CDCgov ww-inference-model issues

CDCgov / 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

18 stars 2 forks source link

issues

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2024-08-08 update : adding spatial to wwinference model.

#56 cbernalz closed 3 months ago
10
Combining error messages with `checkmate::check_x()` output and `cli::cli_abort()`

#55 kaitejohnson closed 3 months ago
1
Testing for key functions

#54 kaitejohnson closed 3 months ago
6
2024-08-07 update : adding matrix normalization func. and using AR1 in spatial func.

#53 cbernalz closed 3 months ago
1
Adding fixed geometric mean marginal variance correlation matrix correction function

#52 cbernalz closed 3 months ago
0
Standardize to use `count_data` in all functions

#51 kaitejohnson closed 3 months ago
2
Use `ar1.stan` in the new spatial functions

#50 kaitejohnson closed 3 months ago
0
Standardize and stabilize outputs of `wwinference()` wrapper function

#49 kaitejohnson closed 2 months ago
2
Tests for autoindexing

#48 dylanhmorris closed 3 months ago
0
Slight tweak to the centered code

#47 kaitejohnson closed 3 months ago
0
Add modularity in pre-processing/stan model to vary spatial correlation functions

#46 kaitejohnson opened 3 months ago
0
Modify vignette to describe the distance data (as this represents a new input dataset).

#45 kaitejohnson opened 3 months ago
2
Incorporate stan spatial functions into `wwinference.stan`

#44 kaitejohnson closed 3 months ago
0
IHR(t) should be on the time of infection, not time of admissions

#43 kaitejohnson opened 3 months ago
4
Parameterize weekday effect with a Dirichlet

#42 kaitejohnson closed 3 months ago
2
Decomposing a MVN

#41 kaitejohnson closed 3 months ago
4
Quick fix to R(t) plots and markdown rendering

#40 kaitejohnson closed 3 months ago
0
2024-07-30 update : added exp decay func test.

#39 cbernalz closed 3 months ago
6
Adding unit tests for spatial functions.

#38 cbernalz closed 3 months ago
0
Input hospital admissions and wastewater data checks

#37 kaitejohnson closed 3 months ago
4
Example set of tests for `flag_as_ww_outliers()`

#36 kaitejohnson closed 3 months ago
0
Consider constraining site-level R(t) deviations to sum to 0

#35 kaitejohnson opened 4 months ago
2
2024-07-22 update : added stan spatial funcs.

#34 cbernalz closed 3 months ago
4
Update pkgdown.yaml

#33 kaitejohnson closed 4 months ago
2
Add an example of a pipeline with a config

#32 kaitejohnson opened 4 months ago
1
30 updating package data in spatial ww branch

#31 cbernalz closed 4 months ago
0
Updating package data in spatial-ww branch.

#30 cbernalz closed 4 months ago
0
Modularize the functions in the `generate_simulated_data()` function

#29 kaitejohnson closed 3 months ago
10
Stan spatial functions.

#28 cbernalz closed 3 months ago
15
Add testing for key functions

#27 kaitejohnson closed 3 months ago
1
Adding spatial components to spatial-main.

#26 cbernalz closed 4 months ago
1
Forward simulation spatially correlated unadjusted reproduction number

#25 cbernalz closed 4 months ago
0
10 add hosp admissions only model functionality

#24 kaitejohnson closed 4 months ago
5
Set up caching of `wwinference.Rmd` vignette in R-cmd-check

#23 kaitejohnson closed 3 months ago
2
Add mermaid diagram to `model_definition.md`

#22 kaitejohnson opened 4 months ago
0
Make the small added value for `log_conc` configurable

#21 dylanhmorris opened 4 months ago
0
Make init generation function more generic

#20 dylanhmorris closed 3 months ago
1
Remove automatic directory mode setting unless strictly needed

#19 dylanhmorris opened 4 months ago
0
Clarify role of `get_stan_data` compared to data pre-processing functions

#18 dylanhmorris opened 4 months ago
0
Avoid the `assign(param_names[i])` construct

#17 dylanhmorris closed 3 months ago
1
Add diagnostic flag for the maximum rhat

#16 kaitejohnson opened 4 months ago
0
Remove the many default arguments from the `generate_simulated_data()` function

#15 kaitejohnson opened 4 months ago
0
Link to package functions in documentation

#14 kaitejohnson opened 4 months ago
0
Remove redundant `pkg::fun()` when `importFrom(pkg, fun)` already present in NAMESPACE

#13 kaitejohnson opened 4 months ago
0
Make generation of data spines in post processing separate functions

#12 kaitejohnson opened 4 months ago
1
Port over the existing tests and set up CI

#11 kaitejohnson closed 4 months ago
3
Add hospital admissions only mode functionality

#10 kaitejohnson closed 4 months ago
0
Port over model tests + add testing to package functions

#9 kaitejohnson closed 4 months ago
0
Set-up R package CI

#8 kaitejohnson closed 4 months ago
1
README and model definition draft

#7 kaitejohnson closed 4 months ago
0

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