mac-theobio McMasterPandemic issues

mac-theobio / McMasterPandemic

SEIR+ model

GNU General Public License v3.0

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Multiple steps per day

#93 stevencarlislewalker opened 3 years ago
1
Refactor file structure on TMB branch

#92 stevencarlislewalker closed 3 years ago
0
Function for converting flex model into TMB AD function

#91 stevencarlislewalker closed 3 years ago
0
Spec for hazard simulation -- v0.0.5

#90 stevencarlislewalker closed 3 years ago
0
Develop R code for https://github.com/mac-theobio/McMasterPandemic/blob/tmb/notes/indexing/tmb_data_struct_v2.md

#89 stevencarlislewalker closed 3 years ago
0
Test TMB gradient

#88 stevencarlislewalker closed 3 years ago
2
Add `tmb` flag to `run_sim`

#87 stevencarlislewalker closed 3 years ago
1
Write spec versioning document and roadmap

#86 stevencarlislewalker closed 3 years ago
0
Implement `C++`/`TMB` code for spec v0.0.3/v0.0.4 -- piece-wise constant time varying parameters

#85 stevencarlislewalker closed 3 years ago
0
Finish documenting spec versions 0.0.3/0.0.4 -- piece-wise constant time varying parameters

#84 stevencarlislewalker opened 3 years ago
0
Test C++ implementation of spec 0.0.2

#83 stevencarlislewalker closed 3 years ago
0
Implement the first spec version (0.0.1) of the TMB data structure for representing rate matrix models

#82 stevencarlislewalker closed 3 years ago
0
Index-based approach to taking a simulation step

#81 stevencarlislewalker closed 3 years ago
0
Create test case out of https://github.com/mac-theobio/McMasterPandemic/blob/tmb/notes/example.R and https://github.com/mac-theobio/McMasterPandemic/blob/tmb/notes/exampleTMB.R

#80 stevencarlislewalker closed 3 years ago
1
Simple SIR model in TMB to test if indexing sparse matrix _parameters_ causes TMB to compute incorrect gradients

#79 stevencarlislewalker closed 3 years ago
0
Develop simple state variable simulation (spec version 0.0.2)

#78 stevencarlislewalker closed 3 years ago
0
Make a plan to pull out the computation of the indices on the R side

#77 stevencarlislewalker closed 3 years ago
2
Merge/rebase master back into the tmb branch before we get too far out-of-sync

#76 stevencarlislewalker closed 3 years ago
9
Getting Started Vignette is 118 Pages

#75 stevencarlislewalker closed 3 years ago
12
Add a `TMB_do_step` function to the package

#74 stevencarlislewalker closed 3 years ago
5
enable input of a vector of parameters through the `time_pars` functionality

#73 papsti opened 3 years ago
2
Use --no-lock in dependencies.R

#72 stevencarlislewalker opened 3 years ago
0
Create branch for TMB refactoring project

#71 stevencarlislewalker closed 3 years ago
0
Set up development environment for TMB refactoring project

#70 stevencarlislewalker closed 3 years ago
3
Build initial TMB example to get Weiguang started

#69 stevencarlislewalker closed 3 years ago
1
can we refactor/get rid of fixed_pars?

#68 bbolker opened 3 years ago
0
make gh-pages to redirect from bbolker.github.io/McMasterPandemic?

#67 bbolker opened 3 years ago
0
rename long filenames

#66 matthewcso closed 3 years ago
1
Backcompatiblity not working for `flex_timevar` feature

#65 papsti opened 3 years ago
0
Investigate new test_calibrate failure caused by merge

#64 matthewcso opened 3 years ago
1
Fix Roxygen documentation

#63 matthewcso closed 3 years ago
3
no visible bindings for R CMD CHECK

#62 matthewcso closed 3 years ago
2
Reduce the length of a lot of file names (potentially ignorable? It's just a note...)

#61 matthewcso closed 3 years ago
1
rescue pkgdown stuff

#60 bbolker closed 3 years ago
3
leftover test needed from flex_timevar

#59 bbolker closed 3 years ago
1
Various problems with examples introduced by ip_devel merge

#58 matthewcso closed 3 years ago
5
Dashes on lines should match the scale of the vaccination rates…

#57 bwinton closed 3 years ago
4
Silent conflict between `opt_pars$time_params` and `time_args$params_timevar` in `calibrate()`

#56 papsti opened 3 years ago
0
issue with `coef.fit_pansim(., "all")` when no base parameters were fitted (just rel vals)

#55 papsti opened 3 years ago
0
forecast CIs based on sampled parameter value instead of on MLE

#54 papsti closed 3 years ago
1
switch col_multiply to use M*v

#53 matthewcso closed 3 years ago
0
explore faster sweep on sparse matrices:

#52 matthewcso closed 3 years ago
5
exponential growth rate calculation

#51 davidearn opened 3 years ago
8
fix getting_started.Rnw, use pkgdown.extras

#50 matthewcso closed 3 years ago
0
Potential issue with calibration with do_hazard=TRUE

#49 matthewcso opened 3 years ago
1
fix make style (add import stringr), re-run styling

#48 matthewcso closed 3 years ago
0
Add link to github pages with documentation

#47 stevencarlislewalker closed 3 years ago
0
convert getting_started to rmarkdown

#46 bbolker closed 3 years ago
2
merging master to pkgdown to rebuild vignettes

#45 matthewcso closed 3 years ago
0
Create docs folder using pkgdown, add new suggests

#44 matthewcso closed 3 years ago
5

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