HopkinsIDD/gavi_vimc_cholera

Issues

• Potential Update in the Future

  #73 opened a year ago by KaiyueZou
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• A small typo detected that didn't impact the model output

  #66 opened 2 years ago by KaiyueZou
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• load_baseline_incidence

  #63 opened 2 years ago by Hanmeng-Xu
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• load_shapefile_by_country

  #62 opened 2 years ago by Hanmeng-Xu
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• surveillance_true_confirmation_rate

  #61 opened 2 years ago by Hanmeng-Xu
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• surveillance_pop_weighted_incid

  #60 opened 2 years ago by Hanmeng-Xu
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• load_worldpop_by_country

  #59 opened 2 years ago by Hanmeng-Xu
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• align_rasters

  #58 opened 2 years ago by eclee25
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• Noted: The mean incidence rate raster is used for district-level vaccination decision-making process for now

  #38 opened 2 years ago by KaiyueZou
  1

• The external dataset that contains the confirmation rate has not been created and there is no code to accommodate its reading in yet

  #43 opened 2 years ago by KaiyueZou
  1

• Maybe create a separate check on "no-vaccination" scenario to boost efficiency

  #44 opened 2 years ago by KaiyueZou
  1

• Each year's newly updated incidence rates are averaged across layers, on which is the targeting decision based

  #47 opened 2 years ago by KaiyueZou
  1

• Now all the input raster are saved in memory, which may be burdensome and slow down the process

  #48 opened 2 years ago by KaiyueZou
  1

• Noted: the true cases are saved as external dataset, but the suspected cases will be transferred around for vacc decision-making purposes

  #49 opened 2 years ago by KaiyueZou
  1

• Noted: now across each year, the same district will be assigned with a different confirmation rate value

  #50 opened 2 years ago by KaiyueZou
  1

• Error message in surveillance_add_rc_new_row() function

  #56 opened 2 years ago by Hanmeng-Xu
  1

• Error message when running the no-vaccination scenarios.

  #57 opened 2 years ago by Hanmeng-Xu
  1

• Question about surveillance_create_expectedCases()

  #55 opened 2 years ago by Hanmeng-Xu
  1

• Noted: the NA district-level incidence rate will be replaced by 0 for simplicity purpose

  #54 opened 2 years ago by KaiyueZou
  0

• Doesn't support country-level skip years because both levels of districts are being simulated and they have different latest tagetted years

  #53 opened 2 years ago by KaiyueZou
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• The first year of incidence rate read in doesn't have incidence trend implemented yet

  #41 opened 2 years ago by KaiyueZou
  1

• Noted: lambda and pop raster sometimes don't agree with each other in those areas covered by rivers

  #52 opened 2 years ago by KaiyueZou
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• Noted: now we assume that the population raster during the same year remains constant -- from the beginning of the year when vacc is being carried out to the end of the year when the cases are summarized

  #51 opened 2 years ago by KaiyueZou
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• A better way to organize the raw output

  #46 opened 2 years ago by KaiyueZou
  1

• Noted: now we assume that the vacc happens at the beginning of each year and will affect that year's cases

  #45 opened 2 years ago by KaiyueZou
  0

• Noted: check package versions if exactextractr::exact_extract doesn't work as supposed

  #42 opened 2 years ago by KaiyueZou
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• Noted: Now running each threshold and surveillance separately

  #40 opened 2 years ago by KaiyueZou
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• Noted: every year's updated incidence will only be used to aid vacc decision-making, not to change the underlying spatial incidence rate raster

  #39 opened 2 years ago by KaiyueZou
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• Make the admin level incidence rate calculation population weighted

  #37 opened 2 years ago by KaiyueZou
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• Be able to set random seed

  #22 opened 2 years ago by eclee25
  1

• Very tight uncertainty bounds for the non-raster countries

  #36 opened 3 years ago by KaiyueZou
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• Lit review on healthcare seeking behavior for AWD in adults

  #35 opened 3 years ago by eclee25
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• Ability to specify secular trend settings in config file

  #34 opened 3 years ago by eclee25
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• Diagnostic report enhancement

  #31 opened 3 years ago by KaiyueZou
  1

• Transfer raster files without corrupting them

  #18 opened 3 years ago by KaiyueZou
  1

• Bangladesh raster data is still on hold

  #13 opened 3 years ago by KaiyueZou
  1

• Update ocv_ve_overtime.csv to include new OCV VE studies

  #33 opened 3 years ago by eclee25
  1

• Add more documentation for how to run model in wiki

  #24 opened 3 years ago by eclee25
  1

• More retrieve functions to get the burden template (stochastic) and a stochastic parameters template

  #28 opened 3 years ago by KaiyueZou
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• Parallel computing issue

  #30 opened 3 years ago by KaiyueZou
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• Incidence data for Iraq and Iran not provided by WHO

  #26 opened 3 years ago by KaiyueZou
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• Reconsider non-raster incidence data assignment

  #23 opened 3 years ago by eclee25
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• make a diagnostic report template

  #12 opened 3 years ago by eclee25
  1

• New touchstone compatibility check

  #20 opened 3 years ago by KaiyueZou
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• (URGENT) Get the old model (with old touchstone) run on the server

  #19 opened 3 years ago by KaiyueZou
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• An auto-check file to run prior to the main model

  #21 opened 3 years ago by KaiyueZou
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• Non-interactive ways to install R packages needed for the model

  #14 opened 3 years ago by KaiyueZou
  1

• Change the Windows "\\" to Linux "//" in R scripts

  #15 opened 3 years ago by KaiyueZou
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• Log into Montagu API in Non-interactive ways

  #16 opened 3 years ago by KaiyueZou
  1

• Unwanted exports in NAMESPACE

  #17 opened 3 years ago by KaiyueZou
  1