From 49b5d4ce207aa48bccab09bb4ec9dc64a05b842e Mon Sep 17 00:00:00 2001
From: Charlie Wright <80007059+wcwr@users.noreply.github.com>
Date: Wed, 12 Mar 2025 10:24:37 -0500
Subject: [PATCH 1/2] Update utils.R

Add alpha to logit2 function
---
 R/utils.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index 14218cb..505fe15 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -20,7 +20,10 @@ utils::globalVariables(c("channel"))
 
 # Internal functions -----------------------------------------------------------
 
-logit2 <- function(x) log2(x) - log2(1 - x)
+logit2 <- function(x, alpha = 1e-5) {
+  #Protect against values exactly 0 or 1 by adding some small alpha
+  log2((x + alpha) / (1 - x + alpha))
+}
 
 ilogit2 <- function(x) 2^x / (1 + 2^x)
 

From 0588d3bfdb76842b39f811b2b0323365a3531d61 Mon Sep 17 00:00:00 2001
From: Charlie Wright <80007059+wcwr@users.noreply.github.com>
Date: Wed, 12 Mar 2025 10:27:28 -0500
Subject: [PATCH 2/2] Update logit2.Rd

Describe alpha in logit2 function
---
 man/logit2.Rd | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/man/logit2.Rd b/man/logit2.Rd
index 64430b4..d66bc51 100644
--- a/man/logit2.Rd
+++ b/man/logit2.Rd
@@ -1,23 +1,24 @@
 \name{logit2}
 \alias{logit2}
 \alias{ilogit2}
-\title{
-  logit in base 2.
-}
+\title{Logit in base 2 with offset}
 \description{
-  Utility functions for computing logit and inverse logit in base 2.
+  Utility functions for computing the logit and inverse logit in base 2.
+  \code{logit2} includes an \code{alpha} parameter to add a small offset,
+  which helps avoid infinite values when \code{x} is exactly 0 or 1.
 }
 \usage{
-logit2(x)
-ilogit2(x)
+  logit2(x, alpha = 1e-5)
+  ilogit2(x)
 }
 \arguments{
-  \item{x}{A numeric vector.}
+  \item{x}{A numeric vector of values (typically beta values between 0 and 1).}
+  \item{alpha}{A small positive numeric offset (default is \code{1e-5}) added to both the numerator and denominator in the logit transform.}
 }
-\value{A numeric vector.}
+\value{A numeric vector of transformed values.}
 \author{
   Kasper Daniel Hansen \email{khansen@jhsph.edu}.
 }
 \examples{
-logit2(c(0.25, 0.5, 0.75))
+  logit2(c(0.25, 0.5, 0.75))
 }