knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-", fig.width = 6, fig.height = 5, dev = "ragg_png" )
spant provides a full suite of tools to build automated analysis pipelines for Magnetic Resonance Spectroscopy (MRS) data. The following features and algorithms are included:
Download and install the latest version of R (https://cloud.r-project.org/), or with your package manager if using a recent Linux distribution, eg sudo apt install r-base
.
It is also strongly recommended to install RStudio Desktop (https://rstudio.com/products/rstudio/download) to provide a modern environment for interactive data analysis.
Once R and RStudio have been installed, open the RStudio application and type the following in the Console (lower left panel) to install the latest stable version of spant:
install.packages("spant", dependencies = TRUE)
Or the the development version from GitHub (requires the devtools
package):
install.packages("devtools") devtools::install_github("martin3141/spant", ref = "devel", dependencies = TRUE)
Quick introduction to the basic analysis workflow : https://martin3141.github.io/spant/articles/spant-intro.html
Short tutorials : https://martin3141.github.io/spant/articles/
Function reference : https://martin3141.github.io/spant/reference/
Once the spant library has been loaded with library(spant)
, type ?spant
on the console for instructions on how to access the offline documentation. Note that offline help on the available functions can be quickly shown in RStudio using ?function_name
, eg ?read_mrs
.
CRAN packages need to be compiled on Linux, and therefore you may need to ensure some additional system libraries are installed. spant may be installed from a clean installation of Ubuntu 20.04 with the following commands pasted into the terminal:
```{ubuntu install, eval = FALSE} sudo apt install -y r-base libcurl4-openssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff5-dev mkdir -p ~/R/x86_64-pc-linux-gnu-library/3.6 Rscript -e 'install.packages("spant", dependencies = TRUE)'
## Ubuntu 21.10 installation ```{ubuntu 2110 install, eval = FALSE} sudo apt install -y r-base libcurl4-openssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff5-dev mkdir -p ~/R/x86_64-pc-linux-gnu-library/4.0 Rscript -e 'install.packages("spant", dependencies = TRUE)'
Firstly install Anaconda in the standard way for your platform: https://docs.anaconda.com/anaconda/install/index.html.
Create a text file, called spant_requirements.yml
, containing the following:
```{conda yml, eval = FALSE} name: spant channels: - conda-forge - r dependencies: - r-base - r-essentials - r-abind - r-plyr - r-foreach - r-pracma - r-stringr - r-signal - r-matrixcalc - r-minpack.lm - r-nnls - r-r.utils - r-graphicsqc - r-expm - r-smoother - r-readr - r-magrittr - r-ptw - r-mmand - r-RNifti - r-RNiftyReg - r-fields - r-MASS - r-numDeriv - r-nloptr - r-irlba - r-tibble - r-jsonlite - r-viridisLite - r-shiny - r-miniUI - r-knitr - r-rmarkdown - r-testthat - r-ragg - r-doParallel
Create and activate the environment: ```{conda, eval = FALSE} conda env create -f spant_requirements.yml conda activate spant
Start R and install spant in the usual way:
install.packages("spant", dependencies = TRUE)
Big thanks to João M.C. Teixeira for figuring out this method of install.
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