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CDCgov
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ww-inference-model
An in-development R package and a Bayesian hierarchical model jointly fitting multiple "local" wastewater data streams and "global" case count data to produce nowcasts and forecasts of both observations
https://cdcgov.github.io/ww-inference-model/
Apache License 2.0
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Infection to count delay length should be the length of the unobserved exponential growth period
#67
kaitejohnson
opened
2 months ago
0
Review initialization approach, document it more, and possibly make it more generic
#66
dylanhmorris
opened
2 months ago
0
Infection feedback strength for simulated data should be configurable
#65
dylanhmorris
closed
1 month ago
2
Tweak / plot size in vignette plots
#64
dylanhmorris
opened
2 months ago
3
Add test coverage with Github token
#63
kaitejohnson
opened
2 months ago
0
geom_line => geom_step
#62
dylanhmorris
closed
2 months ago
0
Specify all inputs to `generate_simulated_data()` or draw from prior as default
#61
kaitejohnson
opened
2 months ago
0
Posterior predictive distributions should be piecewise constant?
#60
athowes
closed
2 months ago
1
49 output class creation
#59
kaitejohnson
closed
1 month ago
10
Adding class and methods for wwinference model fit
#58
gvegayon
closed
1 month ago
4
Allow user to generate simulated data without auxiliary site/subpop
#57
kaitejohnson
opened
2 months ago
0
2024-08-08 update : adding spatial to wwinference model.
#56
cbernalz
closed
1 month ago
10
Combining error messages with `checkmate::check_x()` output and `cli::cli_abort()`
#55
kaitejohnson
closed
2 months ago
1
Testing for key functions
#54
kaitejohnson
closed
2 months ago
6
2024-08-07 update : adding matrix normalization func. and using AR1 in spatial func.
#53
cbernalz
closed
2 months ago
1
Adding fixed geometric mean marginal variance correlation matrix correction function
#52
cbernalz
closed
2 months ago
0
Standardize to use `count_data` in all functions
#51
kaitejohnson
closed
1 month ago
2
Use `ar1.stan` in the new spatial functions
#50
kaitejohnson
closed
2 months ago
0
Standardize and stabilize outputs of `wwinference()` wrapper function
#49
kaitejohnson
closed
1 month ago
2
Tests for autoindexing
#48
dylanhmorris
closed
2 months ago
0
Slight tweak to the centered code
#47
kaitejohnson
closed
2 months ago
0
Add modularity in pre-processing/stan model to vary spatial correlation functions
#46
kaitejohnson
opened
2 months ago
0
Modify vignette to describe the distance data (as this represents a new input dataset).
#45
kaitejohnson
opened
2 months ago
2
Incorporate stan spatial functions into `wwinference.stan`
#44
kaitejohnson
closed
1 month ago
0
IHR(t) should be on the time of infection, not time of admissions
#43
kaitejohnson
opened
2 months ago
4
Parameterize weekday effect with a Dirichlet
#42
kaitejohnson
closed
1 month ago
2
Decomposing a MVN
#41
kaitejohnson
closed
2 months ago
4
Quick fix to R(t) plots and markdown rendering
#40
kaitejohnson
closed
2 months ago
0
2024-07-30 update : added exp decay func test.
#39
cbernalz
closed
2 months ago
6
Adding unit tests for spatial functions.
#38
cbernalz
closed
2 months ago
0
Input hospital admissions and wastewater data checks
#37
kaitejohnson
closed
2 months ago
4
Example set of tests for `flag_as_ww_outliers()`
#36
kaitejohnson
closed
2 months ago
0
Consider constraining site-level R(t) deviations to sum to 0
#35
kaitejohnson
opened
2 months ago
2
2024-07-22 update : added stan spatial funcs.
#34
cbernalz
closed
2 months ago
4
Update pkgdown.yaml
#33
kaitejohnson
closed
3 months ago
2
Add an example of a pipeline with a config
#32
kaitejohnson
opened
3 months ago
1
30 updating package data in spatial ww branch
#31
cbernalz
closed
3 months ago
0
Updating package data in spatial-ww branch.
#30
cbernalz
closed
3 months ago
0
Modularize the functions in the `generate_simulated_data()` function
#29
kaitejohnson
closed
1 month ago
10
Stan spatial functions.
#28
cbernalz
closed
2 months ago
15
Add testing for key functions
#27
kaitejohnson
closed
2 months ago
1
Adding spatial components to spatial-main.
#26
cbernalz
closed
3 months ago
1
Forward simulation spatially correlated unadjusted reproduction number
#25
cbernalz
closed
2 months ago
0
10 add hosp admissions only model functionality
#24
kaitejohnson
closed
2 months ago
5
Set up caching of `wwinference.Rmd` vignette in R-cmd-check
#23
kaitejohnson
closed
1 month ago
2
Add mermaid diagram to `model_definition.md`
#22
kaitejohnson
opened
3 months ago
0
Make the small added value for `log_conc` configurable
#21
dylanhmorris
opened
3 months ago
0
Make init generation function more generic
#20
dylanhmorris
closed
1 month ago
1
Remove automatic directory mode setting unless strictly needed
#19
dylanhmorris
opened
3 months ago
0
Clarify role of `get_stan_data` compared to data pre-processing functions
#18
dylanhmorris
opened
3 months ago
0
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