From 28581f9adae22637fbbf87992138687b7cdeea5f Mon Sep 17 00:00:00 2001
From: Daniel Claborne <dmclaborne@gmail.com>
Date: Thu, 11 Jan 2024 11:26:55 -0800
Subject: [PATCH] add new get/set functions to reference index

---
 _pkgdown.yml               | 4 ++++
 man/calc_element_ratios.Rd | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index fb8be25..feb9edf 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -116,6 +116,7 @@ reference:
   - '`getDBEoColName`'
   - '`getEDataColName`'
   - '`getElCompColName`'
+  - '`getElementColName`'
   - '`getExtractionColName`'
   - '`getFDataColName`'
   - '`getGibbsColName`'
@@ -138,6 +139,7 @@ reference:
   - '`getOxygenColName`'
   - '`getPCRatioColName`'
   - '`getPhosphorusColName`'
+  - '`getRatioColName`'
   - '`getReactionColName`'
   - '`getSulfurColName`'
 - title: Example data objects
@@ -184,6 +186,7 @@ reference:
   - setDBEoColName
   - setEDataColName
   - setElCompColName
+  - setElementColName
   - setExtractionColName
   - setFDataColName
   - setGibbsColName
@@ -206,6 +209,7 @@ reference:
   - setOxygenColName
   - setPCRatioColName
   - setPhosphorusColName
+  - setRatioColName
   - setReactionColName
   - setSulfurColName
   - transformation_counts
diff --git a/man/calc_element_ratios.Rd b/man/calc_element_ratios.Rd
index b57029f..63b447e 100644
--- a/man/calc_element_ratios.Rd
+++ b/man/calc_element_ratios.Rd
@@ -9,7 +9,7 @@ calc_element_ratios(ftmsObj, ratios = NULL)
 \arguments{
 \item{ftmsObj}{an object of class 'peakData' or 'compoundData', typically a result of \code{\link{as.peakData}} or \code{\link{mapPeaksToCompounds}}. e_meta must be present.}
 
-\item{ratios}{a matrix of size 2xN where N is the number of ratios to calculate. Defaults to O:C, H:C, N:C, P:C, N:P. As a matrix:\tabular{lllll}{
+\item{ratios}{a matrix of size 2xN where N is the number of ratios to calculate. Defaults to calculating O:C, H:C, N:C, P:C, and N:P. As a matrix:\tabular{lllll}{
    O \tab H \tab N \tab P \tab N \cr
    C \tab C \tab C \tab C \tab P \cr
 }}