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Issue 735: Fix truncation slicing when t < truncation #736

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Merged
merged 9 commits into from
Aug 9, 2024
Merged

Issue 735: Fix truncation slicing when t < truncation #736

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c25b97f
Fix truncation slicing when t < truncation
seabbs Aug 7, 2024
63131e9
add news item
seabbs Aug 7, 2024
f7ddc9e
add unit tests for truncate vs relying on integration testing
seabbs Aug 7, 2024
bbd9271
add documentation for observation models
seabbs Aug 7, 2024
a67d882
Apply suggestions from code review
seabbs Aug 7, 2024
1e937a7
hack around truncate overloading
seabbs Aug 7, 2024
8453729
use the correct stan functions
seabbs Aug 7, 2024
6e5dff3
rename truncate -> truncate_obs
seabbs Aug 8, 2024
b630024
Update NEWS.md
seabbs Aug 9, 2024
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hack around truncate overloading
  • Loading branch information
@seabbs
seabbs committed Aug 8, 2024
commit 1e937a70bfad213773d64cc0a673bfd4a3bfb8af
4 changes: 3 additions & 1 deletion tests/testthat/setup.R
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Expand Up @@ -9,9 +9,11 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
if (!(tolower(Sys.info()[["sysname"]]) %in% "windows")) {
suppressMessages(
expose_stan_fns(files,
target_dir = system.file("stan/functions", package = "EpiNow2")
target_dir = "inst/stan/functions"
)
)
# avoid problems due to base::truncate
stan_truncate <- truncate
}
}

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8 changes: 4 additions & 4 deletions tests/testthat/test-stan-truncate.R
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Expand Up @@ -5,26 +5,26 @@ test_that("truncate() can perform truncation as expected", {
reports <- c(10, 20, 30, 40, 50)
trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2)
expected <- c(reports[1], reports[2:5] * trunc_rev_cmf)
expect_equal(truncate(reports, trunc_rev_cmf, FALSE), expected)
expect_equal(stan_truncate(reports, trunc_rev_cmf, FALSE), expected)
})

test_that("truncate() can perform reconstruction as expected", {
reports <- c(10, 20, 15, 8, 10)
trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2)
expected <- c(reports[1], reports[2:5] / trunc_rev_cmf)
expect_equal(truncate(reports, trunc_rev_cmf, TRUE), expected)
expect_equal(stan_truncate(reports, trunc_rev_cmf, TRUE), expected)
})

test_that("truncate() can handle longer trunc_rev_cmf than reports", {
reports <- c(10, 20, 30)
trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2, 0.1)
expected <- reports * trunc_rev_cmf[3:5]
expect_equal(truncate(reports, trunc_rev_cmf, FALSE), expected)
expect_equal(stan_truncate(reports, trunc_rev_cmf, FALSE), expected)
})

test_that("truncate() can handle reconstruction with longer trunc_rev_cmf than reports", {
reports <- c(10, 16, 15)
trunc_rev_cmf <- c(1, 0.8, 0.5, 0.2, 0.1)
expected <- reports / trunc_rev_cmf[3:5]
expect_equal(truncate(reports, trunc_rev_cmf, TRUE), expected)
expect_equal(stan_truncate(reports, trunc_rev_cmf, TRUE), expected)
})