The R package pointapply contains the code and data to reconstruct the publication: Martin Schobben, Michiel Kienhuis, and Lubos Polerecky. 2021. New methods to detect isotopic heterogeneity with Secondary Ion Mass Spectrometry, preprint on Eartharxiv.
This paper assesses the performance of the application of the diag_R()
function of the sister package point (Schobben 2022) in detecting
isotope heterogeneity in natural substrates.
The data is stored on the Zenodo repository pointdata.
The data can be directly downloaded with download_point(), which is
build around zen4R (Blondel 2022).
# Download
download_point()Use the function render_paper() and specify the directory to save the
paper. Make sure to have latex installed on your system. Check e.g.,
https://yihui.org/tinytex/ for a light weight LaTeX version.
# install.packages('tinytex')
# Knit
render_paper(title = "Schobbenetal_SIMS_method", output_dir = "mydir")The construction of the R (R Core Team 2022) package pointapply and associated documentation was aided by the packages; devtools (Wickham, Hester, et al. 2021), roxygen2 (Wickham, Danenberg, et al. 2021), testthat (Wickham 2022), vdiffr (Henry et al. 2022), cpp11 (Hester and François 2021), and fs (Hester, Wickham, and Csárdi 2021).
The book: R packages: organize, test, document, and share your code, by Wickham (2015) is a great guide for learning how to build packages.
In addition, this package relies on a set of external packages from the tidyverse universe, including: dplyr (Wickham et al. 2022), tidyr (Wickham and Girlich 2022), tibble (Müller and Wickham 2021), stringr (Wickham 2019), magrittr (Bache and Wickham 2022), and purrr (Henry and Wickham 2020) for data manipulation.
Data plots are constructed with ggplot2 (Wickham, Chang, et al. 2021; Wickham 2016), ggrepel (Slowikowski 2021), RColorBrewer (Neuwirth 2022), and scales (Wickham and Seidel 2022)
The package rlang (Henry and Wickham 2022) was used for tidy evaluation.
Some specialised packages where used, notably; readmat for loading the matlab LANS files (readmat?) and MASS (Ripley 2022; Venables and Ripley 2002) for 2D density estimates.
The data download from Zenodo with an api is facilitated by zen4R (Blondel 2022).
The documentation and paper was written with knitr (Xie 2022b, 2014, 2015), rmarkdown (Allaire, Xie, McPherson, et al. 2022; Xie, Allaire, and Grolemund 2018; Xie, Dervieux, and Riederer 2020), bookdown (Xie 2022a, 2016), pkgdown (Wickham, Hesselberth, and Salmon 2022), rticles (Allaire, Xie, Dervieux, et al. 2022) and bibtex (Francois 2020).
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("MartinSchobben/pointapply", build_vignettes = TRUE)The data figures can be constructed with the functions contain in this package. The following vignettes detail all these operations in a coherent story line.
Data:
- Synthetic data for validation of model performance and Figure 2 and
3 and Supplementary Figure 1 (
vignette("simulation")). - Real data reading and processing and Supplementary Figure 2
(
vignette("data")).
Because of the excessive file-sizes of ion count data, the data is
stored externally on Zenodo,
and can be accessed with the function download_point().
Figures:
- Evaluation of model performance; Figures 4 and 5
(
vignette("performance")). - Raster images and scatter plots of real SIMS
13C/12C analyses; Figures 6–8 and
Supplementary Figures 7 and 8 (
vignette("raster")). - Regression diagnostics; Supplementary Figures 3–5
(
vignette("regression")). - Accuracy of SIMS isotope analysis; Supplementary Figures 3 and 7
(
vignette("accuracy")).
Allaire, JJ, Yihui Xie, Christophe Dervieux, R Foundation, Hadley Wickham, Journal of Statistical Software, Ramnath Vaidyanathan, et al. 2022. Rticles: Article Formats for r Markdown. https://github.com/rstudio/rticles.
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Bache, Stefan Milton, and Hadley Wickham. 2022. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.
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