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Remove dependency to r #565

Merged
merged 12 commits into from
Jan 5, 2021
Merged

Remove dependency to r #565

merged 12 commits into from
Jan 5, 2021

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ManuelaRunge
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Updated r - python scripts:

  • Rt estimation scripts: using epyestim instead of EpiEstim
  • Iteration comparison script to python (uses hosp_cumul and not hosp_det_cumul as the 'det' channels are missing for last iterations )
  • adjusted batch/shell scripts to call python scripts instead of R and commented out not 'translated R scripts' that are not needed for the weekly deliverables (custom seroprevalence plot, fitting script)
  • deleted old Rfiles that are not needed

@ManuelaRunge ManuelaRunge marked this pull request as draft January 5, 2021 11:49
@ManuelaRunge ManuelaRunge mentioned this pull request Jan 5, 2021
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@ManuelaRunge ManuelaRunge linked an issue Jan 5, 2021 that may be closed by this pull request
remove dependency to using Rstudio in weekly processing workflow #564
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@ManuelaRunge ManuelaRunge marked this pull request as ready for review January 5, 2021 16:01
@ManuelaRunge ManuelaRunge merged commit 1e42e4e into numalariamodeling:master Jan 5, 2021
jacksonllee pushed a commit that referenced this pull request Feb 10, 2021
@ManuelaRunge
Remove dependency to r (#565)
22230c7 
* added python script for estimating Rt
* replaced r iteration comparison script with py script
* added Rt timeline plot to iteration comparison script and updated batch file
* commented channels det vs no det
* cleanup  Rt estimation script
* removed not used R files
* removed rfiles from batch and shell files (commented out seroprevalence plot and fitting script)
* added py epyestim script for LL data
* moved argument specification to function call
* updated requirements txt
* bugfixes
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remove dependency to using Rstudio in weekly processing workflow
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@ManuelaRunge