AquaEnv : An Aqua tic Acid–Base Modelling Env ironment in R

Abstract

AquaEnv is an integrated software package for aquatic chemical model generation focused on ocean acidification and antropogenic CO 2 uptake. However, the package is not restricted to the carbon cycle or the oceans: it calculates, converts, and visualizes information necessary to describe pH, related CO 2 air-water exchange, as well as aquatic acid-base chemistry in general for marine, estuarine or freshwater systems. Due to the fact that it includes the relevant acid-base systems, it can also be applied to pore water systems and anoxic waters. AquaEnv is implemented in the open source programming language R, which allows for a flexible and versatile application: AquaEnv's functionality can be used stand-alone as well as seamlessly integrated into reactivetransport models in the R modelling environment. Additionally, AquaEnv provides a routine to simulate and investigate titrations of water samples with a strong acid or base, as well as a routine that allows for a determination of total alkalinity and total carbonate values from recorded titration curves using non-linear curve-fitting.Keywords Acid-base chemistry Á pH modelling Á Ocean acidification Á Reactive-transport models Á Marine estuarine and freshwater systems Á CO 2 air-sea exchange Á In silico titration Á TA determination Electronic supplementary material The online version of this article

Glacial meltwater and primary production are drivers of strong CO<sub>2</sub> uptake in fjord and coastal waters adjacent to the Greenland Ice Sheet

“…Processing of data was done in R (R Core Team, 2013). The R package CRAN: AquaEnv (Hofmann et al, 2010) was used for acid-base speciation and CO 2 system calculations. We used the carbonate equilibrium constants by Roy et al (1993) with the adaptation by Millero et al (1995) for low salinities.…”

“…(1) using the formulation by Nightingale et al (2000) for the gas transfer coefficient. The pCO 2 concentration of the surface water was calculated from salinity, temperature, TA and DIC using the R package CRAN: AquaEnv (Hofmann et al, 2010). The net community production (NCP) was calculated as the difference between the primary production (PP) and bacterial carbon demand (BCD), and values for the rate of these processes were determined based on monthly rate measurements.…”

Stable carbon isotope biogeochemistry of lakes along a trophic gradient

“…The different components of the CO 2 system were calculated from temperature, laboratory pH and DIC concentrations using a salinity of 0 and the R package AquaEnv (Hofmann et al, 2010). Stable isotope ratios were expressed in the delta notation (δ 13 C), which is the 13 C / 12 C ratio relative to VPDB standard, in parts per thousand (‰).…”

A 1500-year multiproxy record of coastal hypoxia from the northern Baltic Sea indicates unprecedented deoxygenation over the 20<sup>th</sup> century

“…Indeed, total sulfide concentrations of > 100 µM have been reported to prevail in the uppermost centimeters of the sediment column within the SMTZ in an analogous setting in the coastal Baltic Sea . Assuming a salinity and temperature of 5.6 and 9 ºC, respectively (Virtasalo et al, 10 2005) and a pH of 6.6 (our unpublished data) at the sediment-water interface, this total sulfide concentration corresponds to H2Saq concentration of > 70 µM (calculated with R package AquaEnv, Hoffmann et al, 2010), clearly exceeding the requirement of 11 µM H2Saq for the activation of the sulfide-switch (Helz, et al, 1996;Erickson and Helz, 2000). The annual accumulation rate of Mo is expected to be controlled by the duration of the late summer period when the SMTZ is located closest to the sediment surface (Adelson et al, 2001;Helz and Adelson, 2013).…”