NEWS in package ‘CHNOSZ’

Changes in version 2.1.0 (2024-02-11)

NEW FEATURES

Add FAQ.Rmd vignette with the following questions: How is ‘CHNOSZ’ pronounced?, How should CHNOSZ be cited?, What thermodynamic models are used in CHNOSZ?, When and why do equal-activity boundaries depend on total activity?, How can minerals with polymorphic transitions be added to the database?, How can I make a diagram with the trisulfur radical ion (S₃^-)?, In OBIGT, what is the meaning of T for solids, liquids, and gases?, and How can mineral pH buffers be plotted?
Add use.polymorphs argument to subcrt() to allow turning off automatic identification of stable polymorphs. This is used in the FAQ (How can minerals with polymorphic transitions be added to the database?).
Restore ‘EOSregress.R’ and its reverse dependencies eos-regress.Rmd and ‘demo/adenine.R’. Thanks to Kris Fecteau and Kirt Robinson for the suggestion.
mosaic() now handles the situation where the alternate basis species include one of the axis variables on a diagram (by changing the argument names in its internal calls to affinity()) and adjusts the labels for the diagram accordingly (e.g. “total C”, “total S”, etc.). Thanks to Evgeniy Bastrakov for the suggestion.
The environment variable CHNOSZ_BUILD_LARGE_VIGNETTES is used to control dpi in knitr chunk options. Setting this variable results in larger vignettes that are used for the CHNOSZ website; if this variable is unset (as in CRAN checks), a smaller package is built.
rank.affinity() now returns average group rankings as percentage values.

OBIGT DATABASE

subcrt() now outputs ΔG° and issues a warning above the temperature limit for C_P equations for minerals and other ‘⁠CGL⁠’ species. The temperature limit for C_P equations is stored as the opposite (negative) value in OBIGT. The previous behavior of outputting NA for ΔG° and issuing a message is now reserved for phase stability limits (i.e., melting, vaporization, or decomposition). See FAQ.Rmd for details.
Add carrollite (Cu_0.92Co_2.07S₄) from von der Heyden et al. (2024).
Modify cattierite (CoS₂) and linnaeite (Co₃S₄) to use parameters from Pankratz et al. (1987) as listed by Williams-Jones and Vasyukova (2022).
Add 36 charged amino acids from Kitadai (2015) and update several others (Arg⁺, Arg^-, Asp^-, Glu^-, His⁺, Lys⁺, Lys^-, and Tyr^-). Thanks to Grayson Boyer.
In OBIGT(), load ‘Berman_cr.csv’ before ‘inorganic_cr.csv’ so that info("Fe2O3") matches hematite rather than maghemite.
Rename checkGHS() and checkEOS() to check.GHS() and check.EOS() and change the default for return.difference to TRUE.

BUG FIXES

Fix bugs in subcrt() where exceed.Ttr and IS arguments were not applied to automatically balanced reactions.
Fix bug in dPdTtr() where OBIGT database parameters were not converted to Joules. This allows re-activating the tests for quartz (which depend on the computed transition temperature) in ‘test-subcrt.R’.

Changes in version 2.0.0 (2023-03-13)

MAJOR USER-VISIBLE CHANGES

Units of Joules instead of calories are now used by default for the thermodynamic properties output by subcrt(). That is, E.units("J") is the default setting. Scripts that implicitly depend on the previous default setting of E.units("cal") may need to be modified to produce expected output.
A model column has been added to the OBIGT thermodynamic database. This specifies the model for calculating standard thermodynamic properties. Currently available models are ‘⁠H2O⁠’ (water), ‘⁠HKF⁠’ (revised Helgeson-Kirkham-Flowers model for aqueous species), ‘⁠CGL⁠’ (heat capacity equation for crystalline, gas, and liquid species), ‘⁠Berman⁠’ (Berman model for minerals), ‘⁠AD⁠’ (Akinfiev-Diamond model for aqueous species), and ‘⁠DEW⁠’ (Deep Earth Water model, a variation of HKF). All OBIGT data files that can be read using add.OBIGT() must have this column; there is no back-compatibility support for data files in the old format.
Backward compatibility for OBIGT data files without an E_units column has been removed.
Order-of-magnitude (OOM) scaling of heat capacity coefficients for the CGL model in OBIGT data files has been removed. OOM scaling of HKF and DEW model parameters is still in place.
Change license from GPL (>= 2) to GPL-3.

OBIGT DATABASE

Move aqueous CH₄ back to ‘organic_aq.csv’ and move gaseous CH₄ from ‘inorganic_gas.csv’ to ‘organic_gas.csv’.
Modify OBIGT(no.organics = TRUE) to prune the database of organic compounds except CH₄. The ability to remove hundreds of more complex organic compounds while keeping CH₄ is useful for some calculations for abiotic reactions in hydrothermal systems.
Merge ‘biotic_aq.csv’ into ‘organic_aq.csv’.
‘⁠OBIGT/inorganic_cr.csv⁠’: Add cobalt monoxide (CoO), guite (Co₃O₄), and zinc from Robie and Hemingway (1995).
‘⁠OBIGT/inorganic_cr.csv⁠’: Modify linnaeite (Co₃S₄) to use 25 °C parameters from Robie and Hemingway (1995) and heat capacity coefficients from Pankratz et al. (1987).
‘⁠OBIGT/inorganic_cr.csv⁠’: Modify Co-pentlandite (Co₉S₈) to use parameters from Pankratz et al. (1987) as listed by Williams-Jones and Vasyukova (2022).
‘⁠OBIGT/organic_aq.csv⁠’: Correct formulas of Na(Mal)-, K(Mal)-, and Dy(Mal)+. Thanks to Grayson Boyer.

NEW FEATURES: THERMODYNAMIC DATA

Add logB.to.OBIGT() to fit selected thermodynamic parameters (‘⁠G⁠’ and ‘⁠S⁠’ at 25 °C and ‘⁠c1⁠’, ‘⁠c2⁠’, and ‘⁠omega⁠’ HKF coefficients) to formation constants of aqueous species as a function of temperature.
Add vignette custom_data.Rmd with description of database format, data-entry conventions, and examples of customizing the thermodynamic database using add.OBIGT(), mod.OBIGT(), and logB.to.OBIGT().

NEW FEATURES: DIAGRAMS

Add stack_mosaic() to create stacked mosaic diagrams, where the species formed in the first layer become the basis species for the species formed in the second layer. This function implements the procedure for making mosaic diagrams for bimetallic systems described in multi-metal.Rmd.
Add loga_aq argument to mosiac() (also present in new function stack_mosaic()) to control the activity of mosaiced aqueous basis species. This obviates a workaround that was previously used in the Mosaic Stacking 2 section of multi-metal.Rmd.
Add add.alpha() to add alpha value to a color specified in any notation accepted by col2rgb().

NEW FEATURES: PROTEINS

Add function rank.affinity() to calculate means of affinity rankings for specified groups of proteins, intended for evolutionary comparisons. The output of the new function can be used by diagram().
Add an as.residue argument to add.protein() to normalize amino acid compositions by protein length.
Add a check to add.protein() that all new protein IDs (protein name + organism name) are unique.
In affinity(), print a message to indicate whether ionization calculations for proteins are being done.
seq2aa() allows an empty sequence (zero counts of amino acids), useful for intializing a data frame of amino acid composition.

NEW FEATURES: OTHER

NaCl() has been rewritten to include pH dependence (i.e. formation of HCl as well as NaCl) by using affinity() and equilibrate() instead of algebraic equations.
Ion size parameters used in the ‘⁠Bdot⁠’ equation have been moved from the code for nonideal() to ‘extdata/thermo/Bdot_acirc.csv’, which is read into thermo()$Bdot_acirc and can be changed by the user.
The two preceding features are used in a new demo yttrium.R to show speciation of Y-Cl complexes as a function of NaCl concentration, pH, T, and P, after Guan et al. (2020).

REMOVED FEATURES

cgl(), hkf(), and AD() are no longer exported. subcrt() should be used for all calculations of thermodynamic properties.
Remove EOSregress() and the associated demo and vignette.
Remove parallel calculations in read.fasta() and count.aa().
Remove revisit(), findit(), uniprot.aa(), nucleic.formula(), and nucleic.complement().

BUG FIXES

Add stringsAsFactors = FALSE to a cbind() call in mix(), needed for R < 4.0.0. Thanks to Xiaojia Jiang for the bug report.
In multi-metal.Rmd, work around absence of hcl.colors() in R < 3.6.0.
diagram(): Improve handling of length > 1 col, lty and lwd arguments for predominance diagrams. Because field boundaries are drawn for the first species, then that species is removed before drawing boundaries for the second species, and so on, species for which different-colored or -styled lines are desired should be placed at the top of the species list. This change makes possible one less call to diagram() in Mosaic Stacking 1 and 2 in multi-metal.Rmd, and now the entire chalcopyrite field in Mosaic Stacking 2 is bounded by a thick orange line, instead of just the border with bornite.
Improve handling of non-integer coefficients in expr.species(). For example, the result for FeS1.33 was previously incorrectly formatted as FeS_.33 but is now correctly formatted as FeS_1.33.

OTHER CHANGES

The reaction component of the output of subcrt() contains the model for each species.
subcrt() produces an error if an aqueous species with the ‘⁠DEW⁠’ model is requested but the DEW water model isn't activated.
Add a zap argument to mod.OBIGT() to clear parameters of preexisting species (used by logB.to.OBIGT()).
In affinity(), make loga.protein = 0 the default (changed from -3).
Add tests ‘stack_mosaic.R’ and ‘stack_solubility.R’ (these create PDF files for visual inspection of results).
axis.label() produces labels with units delimited by parentheses instead of a comma.
seq2aa() now has the sequence argument first and a default of NA for protein (the protein name).
Remove unused ‘⁠cutoff⁠’ value in thermo()$opt.
Move ibasis argument to first position in describe.basis().

Changes in version 1.4.3 (2022-02-20)

UNIT TESTING

Skip tests on CRAN that fail for M1mac and ATLAS (heat capacity and the second derivative of H₂O density in ‘tinytest/test-AD.R’).

Changes in version 1.4.2 (2022-02-08)

PLANNED API CHANGE

In the next major release of CHNOSZ (to be version 2.0.0), units of Joules instead of calories will be used by default for the thermodynamic properties output by subcrt(). That is, E.units("J") will be the default setting. User scripts that implicitly depend on the current default setting of E.units("cal") will need to be modified to produce expected results after this change is made.

THERMODYNAMIC CALCULATIONS

The AD() function, which provides an implementation of the Akinfiev and Diamond (2003) equation of state for aqueous nonelectrolytes, now calculates entropy, heat capacity, and volume in addition to the previously available Gibbs energy.
For minerals with thermodynamic parameters in the equations of Berman (1988), info() with a numeric argument now lists values of G, H, S, Cp, and V at 25 °C and 1 bar (these were previously shown as NA). Thanks to Evgeniy Bastrakov for suggesting both of these changes.

OBIGT DATABASE

Add H₂WO₄(aq) and Cp coefficients of scheelite (CaWO₄) from Liu et al. (2021).
Add aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl from Miron et al. (2016) and Miron et al. (2017) to ‘GEMSFIT.csv’.
Add pyrobitumen (C₅₄H₄₂) from Helgeson et al. (2009) to ‘organic_cr.csv’.
Move Ar, Xe, CH₄, and CO₂ from ‘organic_aq.csv’ to ‘inorganic_aq.csv’.
Fix formula of CaCl₂ in ‘DEW.csv’. Thanks to Grayson Boyer.
Remove ‘OldAA.csv’ (superseded thermodynamic parameters for amino acids). This file is now available in the JMDplots package.

OTHER CHANGES

Tests are now run using the tinytest package.
Add an add argument to basis() to allow adding a species to an existing set of basis species.
The AkDi() function has been renamed to AD(), and all variables and data files likewise use the acronym AD. In particular, the Akinfiev-Diamond model is activated for an aqueous species by using abbrv = "AD" in thermo()$OBIGT.
Names of functions, variables, and data files now use capitalized ‘⁠Berman⁠’, not ‘⁠berman⁠’.
In ‘vignettes/multi-metal.Rmd’ (“Diagrams with multiple metals”), add a link to the associated paper (Dick, 2021).

REMOVED FUNCTIONS

Remove maxdiff() and expect_maxdiff(), previously used in tests.
Remove read.blast(), id.blast(), write.blast(), def2gi(), and example files in ‘extdata/bison’.
Remove eqdata(), a script for extracting data from EQ3/6 output files.

Changes in version 1.4.1 (2021-04-08)

NEW FEATURES

Add ‘⁠demo/Pourbaix.R⁠’ (Eh-pH diagrams with isosolubility lines, after Pourbaix, 1974). This demo depends on the following two changes.
Revise solubility() to enable calculating overall (i.e. minimum) solubility for multiple minerals. Calculations for multiple minerals are also now used in ‘⁠demo/zinc.R⁠’.
Restore lty.aq and lty.cr arguments to diagram() to control plotting of aq-aq and cr-cr field boundaries.
Add no.organics argument to OBIGT() to load the thermodynamic database without organic species.

DATA UPDATES

‘⁠OBIGT/Berman_cr.csv⁠’: Where possible, use standard abbreviations for mineral names (including hematite (Hem) and magnetite (Mag)), as listed by Whitney and Evans (2010).
‘⁠OBIGT/organic_aq.csv⁠’: Add properties of aqueous fatty acids, saccharides, and other species, and add associated ‘⁠demo/E_coli.R⁠’ (Gibbs energy of biomass synthesis in E. coli, after LaRowe and Amend, 2016).
‘⁠OBIGT/inorganic_aq.csv⁠’: Add properties of aqueous Nb and Ta species from Akinfiev et al., 2020.
‘⁠OBIGT/inorganic_cr.csv⁠’: Add willemite (Zn₂SiO₄) from Robie and Hemingway, 1995 and Barin et al., 1977 (heat capacity equation).
‘⁠OBIGT/inorganic_cr.csv⁠’: Move alunite here from ‘⁠SUPCRT92.csv⁠’.
‘⁠thermo/protein.csv⁠’: Rename ‘⁠CDC2_HUMAN⁠’ to ‘⁠CDK1_HUMAN⁠’ (UniProt: P06493).

OTHER CHANGES

Automatic detection of dissociation reactions was fragile and has been removed from solubility(). The new default (dissociate = FALSE) is to not consider dissociation reactions.
In the return value of diagram(), predominant.values previously only contained affinities (extracted from the values element of the eout argument). Now it has the values for the predominant species extracted from the values actually used to make the plot (the plotvals list in the output), i.e. affinities divided by the balancing coefficients if eout is the output of affinity, or activities if eout is the output of equilibrate. Therefore it can now be used to draw contours or a color image showing the activities of the predominant species. This is used for a diagram in a new preprint (Dick, 2021).
Revise multi-metal.Rmd: Improve mineral abbreviations and placement of labels; use updated DFT energies from Materials Project; add Mosaic Stacking 2 (minerals and aqueous species); add K^eff calculation (Robinson et al., 2021); add ΔG_pbx color scale.
Rename ‘⁠demo/berman.R⁠’ to ‘⁠demo/potassium.R⁠’.
Remove unused limSolve package from Suggests in DESCRIPTION.
Add option thermo()$opt$ionize.aa to control calculation of properties of ionized proteins in affinity().
Fix bug where protein ionization calculations with ionize.aa() were incorrectly affected by the setting of E.units().
The Akinfiev-Diamond model is now activated by setting abbrv = "AkDi" for any aqueous species, instead of setting the charge (z) to NA. This simplifies the more common use case of adding a custom aqueous species to OBIGT with mostly NA parameters.
Remove ‘⁠bases2⁠’ argument from mosaic() (old backward compatibility feature).

Changes in version 1.4.0 (2020-11-11)

MAJOR CHANGES

An add argument has been added to species(). With the default of add = FALSE, loading new species now causes any existing species definition to be deleted. To add species to an existing system, use ‘⁠add = TRUE⁠’. With this change, scripts can be made more concise because species(delete = TRUE) is no longer needed to clear the species definition in a series of calculations for different systems.
The naming convention for methane has changed. The name methane now applies exclusively to the gas; the formula CH4 without a state continues to represent the aqueous species. This behavior is consistent with inorganic gases but differs from most organic substances, where the name refers to the aqueous species. This change was made because in the past there was no way to use info() or subcrt() with a single character argument to identify gaseous methane, which is common in geochemistry. (Note that info("CH4", "gas") can still be used.) A hack to revert to the old behavior, where methane refers primarily to the aqueous species, is mod.OBIGT(info("CH4"), name = "methane").
The all-uppercase acronym OBIGT is used everywhere it appears in file, function, and object names. In particular, the thermodynamic database now is located at thermo()$OBIGT, and functions add.OBIGT() and mod.OBIGT() replace the previous add.obigt() and mod.obigt().
The new default of NULL for limit.water in diagram() causes the main diagram to be overlaid on the fields of water stability (white) and instability (gray). Change this to TRUE to obtain the previous default of masking all parts of the diagram outside of the water stability field.

NEW FEATURES

Add function mash() for combining two diagrams for different systems (i.e., simple overlay of diagrams for two single-metal systems).
Add function mix() for combining two single-metal diagrams with a third diagram for bimetallic species. This can be used to produce diagrams for a binary system with fixed composition of the metals.
Add function rebalance() for making a new diagram by secondary balancing between two systems.
Add a stable argument to mosaic() to use previously calculated stabilities of species (e.g. minerals) for the changing basis species. This allows mosaic() calculations to be linked in series (or "stacked"), for instance to sequentially add metals (Fe, then Cu) to a diagram.
Add vignette multi-metal.Rmd for examples that use these new features to make diagrams for systems with multiple metals (specifically Fe-V and Fe-Cu).

CHANGES TO OBIGT DATABASE

Dates in the ‘⁠date⁠’ column have been converted to use ISO 8601 extended format (e.g. 2020-08-16). The accessory function today(), to render the current date using the previous format, has been removed.
Update species parameters for the 2019 version of the Deep Earth Water (DEW) model (Huang and Sverjensky, 2019).
‘⁠inorganic_aq.csv⁠’, ‘⁠inorganic_aq.csv⁠’: Add arsenopyrite, loellingite, westerveldite, and aqueous As(OH)₃ and AsO(OH)₃ from Perfetti et al., 2008.
‘⁠inorganic_aq.csv⁠’: Add Co-chloride species from Liu et al., 2018.
‘⁠inorganic_aq.csv⁠’: Add metal carbonate and bicarbonate complexes and FeSO₄ from St Clair et al., 2019.
‘⁠inorganic_cr.csv⁠’: Add wustite, manganese, and Mn oxides (manganosite, pyrolusite, bixbyite, and hausmannite) from Robie and Hemingway, 1995.
‘⁠inorganic_cr.csv⁠’: Add amorphous Mn(OH)₂ from Wagman et al., 1982 (GHS) and Senoh et al., 1998 (estimated Cp values).
‘⁠inorganic_cr.csv⁠’: Add huebnerite (MnWO₄) from Liu and Xiao, 2020.
‘⁠inorganic_cr.csv⁠’: Add linnaeite (Co₃S₄) and Co-pentlandite (Co₉S₈) from Vaughan and Craig, 1978 and cattierite (CoS₂) and cobalt from Robie and Hemingway, 1995.
Add GHS and Cp at 25 °C for almandine, dickite, fluorphlogopite, glaucophane, grunerite, halloysite, larnite, pyrope (‘⁠SUPCRT92.csv⁠’) and bromellite (‘⁠inorganic_cr.csv⁠’) from Robie and Hemingway, 1995.
‘⁠inorganic_cr.csv⁠’: Correct formulas for number of H₂O in some As-bearing minerals.
‘⁠SUPCRT92.csv⁠’: Change lowercase to uppercase "A" (Angstrom) in names of minerals with suffixes indicating interlayer spacing (amesite, clinochlore, cronstedtite, daphnite).
Remove bracketed suffixes in references (e.g. [S92] was used to indicate that the data first appeared in SUPCRT92).
Use uncompressed data files (i.e. ‘⁠.csv⁠’, not ‘⁠.csv.xz⁠’) and rename ‘⁠DEW_aq.csv⁠’ to ‘⁠DEW.csv⁠’.
The package is now installed with the bibtex file for the OBIGT database (‘⁠docs/OBIGT.bib⁠’), which is used by the logKcalc package (https://github.com/jedick/logKcalc).
‘⁠thermo/element.csv⁠’: Add entropies for Am, Pu, Cm, Np from Thoenen et al., 2014 (The PSI/Nagra Chemical Thermodynamic Database 12/07).

DEMOS AND VIGNETTES

Add ‘⁠demo/comproportionation.R⁠’: Gibbs energy of sulfur comproportionation, after Amend et al., 2020.
Add ‘⁠demo/zinc.R⁠’: Solubilities of multiple minerals (zincite and sphalerite).
Revise and simplify ‘⁠anintro.Rmd⁠’ and ‘⁠equilibrium.Rmd⁠’ (converted from ‘⁠equilibrium.Rnw⁠’).
Revise ‘⁠OBIGT.Rmd⁠’ to reduce the size of the HTML file and make deep linking to individual sections work.
Add ‘⁠viglink⁠’ Rd macro so HTML versions of Rd files can link to vignettes.
Remove vignette ‘⁠hotspring.Rnw⁠’ and demos ‘⁠bison.R⁠’ and ‘⁠bugstab.R⁠’. The material is now in the ‘⁠bison.Rmd⁠’ vignette and ‘⁠bugstab.R⁠’ demo in the JMDplots package (https://github.com/jedick/JMDplots).
New demo ‘⁠berman.R⁠’, extracted from ‘⁠berman.Rd⁠’.
Revise demo ‘⁠mosaic.R⁠’ to use mash() to show S and C species together, make better use of transparency, and dy argument to adjust positions of labels.

DIAGRAM IMPROVEMENTS

Change default resolution in affinity() from 128 to 256. This greatly improves the appearance of diagrams made with the default settings.
which.pmax() was rewritten to speed up identification of predominant species, and the drawing of field boundaries in diagram() was made more efficient. The latter change has prompted the removal of the ‘⁠lty.aq⁠’ and ‘⁠lty.cr⁠’ arguments from diagram().
Add a bottom argument to ratlab() to allow changing the ion in the denominator to something other than H⁺.
The ‘⁠srt⁠’, dx (new), and ‘⁠dy⁠’ arguments in diagram() can now be used to rotate and adjust the position of field labels, not only line labels. This and other arguments (‘⁠cex⁠’, ‘⁠col⁠’, ‘⁠col.names⁠’, ‘⁠font⁠’, ‘⁠family⁠’, ‘⁠bold⁠’, ‘⁠italic⁠’) can have length > 1 to apply different settings to each species.
Add a min.area argument to diagram() to specify the minimum area of fields that should be labeled. This is useful for removing labels from small fields on crowded diagrams.
The list returned by diagram() now includes a predominant.values component, which has the affinities of the predominant species at each grid point. This can be used as shown in the multi-metal.Rmd vignette to compute the Pourbaix energy (ΔG_pbx) for a metastable material.

OTHER CHANGES

subcrt(): replace ‘⁠action.unbalanced⁠’ argument with autobalance, which now provides the ability to prevent autobalancing.
Setting the water model with water() updates the literature references in thermo()$OBIGT.
thermo.refs() shows CHNOSZ version and date.
subcrt() and affinity() use degree symbol (°C) in messages.
Change thermo$... to thermo()$... in messages and comments.
mosaic() now allows a blend argument of length > 1 to apply a specific setting to each group of basis species.
Fix ‘⁠palply.Rd⁠’ for new warning about “Non-file package-anchored link(s) in documentation object” in R CMD check.
Remove wjd() (implementation of Gibbs energy minimization method from White et al., 1958) and demo wjd.R and supporting data file.
Add "QCa" as a keyword for preset species in basis() (glutamine, cysteine, acetic acid, H₂O, O₂).
Add T and P arguments to retrieve() to require that species have non-NA values of standard Gibbs energy at this temperature and pressure.
Change defaults in mod.buffer() to be more suitable for mineral buffers (state = "cr" and logact = 0).
Remove extdata/supcrt (scripts to read SUPCRT data files).
Convert this NEWS file to Rd format.