBio_2022
@kelly-sovacool
Add TODOs
321110f
@kelly-sovacool
Get & combine model predictions
f4c2f8c
@kelly-sovacool
Specify mamba as conda frontend
8812dc4
@kelly-sovacool
Fix typo
9f07139
@kelly-sovacool
Use functions from mikropml dev version
e27dc5b
@kelly-sovacool
Don't use script as input
dbe3cd3 
Required for compatibility as a module for snakedeploy
@kelly-sovacool
Remove script paths from input
fedc6cb
@kelly-sovacool
Deprecated combine_benchmarks script
5cfff3d
@kelly-sovacool
Move Rmd to scripts dir
42339b5
@kelly-sovacool
Merge branch 'main' into plot-rocs
f6e7099
@kelly-sovacool
Tweak graphviz image filepaths
81967a2
@kelly-sovacool
Commit results of graph & container jobs
f109128
@kelly-sovacool
Fix path to report
8e76261
@kelly-sovacool
Tweak gh actions bot config
91b5104
@kelly-sovacool
Use conda env for github actions workflow
7ed3b72
@kelly-sovacool
Add log files
3116e37
@kelly-sovacool
Shell magic for conda env
d07cb52
@kelly-sovacool
Only print feature importance header if it ran
9560842
@kelly-sovacool
Don't run feature importance for test config
44d8f5b
@kelly-sovacool
Don't track results figures
a66ab66
@kelly-sovacool
Use post-deployment script to install mikropml dev version
23bd8e1
github-actions bot and others added 25 commits January 11, 2023 16:17
@github-actions
🎨 Style R code
de9c97b
@github-actions
🎨 Style Python & Snakemake code 🐍
4732711
@github-actions
🐳 Update Dockerfile
85cad35
@kelly-sovacool
Rename predict -> calc_model_sensspec
e92a577
@kelly-sovacool
Merge branch 'plot-rocs' of https://github.com/SchlossLab/mikropml-sn…
36b9f0f 
…akemake-workflow into plot-rocs
@kelly-sovacool
Ignore results
e4ce55a
@kelly-sovacool
Use separate graphviz env
4449564
@kelly-sovacool
Try installing fs too?
4113401
@kelly-sovacool
Use mikropml v1.5.0
e576b66
@kelly-sovacool
Merge branch 'main' into plot-rocs
b6b031e
@kelly-sovacool
Add rulegraph to report & pass configfile to rulegraph/dag command
2db7802
@kelly-sovacool
Note config file path in report
5bf5fd8
@kelly-sovacool
Tweak git commit if/else
b30da80
@kelly-sovacool
Merge b30da80 into cea9ee9
224a3f1
@github-actions
🎨 Style Python & Snakemake code 🐍
e4cc386
@github-actions
🐳 Update Dockerfile
df27436
@kelly-sovacool
Remove comments after smk args
f74419c
@kelly-sovacool
Merge f74419c into cea9ee9
d4a57ff
@kelly-sovacool
get_feature_importance() no longer takes train_data
ef602f9
@kelly-sovacool
Merge ef602f9 into 191cc94
9325d1c
@kelly-sovacool
Find feature importance in test config
be676db 
So CI can catch potential errors
@kelly-sovacool
Merge branch 'plot-rocs' of https://github.com/SchlossLab/mikropml-sn…
3de3fe4 
…akemake-workflow into plot-rocs
@kelly-sovacool
Merge 3de3fe4 into 191cc94
6d11295
@kelly-sovacool
Re-run example on GL
ff59921
@kelly-sovacool
Merge branch 'plot-rocs' of https://github.com/SchlossLab/mikropml-sn…
25ade40 
…akemake-workflow into plot-rocs
@kelly-sovacool kelly-sovacool marked this pull request as ready for review January 20, 2023 22:29
@kelly-sovacool kelly-sovacool merged commit 242011a into main Jan 21, 2023
@kelly-sovacool kelly-sovacool deleted the plot-rocs branch January 21, 2023 03:29
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Plot ROC curves
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@kelly-sovacool