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174 cmdstanr sample args #175

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Sep 27, 2024
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65312a5
add all non depracted cmdstanr::sample args to mcmc options
kaitejohnson Sep 19, 2024
4ae40f3
set show messages to false in the test data mcmc options
kaitejohnson Sep 19, 2024
d65a5cc
update test data
kaitejohnson Sep 19, 2024
10711ed
add documentation for refresh
kaitejohnson Sep 19, 2024
4ae2e9d
update tests to expect all args to mcmc_options
kaitejohnson Sep 19, 2024
7543c2b
replace very verbose handling of passing cmdstanr::sample with a do.call
kaitejohnson Sep 19, 2024
35754b5
replace very verbose handling of passing cmdstanr::sample with a do.call
kaitejohnson Sep 19, 2024
221304c
update docs
kaitejohnson Sep 19, 2024
dcb5dc0
fix test
kaitejohnson Sep 19, 2024
702db94
try to suppress ESS warning
kaitejohnson Sep 19, 2024
7d4e01f
Update tests/testthat/test_ww_model.R
kaitejohnson Sep 19, 2024
4831258
set fit_opts as an empty list
kaitejohnson Sep 19, 2024
c780542
replace test with checkmate
kaitejohnson Sep 19, 2024
a25cac1
Merge branch '174-cmdstanr-sample-args' of https://github.com/CDCgov/…
kaitejohnson Sep 19, 2024
8447704
add wrapper function to silence warnings on mcmc tests
kaitejohnson Sep 19, 2024
5dc640c
Update R/wwinference.R
kaitejohnson Sep 22, 2024
2dba97b
remove extra args from get mcmc options
kaitejohnson Sep 22, 2024
3dc8b95
fix example and rerun documentation
kaitejohnson Sep 22, 2024
3c76895
add checkmates expect names to only allow cmdstanr$ sample args to be…
kaitejohnson Sep 22, 2024
f7d7d39
make get_mcmc_options an internal function
kaitejohnson Sep 22, 2024
ccc7792
modify wwinference call to pass a list not function to fit_opts
kaitejohnson Sep 22, 2024
0a9c49b
fix call to get number of chains
kaitejohnson Sep 22, 2024
9965832
update package data
kaitejohnson Sep 22, 2024
47ec753
modify language in vignette to no longer reference get_mcmc_options
kaitejohnson Sep 22, 2024
388a81c
Update R/wwinference.R
kaitejohnson Sep 22, 2024
6e41735
update documentation
kaitejohnson Sep 22, 2024
be2aaa3
run precommit
kaitejohnson Sep 22, 2024
fc635a2
remove example for function thts not exported
kaitejohnson Sep 22, 2024
1932126
fix test
kaitejohnson Sep 22, 2024
4af34d6
modify test data and rerun
kaitejohnson Sep 22, 2024
94900a6
Update R/wwinference.R
kaitejohnson Sep 23, 2024
53f4772
Update R/wwinference.R
kaitejohnson Sep 23, 2024
811c4f3
Update R/wwinference.R
kaitejohnson Sep 23, 2024
fea1582
Update R/wwinference.R
kaitejohnson Sep 23, 2024
d02c83c
Update R/wwinference.R
kaitejohnson Sep 23, 2024
8aeddc0
Update R/wwinference.R
kaitejohnson Sep 23, 2024
abac574
Update R/wwinference.R
kaitejohnson Sep 23, 2024
68db82c
Update R/wwinference.R
kaitejohnson Sep 23, 2024
5bff3df
Update R/wwinference.R
kaitejohnson Sep 23, 2024
77c7b73
Update R/wwinference.R
kaitejohnson Sep 23, 2024
1608f23
Update R/wwinference.R
kaitejohnson Sep 23, 2024
3bc1ac1
Update R/wwinference.R
kaitejohnson Sep 23, 2024
a255fc2
Update R/wwinference.R
kaitejohnson Sep 23, 2024
f202eb0
Update R/wwinference.R
kaitejohnson Sep 23, 2024
c2c65a1
export function and remove args that are already defaults
kaitejohnson Sep 23, 2024
f684518
fix tests
kaitejohnson Sep 23, 2024
c594a28
fix test, add formalArgs to imports
kaitejohnson Sep 23, 2024
d7d77e7
remove parallel chains and set to default, document things
kaitejohnson Sep 23, 2024
43571c1
Update R/wwinference.R
kaitejohnson Sep 24, 2024
718ebcf
Update R/wwinference.R
kaitejohnson Sep 24, 2024
606eff3
update docs
kaitejohnson Sep 24, 2024
becd549
run precommit and add new test
kaitejohnson Sep 24, 2024
dc67274
add reg exp to test
kaitejohnson Sep 24, 2024
d94d580
add setting mc cores to 4
kaitejohnson Sep 24, 2024
b0ffc23
add the chains back so that we use them in inits
kaitejohnson Sep 24, 2024
d70c609
update test data
kaitejohnson Sep 24, 2024
acd0c4b
Merge branch 'main' into 174-cmdstanr-sample-args
dylanhmorris Sep 24, 2024
6d7a305
remove methods formal args from package
kaitejohnson Sep 24, 2024
492d793
Merge branch '174-cmdstanr-sample-args' of https://github.com/CDCgov/…
kaitejohnson Sep 24, 2024
ee27de0
try updating testing data
kaitejohnson Sep 25, 2024
a6e78b0
Update R/wwinference.R
kaitejohnson Sep 26, 2024
1489d7c
Update R/wwinference.R
kaitejohnson Sep 26, 2024
cfe8b0a
fix documentation
kaitejohnson Sep 26, 2024
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4 changes: 2 additions & 2 deletions tests/testthat/test_ww_model.R
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@ test_that("Test the wastewater inference model on simulated data.", {
#######
# run model briefly on the simulated data
#######
withr::with_seed(5, {
expect_warnin(withr::with_seed(5, {
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fit <- do.call(
wwinference::wwinference,
model_test_data
)
})
}))

params <- model_test_data$model_spec$params
obs_last_draw <- posterior::subset_draws(fit$fit$result$draws(),
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