This package facilitates the reading, processing and visualization of N2O isotope data including drift correction, 17O correction and standards calibration.
As of version 0.4.0, the package is based on the functionality provided
by the isoreader and
isoprocessor packages to load IRMS
data directly from their raw data files and process it. All can be
installed from CRAn or directly from GitHub using the devtools package
(see troubleshooting section below in case of issues
with devtools installs).
install.packages("devtools")
install.packages("isoreader")
devtools::install_github("isoverse/isoprocessor")
devtools::install_github("sebkopf/isorunN2O", build_vignettes = TRUE)For the earlier version that used the now deprecated isoread instead,
run devtools::install_github("sebkopf/isorunN2O", ref = "v0.3.0").
This version unfortunately is no longer supported on newer R versions.
The package includes a tutorial that introduces most functionality and
provides examples of how it works and can be used. Please see the
documentation
here
for details. After the isorunN2O package is installed, the newest
version of this tutorial can also be loaded up as a vignette directly in
R by calling vignette("N2O_data_reduction_tutorial") in the command
line. The RMarkdown file underlying the vignette is available directly
in this repository.
Earlier versions of this package (up to 0.3.0) also include a browser
based application for interactive N2O run monitoring. It can be launched
with the function run_data_viewer(), additional information is
available
here.
For newer versions of this package (>= 0.4.0), this functionality is mostly covered by the much broader graphical user interface of the isoviewer package although it does not yet recreate all of the original functionality of the N2O data viewer. We ask for patience while isoviewer is still in development, it will eventually provide all the original functionality and much more.
On Windows, the above install_github calls can fail because of the
requirement to create zip archieves during some vignette creation steps.
If this is the case, install
Rtools, restart R and
RStudio and try to run the installation again.
If you run into any trouble installing the packages that is not resolved
easily, try installing them again without the vignettes, which are
sometimes the sole culprits, i.e. devtools::install_github(...., build_vignettes = FALSE), which should provide the fully functional
package, just without the vignette tutorial (which you can still check
out online as mentioned in the How to use? section).
The latest version of the devtools package on CRAN (version 1.12.0)
has a bug that causes issues with the installation of package
dependencies, especially on Windows, which usually manifest as errors
during the installation of GitHub packages stating some dependency
(e.g. stringi or dplyr or htmltools, etc. package missing).
Please check this troubleshooting
Gist
for details if you encounter this error.