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epiverse-trace
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finalsize
R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility
https://epiverse-trace.github.io/finalsize/
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Move finalsize specific element from solver function to main finalsize() function
#68
Bisaloo
opened
2 years ago
14
Add test for solver equivalence R
#67
pratikunterwegs
closed
2 years ago
0
Rcpp implementation of final size with risk groups
#66
pratikunterwegs
closed
2 years ago
4
Final size with risk groups using Newton solver
#65
pratikunterwegs
closed
2 years ago
5
Fix test for iterative solver, add epi_spread step
#64
pratikunterwegs
closed
2 years ago
0
Simplify and improve performance of iterative solver
#63
Bisaloo
closed
2 years ago
11
Add solver option to final_size_grps
#62
pratikunterwegs
closed
2 years ago
0
Document final_size_grps solver option
#61
pratikunterwegs
closed
2 years ago
0
Document Newton solver
#60
pratikunterwegs
closed
2 years ago
0
Tests for Newton solver with Polymod data
#59
pratikunterwegs
closed
2 years ago
0
Tests for Newton solver with multiple risk groups
#58
pratikunterwegs
closed
2 years ago
0
Tests for Newton solver with varying r0
#57
pratikunterwegs
closed
2 years ago
0
Add tests for Newton solver in simple cases
#56
pratikunterwegs
closed
2 years ago
0
Implement Newton solver in R
#55
pratikunterwegs
closed
2 years ago
0
Change final size notation to avoid confusion with Pi
#54
pratikunterwegs
closed
2 years ago
0
Iterative solver in final_size_grps missing solver step args
#53
pratikunterwegs
closed
2 years ago
1
Vectorise internal function fn_f in iterative solver
#52
pratikunterwegs
closed
2 years ago
0
Vectorise contact_matrix filling in iterative solver
#51
pratikunterwegs
closed
2 years ago
0
Squash multiple input checks into one stopifnot call
#50
pratikunterwegs
closed
2 years ago
0
Use Kronecker product to replicate contact matrix
#49
pratikunterwegs
closed
2 years ago
0
Document finalsize susc groups R
#48
pratikunterwegs
closed
2 years ago
0
Test final size susc groups R
#47
pratikunterwegs
closed
2 years ago
0
Test finalsize iterative solver R
#46
pratikunterwegs
closed
2 years ago
0
Final size by susc groups in R
#45
pratikunterwegs
closed
2 years ago
0
Final size iterative solver in R
#44
pratikunterwegs
closed
2 years ago
0
Better tests for final size by susceptibility groups
#43
pratikunterwegs
closed
2 years ago
0
R implementation of final size with susceptibility groups
#42
pratikunterwegs
closed
2 years ago
5
R implementation of final_size with susceptibility groups
#41
pratikunterwegs
closed
2 years ago
0
Cpp implementation of final size with susceptibility groups
#40
pratikunterwegs
closed
2 years ago
0
Final epidemic size with susceptibility groups
#39
pratikunterwegs
closed
2 years ago
4
Rcpp
#38
pratikunterwegs
closed
2 years ago
0
Update Rcpp implementation with main
#37
pratikunterwegs
closed
2 years ago
0
Rcpp implementation of final_size
#36
pratikunterwegs
closed
2 years ago
0
Check that Rcpp implementation of finfal_size works
#35
pratikunterwegs
closed
2 years ago
0
Test C++ funs f1 and f2 in Rcpp implementation
#34
pratikunterwegs
closed
2 years ago
0
Test for infections in isolated groups
#33
pratikunterwegs
closed
2 years ago
0
Better tests for finalsize
#32
pratikunterwegs
closed
2 years ago
1
Allow passing single prop_suscep value
#31
pratikunterwegs
closed
2 years ago
0
Check for plausible epidemic final size
#30
pratikunterwegs
closed
2 years ago
0
Check for r0 > 1
#29
pratikunterwegs
closed
2 years ago
0
Remove DS_Store file
#28
pratikunterwegs
closed
2 years ago
0
Create functions to convert between R0 and transmissibility
#27
BlackEdder
closed
1 year ago
4
WIP Improve testing of the final size function
#26
BlackEdder
closed
2 years ago
2
WIP Improve testing of the final size function
#25
BlackEdder
closed
2 years ago
1
Add error/message cases to basic tests
#24
pratikunterwegs
closed
2 years ago
0
More basic checks for final_size arguments
#23
pratikunterwegs
closed
2 years ago
0
Specify initial proportions infected
#22
pratikunterwegs
closed
2 years ago
0
Discussion item: possibly useful functionality elsewhere
#21
sbfnk
opened
2 years ago
1
Dkscc
#20
sbfnk
closed
2 years ago
1
Initial setup as R package
#19
pratikunterwegs
closed
2 years ago
5
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