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p2ra
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Moving `tidy_name` broke `figures/counts-by-pathogen-and-study.py`
#191
dp-rice
closed
1 year ago
1
Improve summary figures
#190
dp-rice
closed
1 year ago
1
`plot_summaries.py` does not check whether there are both incidence and prevalence estimates
#189
dp-rice
closed
1 year ago
0
Revist AAV estimates (currently we use global seroprevalence, even though we have US numbers)
#188
simonleandergrimm
closed
1 year ago
2
Simon aav update
#187
simonleandergrimm
closed
1 year ago
0
Simplify interface for getting public health predictors
#186
dp-rice
closed
1 year ago
1
update table to include nucleic acid, predictor type, and selection round
#185
jeffkaufman
closed
1 year ago
1
Stopped returning incidences for HPV, HCV, and HBV.
#184
simonleandergrimm
closed
1 year ago
0
Extrapolated HPV prevalence to 2020 and 2021.
#183
simonleandergrimm
closed
1 year ago
0
Hep b c fix
#182
simonleandergrimm
closed
1 year ago
0
Simon mcv
#181
simonleandergrimm
closed
1 year ago
0
norovirus: follow flu in only listing GI and GII, not combined
#180
jeffkaufman
closed
1 year ago
0
Display read counts on output figures
#179
dp-rice
closed
1 year ago
0
Add a figure for the P2RA writeup
#178
jeffkaufman
closed
1 year ago
1
Assess HMC mixing statistics
#177
dp-rice
opened
1 year ago
4
Show viral read counts on boxen plots
#176
dp-rice
closed
1 year ago
0
Consider splitting Spurbeck by sample prep method
#175
dp-rice
closed
1 year ago
1
Make output summary table and figures
#174
dp-rice
closed
1 year ago
0
Command line arguments for fit.py
#173
dp-rice
closed
1 year ago
1
Stan output is not deterministic
#172
dp-rice
closed
1 year ago
1
Hierarchical model checking
#171
dp-rice
closed
1 year ago
0
Simon aav update
#170
simonleandergrimm
closed
1 year ago
2
Assess the sensitivity to the prior on mu
#169
dp-rice
closed
1 year ago
0
Summary figures
#168
dp-rice
closed
1 year ago
1
Summary table
#167
dp-rice
closed
1 year ago
0
Simon aav 2
#166
simonleandergrimm
closed
1 year ago
2
Simon bk virus
#165
simonleandergrimm
closed
1 year ago
0
Turn JC Virus and BK Virus estimates into age-adjusted estimates
#164
simonleandergrimm
closed
1 year ago
1
Simon jc virus
#163
simonleandergrimm
closed
1 year ago
0
Add stubs for BKV, JCV, MCV, and AAV2
#162
jeffkaufman
closed
1 year ago
2
Check whether model output changes on pre-submit
#161
dp-rice
closed
1 year ago
1
Update model.md to reflect hierarchical model
#160
dp-rice
closed
1 year ago
0
Get method MGS sample attribute
#159
dp-rice
closed
1 year ago
0
Fit hierarchical model to most viruses
#158
dp-rice
closed
1 year ago
0
Look into how HPV prevalence has changed since 2013-2016
#157
jeffkaufman
closed
1 year ago
2
get all pathogens passing tests
#156
jeffkaufman
closed
1 year ago
0
Expand rna_pathogens
#155
jeffkaufman
closed
1 year ago
0
Simon hep b c extension
#154
simonleandergrimm
closed
1 year ago
0
Investigate if seroprevalence always matches present latent infections.
#153
simonleandergrimm
closed
1 year ago
1
Added a test to identify duplicate prevalences/incidences. Dropped duplicate HSV-1 and HSV-2 seroprevalence estimates.
#152
simonleandergrimm
closed
1 year ago
3
Don't emit zeros for any predictor
#151
jeffkaufman
closed
1 year ago
0
Simon hcv
#150
simonleandergrimm
closed
1 year ago
0
Deal with several incidences/prevalences for same time and location
#149
simonleandergrimm
closed
1 year ago
2
Some viruses give 0 incidences, which break the model
#148
jeffkaufman
closed
1 year ago
0
Add rna_virus dictionary to pathogens
#147
dp-rice
closed
1 year ago
0
Build model for one set of taxids at a time
#146
dp-rice
closed
1 year ago
0
Divide predictions by taxids
#145
jeffkaufman
closed
1 year ago
2
Simon ebv
#144
simonleandergrimm
closed
1 year ago
1
Create estimates for HPV (genital and oral) subtypes, once we have extensive DNA metagenomic sequencing data.
#143
simonleandergrimm
closed
1 year ago
1
Remove estimate for Hepatitis A
#142
jeffkaufman
closed
1 year ago
0
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