add docs

R/match_spec.R

@@ -14,6 +14,7 @@
 #' \code{filter_spec()} filters an Open Specy object.
 #' \code{os_similarity()} EXPERIMENTAL, returns a single similarity metric between two OpenSpecy objects based on the method used. 
 #' @param x an \code{OpenSpecy} object, typically with unknowns.
+#' @param y an \code{OpenSpecy} object to perform similarity search against x.
 #' @param conform Whether to conform the spectra to the library wavenumbers or not.
 #' @param type the type of conformation to make returned by \code{conform_spec()}
 #' @param library an \code{OpenSpecy} or \code{glmnet} object representing the

R/read_ext.R

@@ -94,11 +94,11 @@ read_text <- function(file, colnames = NULL, method = "fread",
   if(sum(grepl("^[0-9]{1,}$",colnames(dt))) > 4){
       wavenumbers <- colnames(dt)[grepl("^[0-9]{1,}$",colnames(dt))]
 
-      spectra <- transpose(dt[,..wavenumbers])
+      spectra <- transpose(dt[,wavenumbers, with = FALSE])
 
       metadata_names <- colnames(dt)[!grepl("^[0-9]{1,}$",colnames(dt))]
 
-      metadata <- dt[,..metadata_names]
+      metadata <- dt[, metadata_names, with = FALSE]
 
       os <- as_OpenSpecy(x = as.numeric(wavenumbers), spectra = spectra, metadata = metadata)
   }