Add logoddsratio-functions (#569)

* Add logoddsratio-functions * news, version bump * fix lints * Apply automatic changes * kill convert_ aliases * add missing prob-change functions * fix * lint and spell check [skip ci] --------- Co-authored-by: strengejacke <[email protected]> Co-authored-by: Mattan S. Ben-Shachar <[email protected]> Co-authored-by: Mattan S. Ben-Shachar <[email protected]>
easystats · Mar 10, 2023 · 66341ee · 66341ee
1 parent 585f7c1
commit 66341ee
Show file tree

Hide file tree

Showing 13 changed files with 369 additions and 173 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -63,6 +63,7 @@ export(F_to_f2)
 export(F_to_omega2)
 export(F_to_r)
 export(arr)
+export(arr_to_logoddsratio)
 export(arr_to_nnt)
 export(arr_to_oddsratio)
 export(arr_to_riskratio)
@@ -88,8 +89,6 @@ export(common_language)
 export(convert_d_to_common_language)
 export(convert_d_to_oddsratio)
 export(convert_d_to_r)
-export(convert_logoddsratio_to_d)
-export(convert_logoddsratio_to_r)
 export(convert_odds_to_probs)
 export(convert_oddsratio_to_d)
 export(convert_oddsratio_to_r)
@@ -101,6 +100,7 @@ export(cov_pooled)
 export(cramers_v)
 export(d_to_cles)
 export(d_to_common_language)
+export(d_to_logoddsratio)
 export(d_to_oddsratio)
 export(d_to_overlap)
 export(d_to_p_superiority)
@@ -165,18 +165,25 @@ export(interpret_vif)
 export(is.rules)
 export(is_effectsize_name)
 export(kendalls_w)
+export(logoddsratio_to_arr)
 export(logoddsratio_to_d)
+export(logoddsratio_to_nnt)
 export(logoddsratio_to_r)
+export(logoddsratio_to_riskratio)
 export(mad_pooled)
 export(mahalanobis_d)
 export(means_ratio)
 export(nnt)
 export(nnt_to_arr)
+export(nnt_to_logoddsratio)
+export(nnt_to_oddsratio)
+export(nnt_to_riskratio)
 export(normalized_chi)
 export(odds_to_probs)
 export(oddsratio)
 export(oddsratio_to_arr)
 export(oddsratio_to_d)
+export(oddsratio_to_nnt)
 export(oddsratio_to_r)
 export(oddsratio_to_riskratio)
 export(omega_squared)
@@ -190,6 +197,7 @@ export(print_md)
 export(probs_to_odds)
 export(r2_semipartial)
 export(r_to_d)
+export(r_to_logoddsratio)
 export(r_to_oddsratio)
 export(rank_biserial)
 export(rank_epsilon_squared)
@@ -201,6 +209,8 @@ export(rb_to_vda)
 export(rb_to_wmw_odds)
 export(riskratio)
 export(riskratio_to_arr)
+export(riskratio_to_logoddsratio)
+export(riskratio_to_nnt)
 export(riskratio_to_oddsratio)
 export(rules)
 export(sd_pooled)

diff --git a/NEWS.md b/NEWS.md
@@ -4,10 +4,17 @@
 
 - `arr()` and `nnt()` for Absolute Risk Reduction or Number Needed to Treat.
 - `oddsratio_to_arr()`, `riskratio_to_arr()`, `nnt_to_arr()` and their inverses.
+- `logoddsratio_to_*()` and `*_to_logoddsratio()` have been added as convenient shortcuts for `oddsratio_to_*(log = TRUE)` and `*_to_oddsratio(log = TRUE)`.
+- Added all missing functions to convert between (log) OR, RR, ARR, and NNT.
 
 ## Changes
 
 - `fei()` gives a more informative error method for invalid table inputs (#566).
+- `convert_*()` aliases are deprecated.
+
+## Breaking Changes
+
+- `*_to_riskratio()` and `riskratio_to_*()` argument `log` not longer converts RR to/from log(RR).
 
 ## Bug fixes
 

diff --git a/R/convert_between_d_to_r.R b/R/convert_between_d_to_r.R
@@ -3,11 +3,11 @@
 #' Enables a conversion between different indices of effect size, such as
 #' standardized difference (Cohen's d), (point-biserial) correlation r or (log) odds ratios.
 #'
-#' @param d Standardized difference value (Cohen's d).
-#' @param r Correlation coefficient r.
+#' @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 OR *Odds ratio* values in vector or data frame.
-#' @param log Take in or output the log of the ratio (such as in logistic models).
+#' @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.
 #'
 #' @family convert between effect sizes
@@ -54,37 +54,21 @@
 #' methods, 8(4), 448.
 #'
 #' @export
-#' @aliases convert_d_to_r
 d_to_r <- function(d, n1, n2, ...) {
   h <- .get_rd_h(n1, n2)
   d / (sqrt(d^2 + h))
 }
 
-#' @export
-convert_d_to_r <- d_to_r
-
-
-
-
-
-
 #' @rdname d_to_r
-#' @aliases convert_r_to_d
 #' @export
 r_to_d <- function(r, n1, n2, ...) {
   h <- .get_rd_h(n1, n2)
   sqrt(h) * r / sqrt(1 - r^2)
 }
 
-#' @export
-convert_r_to_d <- r_to_d
-
-
-
 # OR - d ----------------------------------------------------------------
 
 #' @rdname d_to_r
-#' @aliases convert_oddsratio_to_d
 #' @export
 oddsratio_to_d <- function(OR, log = FALSE, ...) {
   if (log) {
@@ -96,25 +80,13 @@ oddsratio_to_d <- function(OR, log = FALSE, ...) {
   log_OR * (sqrt(3) / pi)
 }
 
-#' @export
-convert_oddsratio_to_d <- oddsratio_to_d
-
-
-
 #' @rdname d_to_r
-#' @aliases convert_logoddsratio_to_d
 #' @export
-logoddsratio_to_d <- function(OR, log = TRUE, ...) {
-  oddsratio_to_d(OR, log = log, ...)
+logoddsratio_to_d <- function(logOR, log = TRUE, ...) {
+  oddsratio_to_d(logOR, log = log, ...)
 }
 
-#' @export
-convert_logoddsratio_to_d <- logoddsratio_to_d
-
-
-
 #' @rdname d_to_r
-#' @aliases convert_d_to_oddsratio
 #' @export
 d_to_oddsratio <- function(d, log = FALSE, ...) {
   log_OR <- d * pi / sqrt(3)
@@ -126,45 +98,41 @@ d_to_oddsratio <- function(d, log = FALSE, ...) {
   }
 }
 
+#' @rdname d_to_r
 #' @export
-convert_d_to_oddsratio <- d_to_oddsratio
+d_to_logoddsratio <- function(d, log = TRUE, ...) {
+  d_to_oddsratio(d, log = log, ...)
+}
 
 
 
 
 # OR - r ----------------------------------------------------------------
 
 #' @rdname d_to_r
-#' @aliases convert_oddsratio_to_r
 #' @export
 oddsratio_to_r <- function(OR, n1, n2, log = FALSE, ...) {
   d_to_r(oddsratio_to_d(OR, log = log), n1, n2)
 }
 
-#' @export
-convert_oddsratio_to_r <- oddsratio_to_r
-
 #' @rdname d_to_r
-#' @aliases convert_logoddsratio_to_r
 #' @export
-logoddsratio_to_r <- function(OR, log = TRUE, ...) {
-  oddsratio_to_r(OR, log = log, ...)
+logoddsratio_to_r <- function(logOR, log = TRUE, ...) {
+  oddsratio_to_r(logOR, log = log, ...)
 }
 
-#' @export
-convert_logoddsratio_to_r <- logoddsratio_to_r
-
-
 
 #' @rdname d_to_r
-#' @aliases convert_r_to_oddsratio
 #' @export
 r_to_oddsratio <- function(r, n1, n2, log = FALSE, ...) {
   d_to_oddsratio(r_to_d(r), log = log, n1, n2)
 }
 
+#' @rdname d_to_r
 #' @export
-convert_r_to_oddsratio <- r_to_oddsratio
+r_to_logoddsratio <- function(r, n1, n2, log = TRUE, ...) {
+  r_to_oddsratio(r, n1, n2, log = log)
+}
 
 
 # Utils -------------------------------------------------------------------

diff --git a/R/convert_between_odds_to_probs.R b/R/convert_between_odds_to_probs.R
@@ -21,15 +21,10 @@
 #' probs_to_odds(0.95)
 #' probs_to_odds(0.95, log = TRUE)
 #' @export
-#' @aliases convert_odds_to_probs
 odds_to_probs <- function(odds, log = FALSE, ...) {
   UseMethod("odds_to_probs")
 }
 
-#' @export
-convert_odds_to_probs <- odds_to_probs
-
-
 #' @export
 odds_to_probs.numeric <- function(odds, log = FALSE, ...) {
   if (log) {
@@ -48,15 +43,11 @@ odds_to_probs.data.frame <- function(odds, log = FALSE, select = NULL, exclude =
 
 
 #' @rdname odds_to_probs
-#' @aliases convert_probs_to_odds
 #' @export
 probs_to_odds <- function(probs, log = FALSE, ...) {
   UseMethod("probs_to_odds")
 }
 
-#' @export
-convert_probs_to_odds <- probs_to_odds
-
 #' @export
 probs_to_odds.numeric <- function(probs, log = FALSE, ...) {
   if (log) {