hySpc-read-spc.Rmd

---
# For vignette ---------------------------------------------------------------
title:       'Import and Export Files with SPC files'
subtitle:    'Tutorial on Spectra File Import from SPC Files for "hyperSpec"'
description: 'Tutorial on spectra file import from SPC Files for "hyperSpec".'
# Authors --------------------------------------------------------------------
author:
  - name: Sang Truong, Claudia Beleites, Vilmantas Gegzna, Roman Kiselev
    email: sttruong@stanford.edu
    corresponding : yes
    affiliation   : Stanford University
# Document -------------------------------------------------------------------
date:        "`r Sys.Date()`"
output:
    bookdown::html_document2:
      base_format: rmarkdown::html_vignette
      toc: yes
      toc_depth: 2
      fig_caption: yes
      number_sections: true
      css:
        - vignette.css
        - style.css
vignette: >
    % \VignetteIndexEntry{Introduction to Package "hySpc.read.spc"}
    % \VignetteKeyword{hySpc.read.spc}
    % \VignettePackage{hySpc.read.spc}
    % \VignetteEngine{knitr::rmarkdown}
    % \VignetteEncoding{UTF-8}
# Citations/References -------------------------------------------------------
link-citations: yes
bibliography: resources/intro-pkg.bib
biblio-style: plain
csl: elsevier-with-titles.csl
# Pkgdown --------------------------------------------------------------------
pkgdown:
  as_is: true
  set_null_theme: no
---


```{r cleanup-hyperspec, include = FALSE}
# Clean up to ensure reproducible workspace ----------------------------------
rm(list = ls(all.names = TRUE))
```

```{r setup, include = FALSE}
# Packages -------------------------------------------------------------------
library(hySpc.read.spc)

# Functions ------------------------------------------------------------------
source("vignette-functions.R", encoding = "UTF-8")

# Settings -------------------------------------------------------------------
source("vignette-default-settings.R", encoding = "UTF-8")

# Temporary options ----------------------------------------------------------
# Change the value of this option in "vignette-default-settings.R"
show_reviewers_notes <- getOption("show_reviewers_notes", TRUE)
```


```{r bib, echo = FALSE, paged.print = FALSE}
dir.create("resources", showWarnings = FALSE)
knitr::write_bib(
  c("hyperSpec"),
  file = "resources/intro-pkg.bib",
  prefix = "R_"
)
```


<!-- This chunk inserts common info about all the vignettes -->

```{r, echo = FALSE, results = "asis"}
res <- knitr::knit_child("list-of-vignettes.md", quiet = TRUE)
cat(res, sep = "\n")
```


<!-- This chunk demonstrates  example of read_spc()-->

```
kaisermap_path <- system.file("extdata/spc.Kaisermap", package = "hySpc.read.spc")
hySpc.read.spc::read_spc(paste0(kaisermap_path,"/ebroAVII.spc"), keys_log2data = TRUE)

labram_path <- system.file("extdata/spc.LabRam", package = "hySpc.read.spc")
hySpc.read.spc::read_spc(paste0(labram_path,"/LabRam-2.spc"))

```