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Remove observe_process() #431

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athowes opened this issue Nov 13, 2024 · 1 comment · Fixed by #439
Closed

Remove observe_process() #431

athowes opened this issue Nov 13, 2024 · 1 comment · Fixed by #439
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athowes commented Nov 13, 2024

In PR #390 we updated the preprocessing functionality, but we left observe_process() in the package. I think if possible we should get rid of this. Similarly, if possible we should get rid of the filter_obs functions.
@athowes athowes added the high Required for next release label Nov 13, 2024
@athowes athowes self-assigned this Nov 13, 2024
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athowes commented Nov 13, 2024 •
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Instances of observe_process() being used (that are not auto generated, or the definition itself):

  • inst/make_hexsticker.R: Line 18
    • observe_process
  • tests/testthat/setup.R: Lines 23, 44, 79
    • observe_process() |>
  • vignettes/approx-inference.Rmd: Line 118
    • observe_process() |>
  • vignettes/ebola.Rmd: Lines 171, 174
    • Line 171: Next, we use observe_process() to add interval censoring columns giving the lower and upper bounds on the primary and secondary event times:
    • Line 174: obs_cens <- observe_process(sierra_leone_ebola_data)
  • vignettes/epidist.Rmd: Lines 160, 161
    • Line 160: # observe_process() should be renamed and include a "daily" i.e. 1 argument
    • Line 161: obs_cens <- obs |> observe_process()
  • vignettes/faq.Rmd: Line 46
    • observe_process() |>

This was referenced Nov 13, 2024
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seabbs added a commit that referenced this issue Nov 19, 2024
@athowes @seabbs
Issue #431: Remove observation process function (#439)
7205068 
* Remove observe_process

* Update NAMESPACE

* Simplify columns created

* Fix names

* Lint fix

* Need to have obs_time in there also

* Set obs_time for Ebola vignette

* Redoc

* Missing part

* Reabase fix for Ebola vignette

* Rebase

* Linter on imports

* Change to nolint strategy

* Increase tol

* Increase tol again

* Update make_hexsticker.R

---------

Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
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Issue #431: Remove observation process function epinowcast/epidist
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