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Merged
remlapmot merged 4 commits into from
Mar 6, 2025
Merged

TwoSampleMR v0.6.11 #598

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0bfa355
Add mr.raps test skips if not installed
remlapmot Mar 4, 2025
30755fa
Remove rsnps as mr.raps now correctly configured
remlapmot Mar 4, 2025
d42a7b0
Bump version
remlapmot Mar 4, 2025
73a429e
Update NEWS.md
remlapmot Mar 4, 2025
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3 changes: 1 addition & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: TwoSampleMR
Title: Two Sample MR Functions and Interface to MRC Integrative
Epidemiology Unit OpenGWAS Database
Version: 0.6.10
Version: 0.6.11
Authors@R: c(
person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-0920-1055")),
Expand Down Expand Up @@ -57,7 +57,6 @@ Suggests:
mr.raps,
MRInstruments,
randomForest,
rsnps,
testthat,
tidyr
VignetteBuilder:
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7 changes: 7 additions & 0 deletions NEWS.md
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@@ -1,3 +1,10 @@
# TwoSampleMR v0.6.11

(Release date 2025-03-06)

* The tests using **mr.raps** are now run conditionally.
* The **rsnps** package has been removed from Suggests because the configuration of **mr.raps** has been corrected.

# TwoSampleMR v0.6.10

(Release date 2025-03-03)
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4 changes: 4 additions & 0 deletions tests/testthat/test_mr.R
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Expand Up @@ -15,13 +15,15 @@ test_that("Test mr(): MR Egger, Weighted median, Inverse variance weighted, Simp
})

test_that("mr.raps", {
skip_if_not_installed("mr.raps")
res2 <- suppressWarnings(mr(dat, method_list = "mr_raps"))
expect_equal(nrow(res2), 1L)
expect_equal(ncol(res2), 9L)
expect_equal(res2[1, "b"], 0.4647, tolerance = 1e-3)
})

test_that("mr.raps over.dispersion option", {
skip_if_not_installed("mr.raps")
params <- default_parameters()
params$over.dispersion <- FALSE
res3 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
Expand All @@ -31,6 +33,7 @@ test_that("mr.raps over.dispersion option", {
})

test_that("mr.raps loss.function option", {
skip_if_not_installed("mr.raps")
params <- default_parameters()
params$loss.function <- "tukey"
res4 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
Expand All @@ -40,6 +43,7 @@ test_that("mr.raps loss.function option", {
})

test_that("mr.raps shrinkage option", {
skip_if_not_installed("mr.raps")
params <- default_parameters()
params$shrinkage <- TRUE
res5 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
Expand Down
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