From 77740e2a90d883a3d4d162049e62c2bf41a3b42b Mon Sep 17 00:00:00 2001
From: "Win Cowger, PhD" <wincowger@gmail.com>
Date: Wed, 23 Oct 2024 14:58:51 -0700
Subject: [PATCH] fix notes, try manage again

---
 R/process_spec.R    | 2 +-
 R/spatial_smooth.R  | 3 +++
 man/process_spec.Rd | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/process_spec.R b/R/process_spec.R
index 2db535b8..011f8466 100644
--- a/R/process_spec.R
+++ b/R/process_spec.R
@@ -11,7 +11,7 @@
 #' If \code{FALSE}, the original data will be returned.
 #' @param adj_intens logical; describing whether to adjust the intensity units.
 #' @param adj_intens_args named list of arguments passed to
-#' \code{\link{smooth_intens}()}.
+#' \code{\link{adj_intens}()}.
 #' @param conform_spec logical; whether to conform the spectra to a new
 #' wavenumber range and resolution.
 #' @param conform_spec_args named list of arguments passed to
diff --git a/R/spatial_smooth.R b/R/spatial_smooth.R
index d20e3540..e9f6c0b9 100644
--- a/R/spatial_smooth.R
+++ b/R/spatial_smooth.R
@@ -37,6 +37,9 @@ spatial_smooth <- function(x, sigma = c(1, 1, 1), ...) {
         stop("The OpenSpecy object must have 'x', 'y', and 'col_id' columns in its metadata.", call. = FALSE)
     }
     
+    #Avoid data.table notes
+    . <- col_id <- y <- wavenumber <- x_idx <- y_idx <- z_idx <- NULL
+    
     # Extract wavenumbers and spectra
     wavenumbers <- x$wavenumber
     spectra <- x$spectra  # data.table with spectra columns
diff --git a/man/process_spec.Rd b/man/process_spec.Rd
index 5a35c4f7..bd8caa76 100644
--- a/man/process_spec.Rd
+++ b/man/process_spec.Rd
@@ -41,7 +41,7 @@ If \code{FALSE}, the original data will be returned.}
 \item{adj_intens}{logical; describing whether to adjust the intensity units.}
 
 \item{adj_intens_args}{named list of arguments passed to
-\code{\link{smooth_intens}()}.}
+\code{\link{adj_intens}()}.}
 
 \item{conform_spec}{logical; whether to conform the spectra to a new
 wavenumber range and resolution.}