.Rbuildignore

+^provoc\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^CITATION\.cff$

CITATION.cff

+# -----------------------------------------------------------
+# CITATION file created with {cffr} R package, v0.2.2
+# See also: https://docs.ropensci.org/cffr/
+# -----------------------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "provoc" in publications use: Joris Huguenin, University of Montpellier, CEFE (2022). provoc : analyze data of VOC by PTR-ToF-MS Vocus. R package version 1.0.5.01. DOI: 10.5281/zenodo.6642830'
+type: software
+license: GPL-3.0-only
+title: 'provoc : analyze data of VOC by PTR-ToF-MS Vocus'
+version: 1.0.5.00
+doi: 10.5281/zenodo.6642830
+abstract: The provoc package has been developed to support PTR-ToF-MS users in their
+  analyses. It has been designed for a quick import of data into R and visualization
+  of the first results in a few minutes. It automatically detects peaks and provides
+  a matrix for further analysis. Some chemometrics functions are proposed.
+authors:
+- family-names: Huguenin
+  given-names: Joris
+  email: joris.huguenin@cefe.cnrs.fr
+preferred-citation:
+  type: software
+  title: 'provoc: analyze data of VOC by PTR-ToF-MS Vocus'
+  authors:
+  - family-names: Huguenin
+    given-names: Joris
+    email: joris.huguenin@cefe.cnrs.fr
+  - family-names: University of Montpellier
+    given-names: CEFE
+  version: 1.0.5.00
+  doi: 10.5281/zenodo.6642830
+  abstract: The provoc package has been developed to support PTR-ToF-MS users in their
+    analyses. It has been designed for a quick import of data into R and visualization
+    of the first results in a few minutes. It automatically detects peaks and provides
+    a matrix for further analysis. Some chemometrics functions are proposed.
+  date-released: '2022-06-10'
+  contact:
+  - family-names: Huguenin
+    given-names: Joris
+    email: joris.huguenin@cefe.cnrs.fr
+  license: GPL-3.0-only
+  year: '2022'
+date-released: '2022-06-15'
+contact:
+- family-names: Huguenin
+  given-names: Joris
+  email: joris.huguenin@cefe.cnrs.fr
+references:
+- type: software
+  title: ALS
+  abstract: 'ALS: Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)'
+  notes: Imports
+  authors:
+  - family-names: Mullen
+    given-names: Katharine M.
+  year: '2022'
+  url: https://CRAN.R-project.org/package=ALS
+  version: '>= 0.0.6'
+- type: software
+  title: baseline
+  abstract: 'baseline: Baseline Correction of Spectra'
+  notes: Imports
+  authors:
+  - family-names: Liland
+    given-names: Kristian Hovde
+    email: kristian.liland@nmbu.no
+  - family-names: Mevik
+    given-names: Bjørn-Helge
+  year: '2022'
+  url: https://CRAN.R-project.org/package=baseline
+  version: '>= 1.3.0'
+- type: software
+  title: dygraphs
+  abstract: 'dygraphs: Interface to ''Dygraphs'' Interactive Time Series Charting
+    Library'
+  notes: Imports
+  authors:
+  - family-names: Vanderkam
+    given-names: Dan
+  - family-names: Allaire
+    given-names: JJ
+  - family-names: Owen
+    given-names: Jonathan
+  - family-names: Gromer
+    given-names: Daniel
+  - family-names: Thieurmel
+    given-names: Benoit
+  year: '2022'
+  url: https://CRAN.R-project.org/package=dygraphs
+  version: '>= 1.1.0'
+- type: software
+  title: graphics
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2022'
+  url: https://www.R-project.org/
+  institution:
+    name: R Foundation for Statistical Computing
+  version: '>= 4.0.0'
+- type: software
+  title: grDevices
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2022'
+  url: https://www.R-project.org/
+  institution:
+    name: R Foundation for Statistical Computing
+  version: '>= 4.0.0'
+- type: software
+  title: magrittr
+  abstract: 'magrittr: A Forward-Pipe Operator for R'
+  notes: Imports
+  authors:
+  - family-names: Bache
+    given-names: Stefan Milton
+    email: stefan@stefanbache.dk
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  year: '2022'
+  url: https://CRAN.R-project.org/package=magrittr
+  version: '>= 2.0.0'
+- type: software
+  title: MALDIquant
+  abstract: 'MALDIquant: Quantitative Analysis of Mass Spectrometry Data'
+  notes: Imports
+  authors:
+  - family-names: Gibb
+    given-names: Sebastian
+    email: mail@sebastiangibb.de
+    orcid: https://orcid.org/0000-0001-7406-4443
+  year: '2022'
+  url: https://CRAN.R-project.org/package=MALDIquant
+  version: '>= 1.19.0'
+- type: software
+  title: rhdf5
+  abstract: 'rhdf5: R Interface to HDF5'
+  notes: Imports
+  authors:
+  - family-names: Fischer
+    given-names: Bernd
+  - family-names: Smith
+    given-names: Mike
+    email: mike.smith@embl.de
+    orcid: https://orcid.org/0000-0002-7800-3848
+  - family-names: Pau
+    given-names: Gregoire
+  year: '2022'
+  url: https://github.com/grimbough/rhdf5
+  version: '>= 2.34.0'
+- type: software
+  title: rmarkdown
+  abstract: 'rmarkdown: Dynamic Documents for R'
+  notes: Imports
+  authors:
+  - family-names: Allaire
+    given-names: JJ
+    email: jj@rstudio.com
+  - family-names: Xie
+    given-names: Yihui
+    email: xie@yihui.name
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: McPherson
+    given-names: Jonathan
+    email: jonathan@rstudio.com
+  - family-names: Luraschi
+    given-names: Javier
+    email: javier@rstudio.com
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevin@rstudio.com
+  - family-names: Atkins
+    given-names: Aron
+    email: aron@rstudio.com
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  - family-names: Cheng
+    given-names: Joe
+    email: joe@rstudio.com
+  - family-names: Chang
+    given-names: Winston
+    email: winston@rstudio.com
+  - family-names: Iannone
+    given-names: Richard
+    email: rich@rstudio.com
+    orcid: https://orcid.org/0000-0003-3925-190X
+  year: '2022'
+  url: https://CRAN.R-project.org/package=rmarkdown
+  version: '>= 2.11.0'
+- type: software
+  title: scales
+  abstract: 'scales: Scale Functions for Visualization'
+  notes: Imports
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  - family-names: Seidel
+    given-names: Dana
+  year: '2022'
+  url: https://CRAN.R-project.org/package=scales
+  version: '>= 1.1.0'
+- type: software
+  title: stats
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2022'
+  url: https://www.R-project.org/
+  institution:
+    name: R Foundation for Statistical Computing
+  version: '>= 4.0.0'
+- type: software
+  title: stringr
+  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
+  notes: Imports
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  year: '2022'
+  url: https://CRAN.R-project.org/package=stringr
+  version: '>= 1.4.0'
+- type: software
+  title: viridis
+  abstract: 'viridis: Colorblind-Friendly Color Maps for R'
+  notes: Imports
+  authors:
+  - family-names: Garnier
+    given-names: Simon
+    email: garnier@njit.edu
+  year: '2022'
+  url: https://CRAN.R-project.org/package=viridis
+  version: '>= 0.6.0'
+- type: software
+  title: utils
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2022'
+  url: https://www.R-project.org/
+  institution:
+    name: R Foundation for Statistical Computing
+  version: '>= 4.0.0'
+- type: software
+  title: xts
+  abstract: 'xts: eXtensible Time Series'
+  notes: Imports
+  authors:
+  - family-names: Ryan
+    given-names: Jeffrey A.
+  - family-names: Ulrich
+    given-names: Joshua M.
+    email: josh.m.ulrich@gmail.com
+  year: '2022'
+  url: https://CRAN.R-project.org/package=xts
+  version: '>= 0.12.0'

DESCRIPTION

+Package: provoc
+Title: analyze data of VOC by PTR-ToF-MS Vocus
+Version: 1.0.5.06
+DOI: 10.5281/zenodo.6642830
+Authors@R: 
+    person(given = "Joris",
+           family = "Huguenin",
+           role = c("aut", "cre"),
+           email = "joris.huguenin@cefe.cnrs.fr")
+Organization: CEFE, University of Montpellier
+Address: Montpellier, France
+Packaged: 2022-06-14; huguenin
+Description: The provoc package has been developed to support PTR-ToF-MS users
+    in their analyses. It has been designed for a quick import of data into R
+    and visualization of the first results in a few minutes. It automatically
+    detects peaks and provides a matrix for further analysis. Some chemometrics
+    functions are proposed. 
+Date/Publication: 2022-06-14
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Imports:
+    baseline (>= 1.3.0),
+    dygraphs (>= 1.1.0),
+    graphics (>= 4.0.0),
+    grDevices (>= 4.0.0),
+    Iso (>= 0.0-18.1),
+    magrittr (>= 2.0.0),
+    MALDIquant (>= 1.19.0),
+    nnls (>= 1.4),
+    rhdf5 (>= 2.34.0),
+    rmarkdown (>= 2.11.0),
+    scales (>= 1.1.0),
+    stats (>= 4.0.0),
+    stringr (>= 1.4.0),
+    viridis (>= 0.6.0),
+    usethis (>= 2.1.0),
+    utils (>= 4.0.0),
+    xts (>= 0.12.0)
+Remotes: 
+    grimbough/rhdf5
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(M.Z)
+export(M.Z.max)
+export(delete.spectra.h5)
+export(det.c)
+export(dy.spectra)
+export(empty.meta)
+export(fx.spectra)
+export(hprint)
+export(import.h5)
+export(import.meta)
+export(ind.acq)
+export(ind.pk)
+export(info.h5)
+export(kinetic.plot)
+export(mcr.voc)
+export(meta.ctrl)
+export(peak.ctrl)
+export(re.calc.T.para)
+export(re.init.T.para)
+import(dygraphs)
+import(grDevices)
+import(graphics)
+import(utils)
+importFrom(Iso,ufit)
+importFrom(MALDIquant,alignSpectra)
+importFrom(MALDIquant,averageMassSpectra)
+importFrom(MALDIquant,binPeaks)
+importFrom(MALDIquant,createMassSpectrum)
+importFrom(MALDIquant,detectPeaks)
+importFrom(MALDIquant,filterPeaks)
+importFrom(MALDIquant,intensityMatrix)
+importFrom(MALDIquant,smoothIntensity)
+importFrom(baseline,baseline.rollingBall)
+importFrom(magrittr,"%>%")
+importFrom(magrittr,add)
+importFrom(magrittr,divide_by)
+importFrom(magrittr,multiply_by)
+importFrom(magrittr,subtract)
+importFrom(nnls,nnls)
+importFrom(rhdf5,H5Fclose)
+importFrom(rhdf5,H5Fopen)
+importFrom(rhdf5,h5closeAll)
+importFrom(rhdf5,h5createFile)
+importFrom(rhdf5,h5ls)
+importFrom(rhdf5,h5write)
+importFrom(rmarkdown,render)
+importFrom(scales,alpha)
+importFrom(stats,approx)
+importFrom(stats,coef)
+importFrom(stats,density)
+importFrom(stats,median)
+importFrom(stats,smooth.spline)
+importFrom(stats,stepfun)
+importFrom(stringr,str_flatten)
+importFrom(stringr,str_pad)
+importFrom(stringr,str_remove_all)
+importFrom(stringr,str_split)
+importFrom(stringr,str_sub)
+importFrom(viridis,viridis)
+importFrom(xts,xts)

inst/devtools_history.R

+usethis::use_build_ignore("devtools_history.R")
+usethis::use_git_ignore(".Rhistory")
+
+# dependance
+
+usethis::use_package("dygraphs")#, min_version = "1.1.0.0")
+usethis::use_package("magrittr")#, min_version = "2.0.0")
+usethis::use_package("MALDIquant")#, min_version = "1.19.0")
+usethis::use_package("rmarkdown")#, min_version = "2.11")
+usethis::use_package("scales")#, min_version = "1.1.0")
+usethis::use_package("stringr")#, min_version = "1.4.0")
+usethis::use_package("usethis")#, min_version = "2.0.0")
+usethis::use_package("viridis")#, min_version = "0.6.0")
+usethis::use_package("xts")#, min_version = "0.12.0")
+usethis::use_dev_package("rhdf5", remote = "grimbough/rhdf5")
+
+
+# CI github
+usethis::use_github_actions()
+usethis::use_github_action(name = "check-standard")
+usethis::use_github_actions_badge("R-CMD-check")

inst/rmarkdown/templates/template-name/skeleton/skeleton.Rmd

+---
+title: "Template Title"
+author: "Your Name"
+date: "The Date"
+output: output_format
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Adding an RMarkdown Template
+
+This file is what a user will see when they select your template. Make sure that you update the fields in the yaml header. In particular you will want to update the `output` field to whatever format your template requires.
+
+This is a good place to demonstrate special features that your template provides. Ideally it should knit out-of-the-box, or at least contain clear instructions as to what needs changing.
+
+Finally, be sure to remove this message!

inst/rmarkdown/templates/template-name/template.yaml

+name: Template Name
+description: >
+   A description of the template
+create_dir: FALSE

inst/rmd/README.Rmd

+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+# knitr::opts_knit$set(root.dir = "C:/Users/huguenin/Documents/R/provoc")
+```
+
+# provoc <a href='https://github.com/JHuguenin/provoc'><img src="https://raw.githubusercontent.com/JHuguenin/provoc/master/inst/img/imgfile.png" align="right" height="138"/></a>
+
+<!-- badges: start -->
+
+[![DOI](https://zenodo.org/badge/425788381.svg)](https://zenodo.org/badge/latestdoi/425788381) [![R-CMD-check](https://github.com/JHuguenin/provoc/workflows/R-CMD-check/badge.svg)](https://github.com/JHuguenin/provoc/actions) [![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/provoc)](https://cran.r-project.org/package=provoc) <!-- [![Coverage status](https://codecov.io/gh/mitchelloharawild/icons/branch/master/graph/badge.svg)](https://codecov.io/gh/mitchelloharawild/icon?branch=master) -->
+
+<!-- badges: end -->
+
+**P**erform a **R**apid **O**verview for **V**olatile **O**rganic **C**ompounds.
+
+The `provoc` package has been developed to support PTR-ToF-MS users in their analyses. It has been designed for a quick import of data into R and visualization of the first results in a few minutes. It automatically detects peaks and provides a matrix for further analysis. Some chemometrics functions are proposed.
+
+It is still a young and wild package that will appreciate feedback and new ideas for its development. Do not hesitate to contact the author to get or provide help.
+
+For cite this package :
+
+-   Joris Huguenin, UMR 5175 CEFE, CNRS, University of Montpellier. provoc: analyze data of VOC by PTR-ToF-MS Vocus. DOI : 10.5281/zenodo.6642830.
+
+# Installation
+
+The **development** version can be installed from GitHub using:
+
+```{r gh-installation, eval = FALSE}
+# install.packages("remotes")
+remotes::install_github("jhuguenin/provoc")
+```
+
+The package requires the update of many dependencies:
+
+-   `baseline`(\>= 1.3.0)
+-   `dygraphs`(\>= 1.1.0)
+-   `graphics`(\>= 4.0.0)
+-   `grDevices`(\>= 4.0.0)
+-   `Iso`(\>= 0.0-18.1)
+-   `magrittr`(\>= 2.0.0)
+-   `MALDIquant`(\>= 1.19.0)
+-   `nnls`(\>= 1.4)
+-   `rhdf5`(\>= 2.34.0)
+-   `rmarkdown`(\>= 2.11.0)
+-   `scales`(\>= 1.1.0)
+-   `stats`(\>= 4.0.0)
+-   `stringr`(\>= 1.4.0)
+-   `viridis`(\>= 0.6.0)
+-   `usethis`(\>= 2.1.0)
+-   `utils`(\>= 4.0.0)
+-   `xts`(\>= 0.12.0)
+
+# Description of function
+
+## Principals functions
+
+-   **import.h5** for import you data. Easy.
+-   **import.meta** custom your analysis plans.
+-   **dy.spectra** & **fx.spectra** look at your dynamic or fixed spectra.
+-   **kinetic.plot** look the kinetic of your VOCs.
+-   **mcr.voc** perform a MCR analysis on your data.
+
+## Secondary functions
+
+### Manage your data
+
+-   if you can't import your files, look them with **info.h5**. After that, delete a corrupted spectra with **delete.spectra.h5**.
+-   peek your meta data with **meta.ctrl** and the peak alignment with **peak.ctrl**.
+-   manage the time of your data with **re.calc.T.para** or revert to original data by **re.init.T.para**.
+-   create a new file "meta_empty.csv" : **empty.meta**.
+
+### Find index or position
+
+-   **ind.acq** return index of spectra for each acquistion.
+-   **ind.pk** return index of peaks.
+-   **det.c** return the index more closed of a decimal number in the numeric vector.
+-   **M.Z** search all peak in accord to a mass number
+-   **M.Z.max** search the highest peak in accord to a mass number
+
+# Usage
+
+```{r load, eval = FALSE}
+library(provoc)
+```
+
+## Importation
+
+Before importing, all h5 files must be placed in a directory named `h5`. This directory must be placed in the working directory. The name of the h5 files placed in the directory may contain the date and time of recording in the form \_yyymmdd_hhmmss. This information will be removed during import. e.g. `00_file_PTR_ToF_MS_20210901_093055.h5` will be renamed `00_file_PTR_ToF_MS` by the import.
+
+Each file is an `acquisition` with several `spectra`.
+
+```{r importation, eval = FALSE}
+# working directory
+wd <- "~/R/data_test/miscalenous" # without final "/"
+setwd(wd) # If you you don't work by project.
+
+# + wd/
+# |  \- h5/
+# |     \- 00_file_PTR_ToF_MS.h5
+# |     \- 01_file_PTR_ToF_MS.h5
+# |     \- 02_file_PTR_ToF_MS.h5
+
+# import
+sp <- import.h5(wd) # or just sp <- import.h5() if you work by project. 
+```
+
+The `import.h5()` function automatically creates a directory named "Figures", a csv file with the meta data "meta_empty.csv" and a list sp. This list contains :
+
+-   `MS` : a big matrix with all data.  
+-   `peaks` : a short matrix with peak intensity.  
+-   `xMS` : vector for the MS abscissa.  
+-   `names` : folder names use in this meta set.  
+-   `wd` : the working directory.  
+-   `acq` : ID use in this meat seta.
+-   `nbr_sp` : the number of spectra for each acquisition.  
+-   `names_acq` : names of spectra.  
+-   `Tinit` : the original date (and time) of spectra.  
+-   `Trecalc` : the recalculated time of spectra (for cumulated several acquisition).  
+-   `workflow` : the list of each operation in the project.  
+-   `mt` : the R meta data.  
+-   `meta` : the Vocus meta data.
+
+You can control part of the analysis with the "meta_empty.csv" file. It is in the form of a table with all the acquisitions imported in rows. The columns are :
+
+-   `names` : names of acquisiton.
+-   `ID` : identifier number.
+-   `nbr_MS` : number of spectra in this acquisition.
+-   `start` : the index where this acquisition begins.
+-   `end` : the index where this acquisition ends.
+-   `used` : `TRUE`/`FALSE` selects the acquisitions useful for the analysis.
+-   `blank (ID)` : (not available) subtract the blank.
+-   `color` : specifies a color.
+-   `concentration` : (not available) specifies a concentration.
+-   `unit` : (not available) and the unit of concentration.
+-   `acq_T0 (ID)` : the T0 ID of the sequence.
+-   `delta_T (s)` : It's possible to adjust the sequence by a shift time in second.
+-   `grp1`, `grp2`, `...` : others free columns for analyzes. Names of columns can be changed.
+
+You can prepare several meta files. By activating or not the acquisitions, it is possible to make different analyses. This allows you to do only one import (often long). You can rename the files meta_1, meta_2 or with more explicit names.
+
+If the import is stopped because of a corrupted file, use `info.h5()` and `delete.spectra.h5()` to correct this file.
+
+If your h5 files are differents, let me know and I can add an option for you.
+ 
+ 
+### Optimize the importation
+
+If you want to improve the data import, there are three options to consider :
+
+-   First, a baseline correction step can be added with: `baseline_correction = TRUE`. When the instrument receives a large number of molecules with the same mass, the detector fluctuates slightly which leaves a visible trace on the spectrogram. This baseline correction is a time consuming but very effective step to improve the analysis.  
+-   Then, the parameters for detecting and aligning the peaks can be adjusted according to the experiment. The package proposes some predefined parameters (see `pk_param`) but the user can modify these parameters (mainly the size of the width of the peak at half height "halfWindowSize" and the signal to noise ratio "SNR"). The quality of these parameters can be visualized thanks to the `ctrl_peak` argument.  
+-   Finally, the argument `skip = X` allows not to import the first X spectra of each file. Typically, in a sequence with several channels, the first spectra will always be polluted by the previous channel. Not importing them saves RAM and computation time. It also allows to import longer sequences in one go.
+
+## Preparation
+
+After the import, a csv file was created in the working directory. This file should look like this:  
+
+<img src="https://raw.githubusercontent.com/JHuguenin/provoc/master/inst/img/meta_empty.PNG" align="center" />  
+
+It is made to be easily opened and closed by excel in Windows10. If your default settings do not allow this facility, let me know and I can add an option for you.  
+
+Once opened, you can edit the information inside to fill in different information such as the color or modality of your samples. Here, the example shows the first three cycles of a sequence with four samples, two with modality A, one with modality B and one blank. There are 12 spectra per sample.  
+With the column acq_T0, I indicate which acquisitions belong to each sample. This is useful for the "time" option when producing the graph. 
+
+<img src="https://raw.githubusercontent.com/JHuguenin/provoc/master/inst/img/meta_1.PNG" align="center" />  
+
+```{r meta data, eval = FALSE}
+sp <- import.meta("meta_1") # without '.csv'
+```
+
+Then, to refine my analysis, I decided to superimpose the T0 of each sample to facilitate the comparison. For this, I removed 300 (600 and 900) seconds because each sample is analyzed for 5 minutes. I also removed my sample 2 with the used column. Finally, I selected only the last 6 spectra (out of 12) by modifying the start column. 
+
+<img src="https://raw.githubusercontent.com/JHuguenin/provoc/master/inst/img/meta_2.PNG" align="center" />  
+
+```{r meta data2, eval = FALSE}
+sp <- import.meta("meta_2")
+```
+
+
+To be able to switch from one graphical representation to another quickly, I created two files meta_1.csv and meta_2.csv that I import according to my needs.  
+
+All operations performed during the analysis are recorded. It is easy to save this trace. Afterwards, you can restart your workflow automatically (not available).
+
+```{r workflow, eval = FALSE}
+saveRDS(sp$workflow, "workflow.rds")
+wf <- readRDS("workflow.rds")
+```
+
+After preparing the meta file, you should recalculate the time with `re.calc.T.para()` if you need to. The other function reinitialize the time.
+
+```{r time gestion, eval = FALSE}
+sp <- re.calc.T.para(sp)
+sp <- re.init.T.para(sp)
+```
+
+Be careful. By default, the "time" option uses a relative T0 from the first spectrum of each acquisition and the "date" option uses the actual date and time of each spectrum. Using the acq_T0 column with the "time" option allows different acquisitions to be sequenced using the T0 of the specified acquisition. Using the acq_T0 column with the "date" option allows you to overlap acquisitions on the T0 of the specified acquisition.
+
+The delta_T column is used to add the specified time (in seconds) to the acquisition.
+
+## Make a plot
+
+With the following three functions, it is really easy to make graphs to explore your data.
+
+`dy.spectra` and `fx.spectra` allow you to make figures of the spectra, respectively dynamically and fixed. You have to fill `sel_sp` with a numerical vector indicating the numbers of the spectra to use (sp$Sacq). For `fx.spectra`, pkm and pkM are the min and max limits.
+
+```{r Spectra plot, eval = FALSE}
+# a dynamic plot :
+dy.spectra(sel_sp = sp$mt$meta[sp$acq,"end"], new_color = FALSE)
+# a standart plot :
+fx.spectra(sel_sp = sp$mt$meta[sp$acq,"end"], pkm = 137, pkM = 137, leg = "l")
+fx.spectra(sel_sp = 1, pkm = 59, pkM = 150)
+```
+
+kinetic.plot plots the evolution of the peaks.
+
+-   `M_num` : Analyzed masses. M.Z(c(69, 205, 157)), M.Z.max(c(69, 205, 157)) or c(69.055, 205.158, 157.021).  
+-   `each_mass` : make a plot for each masse or not. Logical TRUE or FALSE.  
+-   `group` : the name of the meta column that categorizes the groups, or not. e.g. : "grp1" or FALSE.  
+-   `graph_type` : choice "fx" for fixed plot (.tiff) or "dy" for dynamic plot (.html)  
+-   `Y_exp` : y axe exponential or not. Logical TRUE or FALSE.  
+-   `time_format` : x axe with a time ("time") or with a date ("date").
+
+```{r kinetic plot, eval = FALSE}
+kinetic.plot(M_num = M.Z.max(c(59, 137)), each_mass = TRUE,
+                         group = "grp1", graph_type = "dy",
+                         Y_exp = FALSE, time_format = "date")
+```
+
+## Make a MCR
+
+After performing a univariate analysis, Provoc allows a multivariate analysis using the MCR algorithm. This technique is detailed in the article : *Multivariate Curve Resolution (MCR). Solving the mixture analysis problem*(2014). Anna de Juan, Joaquim Jaumot and Roma Tauler. <https://doi.org/10.1039/C4AY00571F>
+
+Currently the constraints of the MCR are by default the same as those of the "alsace" package. They are consistent with an analysis of PTR-ToF-MS data. The function allows to set the number of components used for the RCM (ncMCR) and to specify a variable selection (pk_sel). You can also specify a column from the meta_xxx.csv file that you wish to use to group the spectra according to a modality.
+
+Arguments
+- `ncMCR` : (integer) number of componant of MCR.
+- `grp` : a character string of the group 's column name.
+- `pk_sel` : a vector of selected peaks, or "all".
+- `time_format` :	a charater string "date" or "time".
+- `Li` : the list with spectra (sp).
+
+```{r mcr, eval = FALSE}
+mcr.result <- mcr.voc(ncMCR = 3, grp = "modality", pk_sel = "all", 
+                      time_format = "date", Li = sp)
+```
+
+## Others functions
+
+The package includes several small utility functions.  
+Three of them deserve a clear explanation because they allow you to find the index of peaks or spectra.
+*ind.acq* allows you to find the spectra related to an acquisition. *For example, if you have taken a series of 60 acquisitions, each with 8 spectra, ind.acq allows you to locate the 8 spectra of the 42nd acquisition [ ind.acq(42) #329 330 331 332 333 334 335 336].*
+*ind.pk* works in the same way but on the position of the peaks. This function should not be confused with *M.Z* (or *M.Z.max*) which finds the peaks detected during the import. 
+
+## And now ...
+
+You have everything to work wit provoc. If you have specific needs, questions or remarks, you can contact me quickly at my email address (joris.name [at] cefe.cnrs.fr).
+
+See you

inst/rmd/print_dy_sp.Rmd

+---
+output: html_document
+---
+
+```{r, fig.width=12, fig.height=5, echo=FALSE}
+dygraph(dysp, main = titre) %>%
+    dyAxis("y", label = "Intensity (a.u.)") %>% 
+    dyAxis("x", label = "m/z") %>%
+    dyRangeSelector(keepMouseZoom = TRUE, dateWindow = c(50,200)) %>%
+    dyHighlight(hideOnMouseOut = FALSE, highlightSeriesOpts = list(strokeWidth = 2)) %>% 
+    dyOptions(stackedGraph = FALSE, axisLineWidth = 1.5, fillGraph = TRUE,
+              gridLineColor = "lightblue", colors = dy_color) %>%
+    dyLegend(show = "onmouseover", hideOnMouseOut = TRUE) %>% 
+    dyUnzoom()
+```

inst/rmd/print_dypk_date.Rmd

+---
+output: html_document
+---
+
+```{r, fig.width=12, fig.height=5, echo = FALSE}
+  dygraph(dysp, main = titre) %>%
+      dyAxis("y", label = "Intensity (a.u.)") %>% 
+      dyAxis("x", label = paste("Time")) %>%
+      dyRangeSelector(keepMouseZoom = TRUE) %>%
+      dyOptions(stackedGraph = FALSE, fillGraph = TRUE, colors = dycol,
+                axisLineWidth = 1.5, gridLineColor = "lightblue",
+                connectSeparatedPoints = TRUE) %>% 
+      dyLegend(show = "onmouseover", hideOnMouseOut = TRUE) %>% 
+      dyUnzoom()
+```

inst/rmd/print_dypk_time.Rmd

+---
+output: html_document
+---
+
+```{r, fig.width=12, fig.height=5, echo = FALSE}
+  dygraph(dysp, main = titre) %>%
+      dyAxis("y", label = "Intensity (a.u.)") %>% 
+      dyAxis("x", label = paste("Time (",unit,")")) %>%
+      dyRangeSelector(keepMouseZoom = TRUE) %>%
+      dyOptions(stackedGraph = FALSE, fillGraph = TRUE, colors = dycol,
+                axisLineWidth = 1.5, gridLineColor = "lightblue",
+                connectSeparatedPoints = TRUE) %>% 
+      dyLegend(show = "onmouseover", hideOnMouseOut = TRUE) %>% 
+      dyUnzoom()
+```