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mac-theobio
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McMasterPandemic
SEIR+ model
GNU General Public License v3.0
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Hook up TMB Laplace approximation machinery for regularizing log linear model parameters
#143
stevencarlislewalker
opened
2 years ago
0
Log linear R side
#142
stevencarlislewalker
opened
2 years ago
0
Log linear C++ side
#141
stevencarlislewalker
closed
2 years ago
1
Design data structure for passing log-linear model information to TMB
#140
stevencarlislewalker
closed
2 years ago
1
c++ for negative binomial objective function
#139
stevencarlislewalker
closed
2 years ago
0
C++ to create condensed_state_vector from concatenated_state_vector
#138
stevencarlislewalker
closed
2 years ago
0
make sure to look for time varying multipliers that should be applied on the start date
#137
stevencarlislewalker
closed
2 years ago
1
Add absolute time-varying parameter specification on TMB/C++ side
#136
stevencarlislewalker
closed
2 years ago
1
Consider adding feature for absolute parameter values in `params_timevar`
#135
papsti
closed
2 years ago
6
Move c++ function make_state into the objective function
#134
stevencarlislewalker
opened
2 years ago
0
Harmonize time varying multipliers on the start date with lin_params
#133
stevencarlislewalker
closed
2 years ago
1
By default, every inflow should have an associated outflow
#132
stevencarlislewalker
closed
2 years ago
0
Regular expression validation for formula parser
#131
stevencarlislewalker
closed
2 years ago
1
Welcome back Zach
#130
stevencarlislewalker
closed
2 years ago
1
parallel_accumulators error in flex_spec vignette chunk
#129
bbolker
closed
2 years ago
2
Hardening/testing spec v0.1.1
#128
stevencarlislewalker
closed
2 years ago
0
Passing test of calibration of basic model with make_state on c++ side
#127
stevencarlislewalker
closed
2 years ago
1
Option to start power method from r-side make_state
#126
stevencarlislewalker
closed
2 years ago
1
tmb_status reported inconsistently
#125
stevencarlislewalker
closed
2 years ago
1
Option to utilize R-based `make_state` during calibration
#124
stevencarlislewalker
closed
2 years ago
0
some tests failing on the master branch
#123
papsti
opened
2 years ago
1
Add status indicator back from c++
#122
stevencarlislewalker
closed
2 years ago
2
Add option to round initial state
#121
stevencarlislewalker
opened
2 years ago
8
Add separate do_hazard for linearization
#120
stevencarlislewalker
closed
2 years ago
0
Update `make_state` avoidance once spec version 0.1.1 is complete
#119
stevencarlislewalker
closed
2 years ago
0
test vaccination+variant model with flex approach
#118
stevencarlislewalker
closed
2 years ago
0
pass `tv_mult` as a parameter so that it can be optimized
#117
stevencarlislewalker
closed
2 years ago
0
Integrals of count vectors should be done in R, not C++
#116
stevencarlislewalker
closed
2 years ago
1
Rename variables on both C++ and R sides
#115
stevencarlislewalker
closed
2 years ago
1
Do `make_state` on the `C++` side
#114
stevencarlislewalker
closed
2 years ago
0
Write draft spec ver 0.1.1
#113
stevencarlislewalker
closed
2 years ago
0
test model calibration
#112
stevencarlislewalker
closed
2 years ago
0
`do_hazard` not getting passed through `make_base_model`
#111
stevencarlislewalker
closed
2 years ago
1
enable passing of age-structured parameters in `params_timevar` argument for sims
#110
papsti
opened
2 years ago
0
test for time varying parameters in a vaccination model
#109
stevencarlislewalker
closed
2 years ago
0
Test two-dose vaccination model without time varying parameters using TMB framework
#108
stevencarlislewalker
closed
2 years ago
0
Sums of parameters and state variables that can be used in rate matrix computations (R side
#107
stevencarlislewalker
closed
2 years ago
0
Sums of parameters and state variables that can be used in rate matrix computations
#106
stevencarlislewalker
closed
2 years ago
0
Handle the case of division by zero in rate matrix updates
#105
stevencarlislewalker
closed
2 years ago
0
Compute sums of state variables grouped by vaccine categories without `condense_state`
#104
stevencarlislewalker
opened
2 years ago
1
Allow vectors in and out of rate matrix expressions
#103
stevencarlislewalker
closed
2 years ago
0
Update piecewise time varying parameters on the C++ side
#102
stevencarlislewalker
closed
2 years ago
0
Make sure that initial and final values are added to the report
#101
stevencarlislewalker
closed
2 years ago
1
Explain or fix unused variable warnings coming from compilation of `macpan.cpp`
#100
stevencarlislewalker
closed
2 years ago
1
Add changing force of infection to results from `run_sim`
#99
stevencarlislewalker
closed
2 years ago
0
Add a new vector, concatenated_ratematrix_elements , to the report in TMB
#98
stevencarlislewalker
closed
2 years ago
1
Document model structure objects
#97
stevencarlislewalker
closed
2 years ago
1
Default dll for make_macpan_tmb_fun
#96
stevencarlislewalker
closed
3 years ago
1
More gracefully handle printouts from cpp files in the tmb test harness located at `inst/tmb`
#95
stevencarlislewalker
closed
3 years ago
8
C++ for spec version 0.0.5
#94
stevencarlislewalker
closed
3 years ago
2
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