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Multicountry setup #347

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Multicountry setup #347

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javierps
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@javierps javierps commented Apr 4, 2023

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javierps and others added 30 commits March 10, 2023 11:17
@javierps
first pass at admin_lev specific observation models with overdispersion
cb0321a
@javierps
add prior on the inverse over dispersion parameters
1d51a34
@javierps
Fix admin level indexing
1e983e5
@javierps
typo
9251fa5
@javierps
Modify 0-sum constraint to use QR decomposition as proposed in https:…
3b67692 
…//discourse.mc-stan.org/t/test-soft-vs-hard-sum-to-zero-constrain-choosing-the-right-prior-for-soft-constrain/3884/31
@javierps
drop censored 0 cases
1889737
@javierps
add print statements
48eeb39
@javierps
fix get censoring inds
b5d698f
@javierps
commented print statement to debug grad issue
5d8f792
@javierps
fix typo
fa34c41
@javierps
update map_obs_loctime vectors
5fcafb3
@javierps
fix censored_zero_inds and wider prior on od param for lower level ad…
36c4136 
…min units
@javierps
add pooling for od param for lower level units
56d3861
@javierps
update generated quantities
28033e6
@javierps
update poolin line
4c6002b
@javierps
generated quantities for pooled model
b51c1fa
@javierps
titghen prior on hierarchical mean
7f2604f
@javierps
tigthen prior on sd of subnational level od_param in non-hierarchical…
f987a78 
… model.
@javierps
add print statment for the number of cases in admin levels that are NA
d736af0
@javierps
update priors
757fca2
@javierps
use config to pass parameters for the od prior and add corresponding …
32d6af1 
…check functions
@javierps
update set_parameters and get_all_config_options
2df05e1
@javierps
rename pooled model stan file
097a883
@javierps
temporary fix to initial values with new obsmodels
329a15b
@KaiyueZou
fixed small error when generating configs
cdda4a4
@javierps
update prior on std_dev_w with inv_gamma
0780f4e
@javierps
hardcode prior of sd_w
5557bec
@javierps
Merge branch 'dev_new_obsmodel' of github.com:hopkinsidd/cholera-mapp…
1c4c5b8 
…ing-pipeline into dev_new_obsmodel
@javierps
update genquant to take std_dev_w instead of log_std_dev_w
4552d12
@javierps
Merge branch 'dev' into dev_new_obsmodel
e8bf3fc
javierps and others added 30 commits April 4, 2023 21:43
@javierps
spare memory
95093c5
@javierps
add check functions for ncpus_parallel_prep and do_parallel_prep
8e41ca1
@javierps
Merge branch 'dev' into dev_parallel_aggregation
c8c28a6
@javierps
only snap observations for which the TL and TR are in different time …
f586602 
…slices
@javierps
Merge branch 'dev_parallel_aggregation' of github.com:hopkinsidd/chol…
ef8ac2b 
…era-mapping-pipeline into dev_parallel_aggregation
@javierps
clean check_snap_tol from merge
45c32f5
@javierps
update test config to test censoring, aggregation and in parallel
03e0389
@javierps
update number of parallel chunks based on n_cpus and rm sf_cases and …
5eb0b57 
…ind_mapping after not used
@javierps
more cleanup
bf404e6
@javierps
fix bug in censoring inds
90076e0
@eclee25
Merge branch 'dev' into dev_parallel_aggregation
96e2343
@javierps
fix remove 0-censored issue
c458aaf
@javierps
memory cleanup
1a46ff3
@javierps
fix close_parallel setup name and add to end of prepare_map_data_revised
fa21789
@javierps
Merge branch 'dev_parallel_aggregation' of github.com:hopkinsidd/chol…
fb71ff6 
…era-mapping-pipeline into dev_parallel_aggregation
@javierps
add snap tol to config checks
abd196a
@javierps
Merge branch 'dev' into dev_new_obsmodel_multicountry
7ca6a95
@javierps
update taxdat namespace
aa3f59a
@javierps
typo in documentation
da4bcb6
@javierps
Merge branch 'dev' into dev_new_obsmodel_multicountry
3a74760
@javierps
merge dev_parallel aggregation
efea24c 
Merge branch 'dev_parallel_aggregation' into dev_new_obsmodel_multicountry

# Conflicts:
#	packages/taxdat/NAMESPACE
#	packages/taxdat/R/setup_helpers.R
#	packages/taxdat/R/stan_input_helpers.R
@javierps
custom initial values using mean rate per country
b98c9d5
@javierps
add location_name to aggregation output
acfdf0b
@eclee25
Merge branch 'dev' into dev_new_obsmodel_multicountry
e4a79ab
@javierps
add location_name within do call
abbf193
@javierps
Merge branch 'dev_new_obsmodel_multicountry' of github.com:hopkinsidd…
82cd34f 
…/cholera-mapping-pipeline into dev_new_obsmodel_multicountry
@javierps
extract u_countries before removing stan_input
b288536
@javierps
fix prepare intial values
da41820
@javierps
fix get_country to account for EMR location region
04778cb
@javierps
Merge branch 'dev' into dev_new_obsmodel_multicountry
520730b
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3 participants
@javierps @KaiyueZou @eclee25