naobservatory/p2ra

Issues

• Add incidence figure scripts to repo

  #232 opened a year ago by simonleandergrimm
  0

• Create HIV estimates for Copenhagen

  #217 opened a year ago by simonleandergrimm
  1

• Reinclude HBV, HSV-2, and AAV-6 in analysis for preprint

  #221 opened a year ago by simonleandergrimm
  0

• Pathogens with subtypes only get model diagnostic plots for one

  #218 opened a year ago by dp-rice
  1

• Turn JC Virus and BK Virus estimates into age-adjusted estimates

  #164 opened a year ago by simonleandergrimm
  1

• Update model.md to reflect hierarchical model

  #160 opened a year ago by dp-rice
  0

• Revist AAV estimates (currently we use global seroprevalence, even though we have US numbers)

  #188 opened a year ago by simonleandergrimm
  2

• Extend HPV Denmark and US estimate to all HPV subtypes

  #201 opened a year ago by simonleandergrimm
  2

• Potentially incorporate the share of positive tests into our influenza underreporting factor. (flag with Dan)

  #129 opened a year ago by simonleandergrimm
  2

• Revisiting DK EBV and CMV estimates, or adding limitation to report:

  #198 opened a year ago by simonleandergrimm
  1

• Identify COVID-19 underreporting factor for the Omicron surge

  #127 opened a year ago by simonleandergrimm
  5

• Investigate if seroprevalence always matches present latent infections.

  #153 opened a year ago by simonleandergrimm
  1

• Consider splitting Spurbeck by sample prep method

  #175 opened a year ago by dp-rice
  1

• Simplify interface for getting public health predictors

  #186 opened a year ago by dp-rice
  1

• Consolidate plotting scripts

  #208 opened a year ago by dp-rice
  1

• Command line arguments for fit.py

  #173 opened a year ago by dp-rice
  1

• Check whether model output changes on pre-submit

  #161 opened a year ago by dp-rice
  1

• Assess HMC mixing statistics

  #177 opened a year ago by dp-rice
  4

• `plot_summaries.py` does not check whether there are both incidence and prevalence estimates

  #189 opened a year ago by dp-rice
  0

• Add more tests for stats.py

  #119 opened a year ago by dp-rice
  0

• Display read counts on output figures

  #179 opened a year ago by dp-rice
  0

• Show viral read counts on boxen plots

  #176 opened a year ago by dp-rice
  0

• Moving `tidy_name` broke `figures/counts-by-pathogen-and-study.py`

  #191 opened a year ago by dp-rice
  1

• Create estimates for HPV (genital and oral) subtypes, once we have extensive DNA metagenomic sequencing data.

  #143 opened a year ago by simonleandergrimm
  1

• Look into how HPV prevalence has changed since 2013-2016

  #157 opened a year ago by jeffkaufman
  2

• Stan output is not deterministic

  #172 opened a year ago by dp-rice
  1

• Make it easier to see what taxids estimates apply to

  #139 opened a year ago by jeffkaufman
  1

• Summary figures

  #168 opened a year ago by dp-rice
  1

• Summary table

  #167 opened a year ago by dp-rice
  0

• Assess the sensitivity to the prior on mu

  #169 opened a year ago by dp-rice
  0

• Apply model to Spurbeck MGS data

  #120 opened a year ago by dp-rice
  1

• Stats: Adjust priors to improve posterior checks

  #116 opened a year ago by dp-rice
  1

• Apply model to more viruses

  #115 opened a year ago by dp-rice
  0

• Expand rna_pathogens

  #155 opened a year ago by jeffkaufman
  0

• Deal with several incidences/prevalences for same time and location

  #149 opened a year ago by simonleandergrimm
  2

• Some viruses give 0 incidences, which break the model

  #148 opened a year ago by jeffkaufman
  0

• Reassess HCV and HBV data.

  #110 opened a year ago by simonleandergrimm
  1

• Consider usefulness of county-level HCV estimates (that were created) and county-level HBV estimates (that weren't yet created)

  #111 opened a year ago by simonleandergrimm
  1

• Currently it is unclear when the NORS Outbreak data starts, only that it ends in 2021.

  #130 opened a year ago by simonleandergrimm
  2

• Add HPV estimates

  #137 opened a year ago by simonleandergrimm
  1

• Bump mgs data tag to fix "Montogmery County"

  #134 opened a year ago by dp-rice
  0

• Minor fix in influenza.py: Changing the variable name `public_health_labs_infections` to `clinical_labs_infections`

  #128 opened a year ago by simonleandergrimm
  3

• Investigate why HIV LA County 2020 is not matching

  #132 opened a year ago by dp-rice
  1

• Get NORS 2022 data

  #84 opened a year ago by jeffkaufman
  1

• Apply model to a second MGS dataset

  #114 opened a year ago by dp-rice
  0

• Stats: run model for more viruses

  #106 opened a year ago by dp-rice
  0

• Undo Rhinovirus commit #ca7a5ff

  #88 opened a year ago by simonleandergrimm
  1

• Use country and state metadata from MGS repo

  #105 opened a year ago by dp-rice
  1

• Add get_location that works like get_dates

  #103 opened a year ago by jeffkaufman
  0

• Improve estimate of prevalence from incidence

  #87 opened a year ago by jeffkaufman
  1