add p0 to oddsratio_to_d

#657

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: effectsize
 Title: Indices of Effect Size
-Version: 0.8.9
+Version: 0.8.9.1
 Authors@R: 
     c(person(given = "Mattan S.",
              family = "Ben-Shachar",
@@ -105,7 +105,7 @@ VignetteBuilder:
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/website:

NEWS.md

@@ -1,3 +1,9 @@
+# effectsize 0.8.9.xxx
+
+## New features
+
+- `oddsratio_to_d()` and related functions gain a `p0` argument for exact conversion between odds ratios and Cohen's _d_.
+
 # effectsize 0.8.9
 
 ## Bug fixes

R/convert_between_d_to_r.R

@@ -6,6 +6,7 @@
 #' @param d,r,OR,logOR Standardized difference value (Cohen's d), correlation
 #'   coefficient (r), Odds ratio, or logged Odds ratio.
 #' @param n1,n2 Group sample sizes. If either is missing, groups are assumed to be of equal size.
+#' @param p0 Baseline risk. If not specified, the _d_ to _OR_ conversion uses am approximation (see details).
 #' @param log Take in or output the log of the ratio (such as in logistic models),
 #'   e.g. when the desired input or output are log odds ratios instead odds ratios.
 #' @param ... Arguments passed to or from other methods.
@@ -70,20 +71,32 @@ r_to_d <- function(r, n1, n2, ...) {
 
 #' @rdname d_to_r
 #' @export
-oddsratio_to_d <- function(OR, log = FALSE, ...) {
+oddsratio_to_d <- function(OR, p0, log = FALSE, ...) {
+  if (missing(p0)) {
+    # Use approximation
+    if (log) {
+      log_OR <- OR
+    } else {
+      log_OR <- log(OR)
+    }
+
+    return(log_OR * (sqrt(3) / pi))
+  }
+
+
   if (log) {
-    log_OR <- OR
-  } else {
-    log_OR <- log(OR)
+    OR <- exp(OR)
   }
 
-  log_OR * (sqrt(3) / pi)
+  odds1 <- OR * probs_to_odds(p0)
+  p1 <- odds_to_probs(odds1)
+  qnorm(p1) - qnorm(p0)
 }
 
 #' @rdname d_to_r
 #' @export
-logoddsratio_to_d <- function(logOR, log = TRUE, ...) {
-  oddsratio_to_d(logOR, log = log, ...)
+logoddsratio_to_d <- function(logOR, p0, log = TRUE, ...) {
+  oddsratio_to_d(logOR, p0, log = log, ...)
 }
 
 #' @rdname d_to_r
@@ -111,14 +124,14 @@ d_to_logoddsratio <- function(d, log = TRUE, ...) {
 
 #' @rdname d_to_r
 #' @export
-oddsratio_to_r <- function(OR, n1, n2, log = FALSE, ...) {
-  d_to_r(oddsratio_to_d(OR, log = log), n1, n2)
+oddsratio_to_r <- function(OR, p0, n1, n2, log = FALSE, ...) {
+  d_to_r(oddsratio_to_d(OR, p0, log = log), n1, n2)
 }
 
 #' @rdname d_to_r
 #' @export
-logoddsratio_to_r <- function(logOR, log = TRUE, ...) {
-  oddsratio_to_r(logOR, log = log, ...)
+logoddsratio_to_r <- function(logOR, p0, n1, n2, log = TRUE, ...) {
+  oddsratio_to_r(logOR, p0, n1, n2, log = log, ...)
 }
 
 
@@ -140,13 +153,11 @@ r_to_logoddsratio <- function(r, n1, n2, log = TRUE, ...) {
 #' @keywords internal
 .get_rd_h <- function(n1, n2) {
   if (missing(n1) && missing(n2)) {
-    h <- 4
-  } else {
-    if (missing(n1)) n1 <- n2
-    if (missing(n2)) n2 <- n1
-    m <- n1 + n2 - 2
-    h <- m / n1 + m / n2
+    return(4)
   }
 
-  h
+  if (missing(n1)) n1 <- n2
+  if (missing(n2)) n2 <- n1
+  m <- n1 + n2 - 2
+  m / n1 + m / n2
 }

tests/testthat/test-convert_between.R

@@ -5,6 +5,21 @@ test_that("oddsratio_to_d", {
   expect_equal(d_to_oddsratio(-0.7994, log = TRUE), -1.45, tolerance = 0.01)
 })
 
+test_that("exact OR to d", {
+  d <- c(0, 0.2, 0.5, 0.8)
+  p0 <- pnorm(0, lower.tail = FALSE)
+  p1 <- pnorm(0, mean = d, lower.tail = FALSE)
+  OR <- probs_to_odds(p1) / probs_to_odds(p0)
+
+  expect_equal(cor(oddsratio_to_d(OR), d), 1, tolerance = 0.0001)
+  expect_equal(oddsratio_to_d(1), 0, tolerance = 0.0001)
+  expect_equal(oddsratio_to_d(OR, p0), d)
+
+  expect_equal(cor(oddsratio_to_r(OR), d_to_r(d)), 1, tolerance = 0.0002)
+  expect_equal(oddsratio_to_r(1), 0, tolerance = 0.0001)
+  expect_equal(oddsratio_to_r(OR, p0), d_to_r(d))
+})
+
 
 test_that("d_to_r", {
   expect_equal(d_to_r(1.1547), 0.5, tolerance = 0.01)