feat: support Sz LCD/GCD tables in read_peaklist

R/read_peaklist.R

@@ -7,7 +7,8 @@
 #' the function with a folder or vector of folders containing the files.
 #' Otherwise, set to\code{FALSE}.
 #' @param format_in Format of files to be imported/converted. Current options
-#' include: \code{chemstation} or \code{shimadzu}.
+#' include: \code{chemstation}, \code{shimadzu_fid}, \code{shimadzu_dad},
+#' \code{shimadzu_lcd}, and \code{shimadzu_gcd}.
 #' @param pattern pattern (e.g. a file extension). Defaults to NULL, in which
 #' case file extension will be deduced from \code{format_in}.
 #' @param data_format Either \code{chromatographr} or \code{original}.
@@ -33,14 +34,16 @@
 
 read_peaklist <- function(paths, find_files,
                         format_in = c("chemstation", "shimadzu_fid",
-                                      "shimadzu_dad"),
+                                      "shimadzu_dad", "shimadzu_lcd",
+                                      "shimadzu_gcd"),
                         pattern = NULL,
                         data_format = c("chromatographr", "original"),
                         metadata_format = c("chromconverter", "raw"),
                         read_metadata = TRUE, progress_bar, cl = 1){
   data_format <- match.arg(tolower(data_format), c("chromatographr", "original"))
   format_in <- match.arg(tolower(format_in),
-                         c("chemstation", "shimadzu_fid", "shimadzu_dad"))
+                         c("chemstation", "shimadzu_fid", "shimadzu_dad",
+                           "shimadzu_lcd", "shimadzu_gcd"))
   if (missing(progress_bar)){
     progress_bar <- check_for_pkg("pbapply", return_boolean = TRUE)
   }
@@ -62,12 +65,18 @@ read_peaklist <- function(paths, find_files,
     parser <- purrr::partial(read_chemstation_reports,
                              data_format = data_format,
                              metadata_format = metadata_format)
-  } else if (grepl("shimadzu", format_in)){
+  } else if (format_in %in% c("shimadzu_dad", "shimadzu_fid")){
     pattern <- ifelse(is.null(pattern), ".txt", pattern)
     parser <- partial(read_shimadzu, what = "peak_table",
                          data_format = "wide",
                          read_metadata = read_metadata,
                          peaktable_format = data_format)
+  } else if (format_in == "shimadzu_lcd"){
+    parser <- partial(read_shimadzu_lcd, what = "peak_table",
+                      data_format="wide", read_metadata=read_metadata)
+  } else if (format_in == "shimadzu_gcd"){
+    parser <- partial(read_shimadzu_gcd, what = "peak_table",
+                      data_format="wide", read_metadata=read_metadata)
   }
 
   if (find_files){
@@ -97,10 +106,10 @@ read_peaklist <- function(paths, find_files,
     data <- lapply(seq_along(data), function(i){
       if (inherits(data[[i]], "list")){
         lapply(data[[i]], function(xx){
-          cbind(sample = file_names[i], xx)
+          cbind(Sample = file_names[i], xx)
         })
       } else {
-        cbind(sample = file_names[i], data[[i]])
+        cbind(Sample = file_names[i], data[[i]])
       }
     })
     class(data) <- "peak_list"

R/read_shimadzu_ascii.R

@@ -306,8 +306,8 @@ read_shimadzu_peaktable <- function(path, x, idx, sep, format_in, format_out){
     t1 <- strsplit(x = x[[table_start + 3]], split = sep)[[1]][time_column]
     decimal_separator <- ifelse(grepl(",", t1), ",", ".")
 
-    peak_tab <- read.csv(path, skip = table_start-1, sep = sep, nrows = nrows,
-                         dec = decimal_separator)
+    peak_tab <- read.csv(path, skip = (table_start-1), sep = sep, nrows = nrows,
+                         dec = decimal_separator, check.names = FALSE)
     if (format_out == "chromatographr"){
       column_names <- switch(format_in, "MC" = c("Ret.Time", "Proc.From",
                                                  "Proc.To", "Area", "Height"),