From 22d23dbb2eba19f4d6dd8ba392599c5eecd4a2aa Mon Sep 17 00:00:00 2001
From: jrmuirhead <jim.muirhead1@gmail.com>
Date: Mon, 25 Mar 2024 15:01:31 -0400
Subject: [PATCH] Proposed fix for issue 146 - missing data and calculation of
 secondary axis scale Jmuirhead/issue146 (#147)

* Update help_secondary.R

Add na.rm = TRUE in calculations of range of to and from

* Propagate na.rm top-down

* Fix plumbing

* Add news bullet

---------

Co-authored-by: Teun van den Brand <tahvdbrand@gmail.com>
---
 NEWS.md               |  2 ++
 R/help_secondary.R    | 20 ++++++++++++--------
 man/help_secondary.Rd |  6 ++++++
 3 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index d35b350..2579a76 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # ggh4x (development version)
 
+* `help_secondary()` has a new `na.rm` argument (#146, thanks @jrmuirhead!)
+
 # ggh4x 0.2.8
 
 This is a small release fixing a NOTE by request. In addition, there are two
diff --git a/R/help_secondary.R b/R/help_secondary.R
index 268b794..364f0d5 100644
--- a/R/help_secondary.R
+++ b/R/help_secondary.R
@@ -20,6 +20,9 @@
 #'  \item{`"sortfit"`}{Sorts the both `primary` and `secondary` independently
 #'  before passing these on to the `"fit"` method.}
 #' }
+#' @param na.rm A `logical(1)`: whether to remove missing values (`TRUE`) or
+#'   propagate missing values (`FALSE`). Applies to the `method = "range"` and
+#'   `method = "max"` methods.
 #' @inheritDotParams ggplot2::sec_axis -trans
 #'
 #' @details The intent is to run this function before starting a plot. The
@@ -69,6 +72,7 @@ help_secondary <- function(
   primary = c(0, 1),
   secondary = c(0, 1),
   method = c("range", "max", "fit", "ccf", "sortfit"),
+  na.rm = TRUE,
   ...
 ) {
   primary   <- enquo(primary)
@@ -82,8 +86,8 @@ help_secondary <- function(
 
   help <- switch(
     method,
-    "range" = help_sec_range(primary, secondary),
-    "max"   = help_sec_max(primary, secondary),
+    "range" = help_sec_range(primary, secondary, na.rm = na.rm),
+    "max"   = help_sec_max(primary, secondary, na.rm = na.rm),
     "fit"   = help_sec_fit(primary, secondary),
     "ccf"   = help_sec_ccf(primary, secondary),
     "sortfit" = help_sec_sortfit(primary, secondary)
@@ -112,9 +116,9 @@ new_sec_axis <- function(trans = NULL, ...) {
 
 # Methods -----------------------------------------------------------------
 
-help_sec_range <- function(from, to) {
-  from   <- range(from)
-  to <- range(to)
+help_sec_range <- function(from, to, na.rm = TRUE) {
+  from   <- range(from, na.rm = na.rm)
+  to <- range(to, na.rm = na.rm)
 
   forward <- function(x) {
     rescale(x, from = to, to = from)
@@ -125,9 +129,9 @@ help_sec_range <- function(from, to) {
   list(forward = forward, reverse = reverse)
 }
 
-help_sec_max <- function(from, to) {
-  from   <- range(from)
-  to <- range(to)
+help_sec_max <- function(from, to, na.rm = TRUE) {
+  from   <- range(from, na.rm = na.rm)
+  to <- range(to, na.rm = na.rm)
 
   forward <- function(x) {
     rescale_max(x, from = to, to = from)
diff --git a/man/help_secondary.Rd b/man/help_secondary.Rd
index f816aaf..a91f3fa 100644
--- a/man/help_secondary.Rd
+++ b/man/help_secondary.Rd
@@ -9,6 +9,7 @@ help_secondary(
   primary = c(0, 1),
   secondary = c(0, 1),
   method = c("range", "max", "fit", "ccf", "sortfit"),
+  na.rm = TRUE,
   ...
 )
 }
@@ -33,9 +34,14 @@ then align the data by truncation. The aligned data is then passed to the
 before passing these on to the \code{"fit"} method.}
 }}
 
+\item{na.rm}{A \code{logical(1)}: whether to remove missing values (\code{TRUE}) or
+propagate missing values (\code{FALSE}). Applies to the \code{method = "range"} and
+\code{method = "max"} methods.}
+
 \item{...}{
   Arguments passed on to \code{\link[ggplot2:sec_axis]{ggplot2::sec_axis}}
   \describe{
+    \item{\code{transform}}{A formula or function of transformation}
     \item{\code{name}}{The name of the secondary axis}
     \item{\code{breaks}}{One of:
 \itemize{