README.md
In elementR: An Framework for Reducing Elemental LAICPMS Data from Solid Structures

elementR :star:

Since its release and during IOS2018, elementR, the R package for data reduction of otolith LA-ICPMS data, is receiving more and more requests for including new features.

We therefore decided to develop a successor of elementR in a collaborative manner to satisfy all of your needs. But for this we need you! Tell us which feature you would like to see included in the successor of elementR or just support the project (https://goo.gl/forms/NxLNbKOb2ZZhOJ4r2). The more support we get, the easier it will be to find funding for a professional developer, so your participation counts!

We really look forward to hear from you!

For more details on the project or on elementR, see elementR website

elementR is an R package facilitating the handling and reduction of elemental microchemistry data obtained from solid-phase LA-ICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The elementR R-package provides:

a set of classes to handle LA-ICPMS data
a reactive user friendly interface running in the web browser to conduct all steps needed for an optimal data reduction while leaving maximum control to the user.

elementR implements R6 R classes and is based on Shiny for it's GUI.

Before installation

Check the version of R installed on your computer (sessionInfo()), must be ≥ 3.2.3, see https://cran.r-project.org/ to update your version.
For Mac users only: elementR package needs XQuartz. Please check, that XQuartz is installed and runs properly on your computer. If not, please visit https://www.xquartz.org/.

The easiest way to get elementR is to install it from CRAN:

install.packages("elementR", dependencies = T)
library(elementR)

Alternatively, you can install the development version (not yet pushed on cran) from GitHub :

#Install elementR's dependencies
pkgs <- c("gdata", "shiny","devtools", "shinyjs", "gnumeric", "R6", "shinydashboard",
    "abind", "stringr", "lmtest", "tcltk", "tcltk2", "reader", "readODS", "readxl", "outliers", "climtrends",
    "EnvStats", "colourpicker", "zoo", "httpuv")

invisible(lapply(pkgs, function(pkgs){
    if(!require(pkgs)){
        install.packages(pkgs, dependencies=TRUE)
    }
}))

#Install elementR
devtools::install_github("charlottesirot/elementR", ref = "master", force = T, dependencies = T)

library(elementR)

For Mac users: during installation elementR will ask to install "XCode/otool". Accept this installation.

If the installation is stuck at the installation of the tcltk package, this probably means that XQuartz does not run properly. Check its validity.

For Linux users: you could need to install additional libraries:

sudo apt-get update
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
sudo apt-get install libxml2-dev
sudo apt-get install libssh2-1-dev

the elementR GUI runs on any web browser. However, as the graphic of the user interface has been developed based on Firefox, authors highly recommend to run elementR under Firefox.

To launch elementR, run the following command in your R console:

runElementR()

If you are new to elementR you are better off starting with a systematic introduction, this can be found in the pdf documentation of this package.

If, despite the :heart: brought during the programming of this R package and writing of this documentation, you have difficulties to install or run elementR, if you have questions about the procedures or calculations, or if you want to report bugs :beetle:, do not hesitate to contact our team elementR.software@gmail.com, to consult the official elementR documentation above or on CRAN or connect with us on GitHub.