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p2ra
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Johnson Flu A: hack together a rough P2RA estimate
#240
jeffkaufman
opened
4 months ago
1
flu: check in data from current season
#239
jeffkaufman
closed
4 months ago
0
Set pseudocounts back to 0.1 infections per week (previously 0.001). Reran fit.py.
#238
simonleandergrimm
closed
7 months ago
1
Added mypy inline comments and fixed tuple mypy issue in plot_summaries.py
#237
simonleandergrimm
closed
8 months ago
1
Changed logic of hatch_zero_counts.
#236
simonleandergrimm
closed
8 months ago
4
Plot reads per prevalence
#235
dp-rice
closed
10 months ago
1
don't italicize RA
#234
jeffkaufman
closed
11 months ago
0
Include vertical lines on charts
#233
jeffkaufman
closed
11 months ago
0
Add incidence figure scripts to repo
#232
simonleandergrimm
opened
11 months ago
0
Also generate by_location_prevalence-violin plot
#231
jeffkaufman
closed
11 months ago
0
Hide Crits-Cristoph Flu predictors, since they're driven entirely by …
#230
jeffkaufman
closed
11 months ago
0
pseudocounts: determine fraction of samples this applies to
#229
jeffkaufman
closed
11 months ago
0
authors: check in script used to determine the set of authors
#228
jeffkaufman
closed
11 months ago
0
print out relevant ra(1%)
#227
jeffkaufman
closed
11 months ago
0
Add bar chart for prevalence
#226
jeffkaufman
closed
11 months ago
1
Pathogens: remove LA-specific HIV estimate
#225
jeffkaufman
closed
11 months ago
0
Switch from ra-1000 to ra-100
#224
jeffkaufman
closed
11 months ago
0
Fit Brinch HIV/HCV
#223
dp-rice
closed
11 months ago
1
Copenhagen estimates for HIV and HCV. Added multiplication method to PrevalenceAbsolute. Edited test.py, as it runs an example test on HIV estimates.
#222
simonleandergrimm
closed
11 months ago
2
Reinclude HBV, HSV-2, and AAV-6 in analysis for preprint
#221
simonleandergrimm
opened
11 months ago
0
Run model with read exclusions
#220
dp-rice
closed
12 months ago
6
Update model documentation
#219
dp-rice
closed
12 months ago
1
Pathogens with subtypes only get model diagnostic plots for one
#218
dp-rice
closed
12 months ago
1
Create HIV estimates for Copenhagen
#217
simonleandergrimm
closed
11 months ago
1
Plot estimates with zero counts differently
#216
dp-rice
closed
12 months ago
1
Refit model with bad MGS pathogens removed
#215
dp-rice
closed
1 year ago
0
Drop HSV-2, HBV, and AAV6
#214
jeffkaufman
closed
1 year ago
0
Add command list_taxids.py
#213
jeffkaufman
closed
1 year ago
0
Generate figures for blog post
#212
dp-rice
closed
1 year ago
0
add generate_numbers_for_discussion
#211
jeffkaufman
closed
1 year ago
0
Bump MGS tag to use deduplicated data and correct set of taxids
#210
dp-rice
closed
1 year ago
0
Rework counts figure
#209
jeffkaufman
closed
1 year ago
3
Consolidate plotting scripts
#208
dp-rice
closed
12 months ago
1
Fit brinch
#207
dp-rice
closed
1 year ago
0
Fixed locations for DK estimates.
#206
simonleandergrimm
closed
1 year ago
0
Changed description of how we extrapolate from Northern European estimates to Denmark.
#205
simonleandergrimm
closed
1 year ago
0
Added JC Virus, BK Virus, and MC Virus estimates for Denmark, fixed US prevalence for MCV
#204
simonleandergrimm
closed
1 year ago
0
Update infra to cover Brinch 2020
#203
jeffkaufman
closed
1 year ago
0
2007 HBV estimate for Denmark, extrapolated to 2015-2018.
#202
simonleandergrimm
closed
1 year ago
0
Extend HPV Denmark and US estimate to all HPV subtypes
#201
simonleandergrimm
closed
12 months ago
2
HPV Denmark estimate, based on a 2016 study of 4000 Danish men.
#200
simonleandergrimm
closed
1 year ago
2
Extrapolated 2006 Dutch CMV seroprevalence to Denmark 2015-2018.
#199
simonleandergrimm
closed
1 year ago
0
Revisiting DK EBV and CMV estimates, or adding limitation to report:
#198
simonleandergrimm
closed
12 months ago
1
Changed extrapolation of EBV from 2020-2021 to 2015-2018.
#197
simonleandergrimm
closed
1 year ago
0
Extrapolated Denmark EBV estimate to 2015-2018
#196
simonleandergrimm
closed
1 year ago
0
Pin `pydantic` to 1.10
#195
dp-rice
closed
1 year ago
1
Simon test branch
#194
simonleandergrimm
closed
1 year ago
0
Extrapolating German HSV estimates to Denmark 2015-2018
#193
simonleandergrimm
closed
1 year ago
0
Extrapolated Northern European AAV seroprevalence in hemophilia patients to Denmark 2015-2018
#192
simonleandergrimm
closed
1 year ago
2
Moving `tidy_name` broke `figures/counts-by-pathogen-and-study.py`
#191
dp-rice
closed
1 year ago
1
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