In stable isotope geochemical calculations, we use a number of different representations of isotopic information and processes (ratios, abundances, delta values, alpha values, epsilon values, fractionation factors, refereence frame shifts, mass balance calculations, mass-independent effects, etc., etc.) that are constantly being converted back and forth and used for different kinds of isotope arithmetic. Very frequently, the tangle of keeping track of this information and how all the calculations are done properly makes code very hard to read, difficult to communicate - or even understand oneself later on, and as anyone knows who’s ever dropped a -1 or x1000 at the wrong place, prone to small mistakes that can make an enormous difference.
The isotopia package uses the S4
object system of R to define elemental isotopic data classes (ratio,
abundance, delta, fractionation_factor and intensity) so that it
can automatically keep track of what is a ratio, what is a delta value
(and is it in permil notation or in ppm), etc., and perform isotope
arithmetic accordingly. The multiple dispatch system of S4 allows any
generic function to be dispached to a method based on the class of the
argument, i.e. a fractionation function can be implemented differentely
whether it is supposed to fractionate an isotope ratio or a delta value.
This allows the user to focus on the actual calculations and communicate
to the reader exactly what each value represents. Most importantly, the
isotope value object structure allows
isotopia to put safeguards in place
against non-sense calculations and makes it easy to implement rigorous,
automatically executed tests for every single formula and computation
(currently there are over 350 tests implemented, see Testing
for a few examples). This means that any time any of the isotopia source
code is modified, it has to pass all the tests that ensure it is
functioning exactly as expected. This kind of test-driven implementation
provides high confidence in the calculations and protects from small
code changes leading to incorrect results and interpretation.
For a detailed guide on how to get started, see this vignette.
The isotopia R package can be
installed directly from GitHub, by using the R
development tools package (devtools). A word of caution that isotopia
is still under active development and development versions include
additional functionality with syntax that might not be backwards
compatible.
# install.packages("devtools") # only needed once
devtools::install_github("isoverse/isotopia")