Merge pull request #597 from remlapmot/mrraps

TwoSampleMR 0.6.10

Author: remlapmot

DESCRIPTION

@@ -1,6 +1,7 @@
 Package: TwoSampleMR
-Title: Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database
-Version: 0.6.9
+Title: Two Sample MR Functions and Interface to MRC Integrative
+    Epidemiology Unit OpenGWAS Database
+Version: 0.6.10
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),
@@ -40,7 +41,6 @@ Imports:
     magrittr,
     MASS,
     meta,
-    mr.raps,
     MRMix,
     MRPRESSO,
     pbapply,
@@ -54,8 +54,10 @@ Suggests:
     car,
     markdown,
     MendelianRandomization,
+    mr.raps,
     MRInstruments,
     randomForest,
+    rsnps,
     testthat,
     tidyr
 VignetteBuilder: 
@@ -64,7 +66,10 @@ Remotes:
     gqi/MRMix,
     mrcieu/MRInstruments,
     MRPRESSO=rondolab/MR-PRESSO,
-    WSpiller/RadialMR
+    qingyuanzhao/mr.raps,
+    WSpiller/RadialMR,
+    ropensci/rsnps
+Additional_repositories: https://mrcieu.r-universe.dev
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NEWS.md

@@ -1,3 +1,15 @@
+# TwoSampleMR v0.6.10
+
+(Release date 2025-03-03)
+
+* The **mr.raps** package was archived from CRAN on 2025-03-01.
+A later version (0.4.1) than was on CRAN (0.2) is available from its GitHub repo <https://github.com/qingyuanzhao/mr.raps>.
+We believe this later version still works as expected in **TwoSampleMR**.
+However, version 0.4.1 depends upon **rsnps** package which is itself now only available on its GitHub repo.
+Hence, we have added both packages to our <https://mrcieu.r-universe.dev/> and added that to the `Additional_repositories` field in the DESCRIPTION.
+We have also moved mr.raps to the soft dependency list (Suggests list) and added rsnps to our Suggests list, both with remotes.
+* Fix to `default_parameters()` helpfile
+
 # TwoSampleMR v0.6.9
 
 (Release date 2025-02-05)

R/mr.R

@@ -12,6 +12,13 @@
 #' }
 mr <- function(dat, parameters=default_parameters(), method_list=subset(mr_method_list(), use_by_default)$obj)
 {
+
+  if ("mr_raps" %in% method_list) {
+    if (!(requireNamespace("mr.raps", quietly = TRUE))) {
+      stop("You can install mr.raps with install.packages('mr.raps', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))")
+    }
+  }
+  
 	mr_tab <- plyr::ddply(dat, c("id.exposure", "id.outcome"), function(x1)
 	{
 		# message("Performing MR analysis of '", x1$id.exposure[1], "' on '", x18WII58$id.outcome[1], "'")
@@ -232,7 +239,7 @@ mr_method_list <- function()
 
 #' List of parameters for use with MR functions
 #'
-#' The default is `list(test_dist = "z", nboot = 1000, Cov = 0, penk = 20, phi = 1, alpha = 0.05, Qthresh = 0.05, over.dispersion = TRUE, loss.function = "huber")`.
+#' The default is `list(test_dist = "z", nboot = 1000, Cov = 0, penk = 20, phi = 1, alpha = 0.05, Qthresh = 0.05, over.dispersion = TRUE, loss.function = "huber", shrinkage = FALSE)`.
 #'
 #' @export
 default_parameters <- function()
@@ -246,8 +253,8 @@ default_parameters <- function()
 		alpha = 0.05,
 		Qthresh = 0.05,
 		over.dispersion = TRUE,
-                loss.function = "huber",
-                shrinkage = FALSE
+    loss.function = "huber",
+    shrinkage = FALSE
 	)
 }
 
@@ -974,6 +981,10 @@ mr_ivw_fe <- function(b_exp, b_out, se_exp, se_out, parameters=default_parameter
 #' @export
 mr_raps <- function(b_exp, b_out, se_exp, se_out, parameters = default_parameters()) {
 
+  if (!(requireNamespace("mr.raps", quietly = TRUE))) {
+    stop("You can install mr.raps with install.packages('mr.raps', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))")
+  }
+  
     data <- data.frame(beta.exposure = b_exp,
                        beta.outcome = b_out,
                        se.exposure = se_exp,

man/default_parameters.Rd

@@ -0,0 +1,49 @@
+# Test mr()
+
+# dat <- make_dat("ieu-a-2", "ieu-a-7")
+load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
+
+test_that("Test mr(): MR Egger, Weighted median, Inverse variance weighted, Simple mode, Weighted mode", {
+  res <- mr(dat)
+  expect_equal(nrow(res), 5L)
+  expect_equal(ncol(res), 9L)
+  expect_equal(res[1, "b"], 0.5025, tolerance = 1e-3)
+  expect_equal(res[2, "b"], 0.3870, tolerance = 1e-3)
+  expect_equal(res[3, "b"], 0.4459, tolerance = 1e-3)
+  expect_equal(res[4, "b"], 0.3402, tolerance = 1e-3)
+  expect_equal(res[5, "b"], 0.3791, tolerance = 1e-1)
+})
+
+test_that("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", {
+  params <- default_parameters()
+  params$over.dispersion <- FALSE
+  res3 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
+  expect_equal(nrow(res3), 1L)
+  expect_equal(ncol(res3), 9L)
+  expect_equal(res3[1, "b"], 0.4682, tolerance = 1e-3)
+})
+
+test_that("mr.raps loss.function option", {
+  params <- default_parameters()
+  params$loss.function <- "tukey"
+  res4 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
+  expect_equal(nrow(res4), 1L)
+  expect_equal(ncol(res4), 9L)
+  expect_equal(res4[1, "b"], 0.4788, tolerance = 1e-3)
+})
+
+test_that("mr.raps shrinkage option", {
+  params <- default_parameters()
+  params$shrinkage <- TRUE
+  res5 <- suppressWarnings(mr(dat, method_list = "mr_raps", parameters = params))
+  expect_equal(nrow(res5), 1L)
+  expect_equal(ncol(res5), 9L)
+  expect_equal(res5[1, "b"], 0.4647, tolerance = 1e-3)
+})