Add lr_ prefix to all exported functions

NAMESPACE

@@ -1,18 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
-export(convert_tocsv)
-export(get_metadata)
-export(get_spec)
-export(parse_abs)
-export(parse_generic)
-export(parse_jaz)
-export(parse_jazirrad)
-export(parse_jdx)
-export(parse_procspec)
-export(parse_roh)
-export(parse_trm)
-export(parse_trt)
-export(parse_ttt)
+export(lr_convert_tocsv)
+export(lr_get_metadata)
+export(lr_get_spec)
+export(lr_parse_abs)
+export(lr_parse_generic)
+export(lr_parse_jaz)
+export(lr_parse_jazirrad)
+export(lr_parse_jdx)
+export(lr_parse_procspec)
+export(lr_parse_roh)
+export(lr_parse_trm)
+export(lr_parse_trt)
+export(lr_parse_ttt)
 importFrom(pbmcapply,pbmclapply)
 importFrom(stats,approx)
 importFrom(stats,setNames)

R/convert_tocsv.R

@@ -3,22 +3,22 @@
 #' @param overwrite logical. Should the function overwrite existing files with
 #' the same name? (defaults to `FALSE`).
 #'
-#' @inheritParams get_spec
+#' @inheritParams lr_get_spec
 #'
 #' @return Convert input files to csv and invisibly return the list of created
 #' file paths
 #'
 #' @section Warning:
 #'
 #' This step loses all metadata associated to the spectra. This metadata is
-#' critical to ensure reproducibility. We recommended you use [get_metadata()]
-#' to extract this information from your raw data
+#' critical to ensure reproducibility. We recommended you use
+#' [lr_get_metadata()] to extract this information from your raw data.
 #'
 #' @importFrom tools file_path_sans_ext
 #' @importFrom utils write.csv
 #'
 #' @export
-convert_tocsv <- function(where = getwd(), ext = "txt", decimal = ".",
+lr_convert_tocsv <- function(where = getwd(), ext = "txt", decimal = ".",
                           sep = NULL, subdir = FALSE,
                           cores = getOption("mc.cores", 2L), ignore.case = TRUE,
                           overwrite = FALSE) {

R/dispatch_parser.R

@@ -6,16 +6,16 @@ dispatch_parser <- function(filename, decimal = ".", sep = NULL) {
 
   switch(
     tolower(file_ext(filename)),
-    procspec = parse_procspec(filename),
-    abs      = parse_abs(filename),
-    roh      = parse_roh(filename),
-    trm      = parse_trm(filename),
-    trt      = parse_trt(filename),
-    ttt      = parse_ttt(filename),
-    jdx      = parse_jdx(filename),
-    jaz      = parse_jaz(filename),
-    jazirrad = parse_jazirrad(filename),
-    parse_generic(filename, decimal = decimal, sep = sep)
+    procspec = lr_parse_procspec(filename),
+    abs      = lr_parse_abs(filename),
+    roh      = lr_parse_roh(filename),
+    trm      = lr_parse_trm(filename),
+    trt      = lr_parse_trt(filename),
+    ttt      = lr_parse_ttt(filename),
+    jdx      = lr_parse_jdx(filename),
+    jaz      = lr_parse_jaz(filename),
+    jazirrad = lr_parse_jazirrad(filename),
+    lr_parse_generic(filename, decimal = decimal, sep = sep)
   )
 
 }

R/get_metadata.R

@@ -2,7 +2,7 @@
 #'
 #' Finds and imports metadata from spectra files in a given location.
 #'
-#' @inheritParams get_spec
+#' @inheritParams lr_get_spec
 #'
 #' @export
 #'
@@ -34,10 +34,10 @@
 #' Animal Behaviour. 2015 Aug 1;106:51–7 (\doi{10.1016/j.anbehav.2015.05.007}).
 #'
 #' @examples
-#' get_metadata(system.file("testdata", package = "lightr"), ext = "ProcSpec",
-#'              subdir = TRUE)
+#' lr_get_metadata(system.file("testdata", package = "lightr"),
+#'                 ext = "ProcSpec", subdir = TRUE)
 
-get_metadata <- function(where = getwd(), ext = "ProcSpec", sep = NULL,
+lr_get_metadata <- function(where = getwd(), ext = "ProcSpec", sep = NULL,
                          subdir = FALSE, subdir.names = FALSE,
                          cores = getOption("mc.cores", 2L),
                          ignore.case = TRUE) {

R/get_spec.R

@@ -3,7 +3,7 @@
 #' Finds and imports reflectance/transmittance/absorbance data from spectra
 #' files in a given location.
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
 #' @param where Folder in which files are located (defaults to current working
 #' directory).
@@ -31,9 +31,9 @@
 #' @importFrom stats approx
 #'
 #' @examples
-#' get_spec(system.file("testdata", package = "lightr"), lim = c(400, 900))
+#' lr_get_spec(system.file("testdata", package = "lightr"), lim = c(400, 900))
 #'
-get_spec <- function(where = getwd(), ext = "txt", lim = c(300, 700),
+lr_get_spec <- function(where = getwd(), ext = "txt", lim = c(300, 700),
                      decimal = ".", sep = NULL, subdir = FALSE,
                      subdir.names = FALSE, cores = getOption("mc.cores", 2L),
                      ignore.case = TRUE) {

R/parse_avantes_binary.R

@@ -2,19 +2,21 @@
 #'
 #' Parse Avantes binary file. <https://www.avantes.com/products/spectrometers>
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
-#' @inherit parse_generic return
+#' @inherit lr_parse_generic return
 #'
 #' @importFrom stats setNames
 #'
 #' @examples
-#' parse_trm(system.file("testdata", "avantes_trans.TRM", package = "lightr"))
-#' parse_roh(system.file("testdata", "avantes_reflect.ROH", package = "lightr"))
+#' lr_parse_trm(system.file("testdata", "avantes_trans.TRM",
+#'                          package = "lightr"))
+#' lr_parse_roh(system.file("testdata", "avantes_reflect.ROH",
+#'                          package = "lightr"))
 #'
 #' @export
 #'
-parse_trm <- function(filename) {
+lr_parse_trm <- function(filename) {
   # Translation of the matlab script from:
   # Copyright: (cc-by) Kotya Karapetyan, 2011.
   # kotya.karapetyan@gmail.com
@@ -108,14 +110,14 @@ parse_trm <- function(filename) {
   return(list(data, metadata))
 }
 
-#' @rdname parse_trm
+#' @rdname lr_parse_trm
 #'
 #' @export
 #'
-parse_abs <- parse_trm
+lr_parse_abs <- lr_parse_trm
 
-#' @rdname parse_trm
+#' @rdname lr_parse_trm
 #'
 #' @export
 #'
-parse_roh <- parse_trm
+lr_parse_roh <- lr_parse_trm

R/parse_avantes_converted.R

@@ -3,17 +3,19 @@
 #' Parse Avantes converted file.
 #' <https://www.avantes.com/products/spectrometers>
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
-#' @inherit parse_generic return
+#' @inherit lr_parse_generic return
 #'
 #' @examples
-#' parse_ttt(system.file("testdata", "avantes_export.ttt", package = "lightr"))
-#' parse_trt(system.file("testdata", "avantes_export2.trt", package = "lightr"))
+#' lr_parse_ttt(system.file("testdata", "avantes_export.ttt",
+#'                          package = "lightr"))
+#' lr_parse_trt(system.file("testdata", "avantes_export2.trt",
+#'                          package = "lightr"))
 #'
 #' @export
 #'
-parse_ttt <- function(filename) {
+lr_parse_ttt <- function(filename) {
 
   # FIXME: grep to find appropriate lines instead of relying on fixed indices
 
@@ -67,8 +69,8 @@ parse_ttt <- function(filename) {
 
 }
 
-#' @rdname parse_ttt
+#' @rdname lr_parse_ttt
 #'
 #' @export
 #'
-parse_trt <- parse_ttt
+lr_parse_trt <- lr_parse_ttt

R/parse_generic.R

@@ -12,14 +12,15 @@
 #'   * a list with metadata including
 #'
 #' @examples
-#' parse_generic(system.file("testdata", "spec.csv", package = "lightr"),
-#'               sep = ",")
-#' parse_generic(system.file("testdata", "CRAIC_export.txt", package = "lightr"))
+#' lr_parse_generic(system.file("testdata", "spec.csv", package = "lightr"),
+#'                  sep = ",")
+#' lr_parse_generic(system.file("testdata", "CRAIC_export.txt",
+#'                              package = "lightr"))
 #'
 #' @export
 #'
 
-parse_generic <- function(filename, decimal = ".", sep = NULL) {
+lr_parse_generic <- function(filename, decimal = ".", sep = NULL) {
 
   seps <- paste0(c("[[:blank:]]", sep), collapse = "|\\")
 

R/parse_jdx.R

@@ -2,20 +2,20 @@
 #'
 #' Parse OceanOptics JCAMP-DX (.jdx) file. <https://oceanoptics.com/>
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
-#' @inherit parse_generic return
+#' @inherit lr_parse_generic return
 #'
 #' @references McDonald RS, Wilks PA. JCAMP-DX: A Standard Form for Exchange of
 #' Infrared Spectra in Computer Readable Form. Applied Spectroscopy.
 #' 1988;42(1):151‑62.
 #'
 #' @examples
-#' parse_jdx(system.file("testdata", "OceanOptics.jdx", package = "lightr"))
+#' lr_parse_jdx(system.file("testdata", "OceanOptics.jdx", package = "lightr"))
 #'
 #' @export
 #'
-parse_jdx <- function(filename) {
+lr_parse_jdx <- function(filename) {
   content <- readLines(filename)
   author <- grep("^##OWNER=", content, value = TRUE)
   author <- gsub("^##OWNER= ", "", author)[1]

R/parse_oceanoptics_converted.R

@@ -2,17 +2,18 @@
 #'
 #' Parse OceanOptics converted file. <https://oceanoptics.com/>
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
-#' @inherit parse_generic return
+#' @inherit lr_parse_generic return
 #'
 #' @examples
-#' parse_jaz(system.file("testdata", "jazspec.jaz", package = "lightr"))
-#' parse_jazirrad(system.file("testdata", "irrad.JazIrrad", package = "lightr"))
+#' lr_parse_jaz(system.file("testdata", "jazspec.jaz", package = "lightr"))
+#' lr_parse_jazirrad(system.file("testdata", "irrad.JazIrrad",
+#'                   package = "lightr"))
 #'
 #' @export
 #'
-parse_jaz <- function(filename) {
+lr_parse_jaz <- function(filename) {
 
   # METADATA
 
@@ -104,8 +105,8 @@ parse_jaz <- function(filename) {
   return(list(data.frame(data_final), metadata))
 }
 
-#' @rdname parse_jaz
+#' @rdname lr_parse_jaz
 #'
 #' @export
 #'
-parse_jazirrad <- parse_jaz
+lr_parse_jazirrad <- lr_parse_jaz

R/parse_procspec.R

@@ -2,21 +2,22 @@
 #'
 #' Parse OceanOptics ProcSpec file. <https://oceanoptics.com/>
 #'
-#' @inheritParams parse_generic
+#' @inheritParams lr_parse_generic
 #'
-#' @inherit parse_generic return
+#' @inherit lr_parse_generic return
 #'
 #' @importFrom xml2 read_xml xml_find_all xml_find_first xml_text
 #'
 #' @references <https://oceanoptics.com/faq/extract-data-procspec-file-without-spectrasuite/>
 #'
 #' @examples
-#' parse_procspec(system.file("testdata", "procspec_files",
-#'                            "OceanOptics_Linux.ProcSpec", package = "lightr"))
+#' lr_parse_procspec(system.file("testdata", "procspec_files",
+#'                               "OceanOptics_Linux.ProcSpec",
+#'                               package = "lightr"))
 #'
 #' @export
 #'
-parse_procspec <- function(filename) {
+lr_parse_procspec <- function(filename) {
   # We let R find the suitable tmp folder to extract files
   tmp <- tempdir()
   on.exit(unlink(tmp))