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mac-theobio
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McMasterPandemic
SEIR+ model
GNU General Public License v3.0
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Undocumented S4
#193
stevencarlislewalker
closed
2 years ago
6
Undocumented code objects
#192
stevencarlislewalker
closed
2 years ago
1
Missing links in documentation
#191
stevencarlislewalker
closed
2 years ago
0
clean up branches, docs
#190
bbolker
closed
2 years ago
5
Differencing in condensation should be able to subset on dates with observed data
#189
stevencarlislewalker
closed
2 years ago
1
Ability to turn off objective function computation when forecasting
#188
stevencarlislewalker
closed
2 years ago
3
Different results between different TMB branch revisions
#187
stevencarlislewalker
closed
2 years ago
2
Waning Immunity
#186
stevencarlislewalker
closed
2 years ago
1
Warnings from TMB
#185
stevencarlislewalker
closed
2 years ago
4
Add option to flow R_vaxdose2 back to S_vaxdose2 at constant rate
#184
stevencarlislewalker
closed
2 years ago
1
C++-side work for regularization and parameter transformation
#183
stevencarlislewalker
closed
2 years ago
0
Throw error when parameter transformation doesn't match prior transformation
#182
stevencarlislewalker
opened
2 years ago
0
Refactor c++ code to move use `simulation_history` for everything that `sp` is currently being used for
#181
stevencarlislewalker
opened
2 years ago
0
Add a make rule that generates the valid_trans, valid_prior_family, etc, from an enum in the c++ code giving the indices associated with each transformation, prior family , etc...
#180
stevencarlislewalker
opened
2 years ago
0
Tests for time varying dispersion parameters using the TMB engine
#179
stevencarlislewalker
opened
2 years ago
0
Fix ggplot2 %+% namespace conflict
#178
stevencarlislewalker
opened
2 years ago
1
Runge-Kutta Steps
#177
stevencarlislewalker
opened
2 years ago
0
Sensitivity Equations
#176
stevencarlislewalker
opened
2 years ago
0
Spikes in simulations at breakpoints
#175
stevencarlislewalker
closed
2 years ago
3
Encapsulate threedosewane model construction in a function
#174
stevencarlislewalker
opened
2 years ago
0
Allow observational stochasticity of simulations with tmb
#173
stevencarlislewalker
closed
2 years ago
0
R side work to support computation of negative binomial likelihood
#172
stevencarlislewalker
closed
2 years ago
1
R side and package work to clean up support of C++ condensation
#171
stevencarlislewalker
closed
2 years ago
0
add_chain function
#170
stevencarlislewalker
opened
2 years ago
0
Replace sp with simulation_history
#169
stevencarlislewalker
opened
2 years ago
0
R-Side for condensation
#168
stevencarlislewalker
closed
2 years ago
0
Remove steps in make state specs that (12-17) that shouldn't be there
#167
stevencarlislewalker
closed
2 years ago
0
R side to compute the q vector for convolution
#166
stevencarlislewalker
closed
2 years ago
0
Warn if time varying parameter dates are outside of start and end dates
#165
stevencarlislewalker
closed
2 years ago
0
Remove the tmb objective function from the sim_args list, and just regenerate it on every call to run_sim
#164
stevencarlislewalker
closed
2 years ago
2
Test forecasting with TMB engine
#163
stevencarlislewalker
closed
2 years ago
1
add_tmb_indices should probably be called update_tmb_indices
#162
stevencarlislewalker
closed
2 years ago
0
Test for appropriate error from find_vec_indices for all missing variable scenarios
#161
stevencarlislewalker
closed
2 years ago
0
Test TMB engine for calibration with multiple data streams
#160
stevencarlislewalker
closed
2 years ago
0
Error in tmb_fun if no tmb_indices
#159
stevencarlislewalker
closed
2 years ago
1
Warn if no outflow
#158
stevencarlislewalker
closed
2 years ago
0
Change argument names in add_outflow
#157
stevencarlislewalker
closed
2 years ago
0
Pass vector of constants to TMB
#156
stevencarlislewalker
opened
2 years ago
0
Modify models.R so that rep_rate and vec_rate from/to arguments do not make explicit calls to rep
#155
stevencarlislewalker
closed
2 years ago
0
Figure out how to make the variolation model work in macpan flex
#154
stevencarlislewalker
closed
2 years ago
0
Allow inverses of complements in rate specifications
#153
stevencarlislewalker
opened
2 years ago
1
Fix flex_intro vignette
#152
stevencarlislewalker
closed
2 years ago
0
Remove commented out experimental code associated with #133
#151
stevencarlislewalker
closed
2 years ago
0
Users shouldn't have to use `expand_params_S0`
#150
stevencarlislewalker
closed
2 years ago
1
It shouldn't be necessary to set `use_flex=TRUE` if `flexmodel` is provided in `run_sim`
#149
stevencarlislewalker
closed
2 years ago
1
Passing test of calibration of variant model with make_state on c++ side
#148
stevencarlislewalker
closed
2 years ago
0
Isolate the causes of small numerical discrepancies in vaccination+variant models
#147
stevencarlislewalker
closed
2 years ago
3
Use `TMB:::FreeADFun` to make sure external pointers are getting removed
#146
stevencarlislewalker
closed
2 years ago
2
Global option to run flagged tests with factory-fresh spec settings
#145
stevencarlislewalker
closed
2 years ago
1
Add option to just update lin_state without jacobian
#144
stevencarlislewalker
closed
2 years ago
1
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