Merge pull request #649 from remlapmot/steiger-issue

TwoSampleMR 0.6.21

Author: remlapmot

.Rbuildignore

@@ -18,3 +18,4 @@ cache$
 ^CITATION\.cff$
 ^README\.html$
 ^\.lintr$
+^inst/sandpit$

.lintr

@@ -4,7 +4,6 @@ linters: linters_with_defaults(
     indentation_linter = NULL,
     infix_spaces_linter = NULL,
     quotes_linter = NULL,
-    brace_linter = NULL,
     commas_linter = NULL,
     whitespace_linter = NULL,
     object_name_linter = NULL,

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.20
+Version: 0.6.21
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,11 @@
+# TwoSampleMR v0.6.21
+
+(Release date 2025-08-11)
+
+* Fixed typos in Steiger related documentation (thanks to @eleanorsanderson and Kaitlin Wade for providing the motivating example for this).
+* Some code cleanup to make debugging easier.
+* Reduced size of installed package by removing some unused files.
+
 # TwoSampleMR v0.6.20
 
 (Release date 2025-08-01)

R/add_metadata.r

@@ -8,30 +8,24 @@
 #'
 #' @export
 #' @return Data frame
-add_metadata <- function(dat, cols = c("sample_size", "ncase", "ncontrol", "unit", "sd"))
-{
+add_metadata <- function(dat, cols = c("sample_size", "ncase", "ncontrol", "unit", "sd")) {
 	stopifnot(is.data.frame(dat))
 	stopifnot("id.exposure" %in% names(dat) | "id.outcome" %in% names(dat))
-	get_info <- function(id, what="exposure", cols)
-	{
+	get_info <- function(id, what="exposure", cols) {
 		info <- ieugwasr::gwasinfo(id)
-		if (nrow(info) == 0)
-		{
+		if (nrow(info) == 0) {
 			message(what, ": none of the IDs found in database")
 			return(NULL)
 		}
-		for (col in cols)
-		{
-			if (!col %in% names(info))
-			{
+		for (col in cols) {
+			if (!col %in% names(info)) {
 				info[[col]] <- NA
 			}
 		}
 		info <- subset(info, select=c("id", cols))
 		names(info) <- paste0(names(info), ".", what)
 		names(info)[names(info) == paste0("sample_size.", what)] <- paste0("samplesize.", what)
-		if ("sample_size" %in% cols)
-		{
+		if ("sample_size" %in% cols) {
 			index <- grepl("ukb-d", info$id) & is.na(info[[paste0("samplesize.", what)]])
 			info[[paste0("samplesize.", what)]][index] <- 300000
 		}
@@ -40,42 +34,32 @@ add_metadata <- function(dat, cols = c("sample_size", "ncase", "ncontrol", "unit
 
 	order_col <- random_string()
 	dat[[order_col]] <- seq_len(nrow(dat))
-	if ("id.exposure" %in% names(dat))
-	{
+	if ("id.exposure" %in% names(dat)) {
 		exposure_id <- unique(dat[["id.exposure"]])
 		info <- get_info(id=exposure_id, what="exposure", cols=cols)
-		if (!is.null(info))
-		{
-			for (x in names(info))
-			{
-				if (! x %in% names(dat))
-				{
+		if (!is.null(info)) {
+			for (x in names(info)) {
+				if (! x %in% names(dat)) {
 					dat[[x]] <- NA
 				}
 
-				for (id in unique(info[["id.exposure"]]))
-				{
+				for (id in unique(info[["id.exposure"]])) {
 					dat[[x]][is.na(dat[[x]]) & dat[["id.exposure"]] == id] <- info[[x]][info[["id.exposure"]] == id]
 				}
 			}
 		}
 	}
 
-	if ("id.outcome" %in% names(dat))
-	{
+	if ("id.outcome" %in% names(dat)) {
 		outcome_id <- unique(dat[["id.outcome"]])
 		info <- get_info(id=outcome_id, what="outcome", cols=cols)
-		if (!is.null(info))
-		{
-			for (x in names(info))
-			{
-				if (! x %in% names(dat))
-				{
+		if (!is.null(info)) {
+			for (x in names(info)) {
+				if (! x %in% names(dat)) {
 					dat[[x]] <- NA
 				}
 
-				for (id in unique(info[["id.outcome"]]))
-				{
+				for (id in unique(info[["id.outcome"]])) {
 					dat[[x]][is.na(dat[[x]]) & dat[["id.outcome"]] == id] <- info[[x]][info[["id.outcome"]] == id]
 				}
 			}