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Change data for dawsonite, scheelite, and ferberite from calories to Joules (as originally reported).
Use correct Cp coefficients for ferberite (2nd term in equation of Wood and Samson, 2000 is off by a factor of 10). Thanks to Xiangchong Liu and David Polya for the bug report and assistance.
Move more carbonates from SUPCRT92 back into the default database: artinite, azurite.
Improve the handling of solids in equilibrate(). They are now excluded from the equilibrium calculation, but their stability fields are calculated using the maximum affinity method (with diagram()). Where solids are stable, logarithms of activities of aqueous species are set to -999, and vice versa. Thanks to Feng Lai for the request and test case.
Remove files Sce.csv.xz and yeastgfp.csv.xz and functions yeastgfp() and yeast.aa(). These have been moved to the JMDplots package (https://github.com/jedick/JMDplots).
Remove protein_refseq.csv.xz (based on RefSeq release 61). An updated version, based on RefSeq release 95, is available in JMDplots.
describe.reaction(): revert the Unicode double arrow. Unlike that, a simple equals sign is displayed correctly on all systems.
Fix bug in unexported function obigt2eos(): lambda (exponent in heat capacity equation) was incorrectly going through a units conversion.
subcrt(): properties of minerals are now output at the listed upper T limit (or transition temperature, for e.g. cr1 -> cr2). Previously, properties were set to NA at, and not only above, the T limit. Thanks to Evgeniy Bastrakov for the bug report.
In mosaic(), set the activities of only aqueous basis species to the total activity, which is taken from the incoming basis() definition. This fixes a bug where activities of minerals (particularly, native sulfur) were unexpectedly changed; their logarithms are now set to 0. Thanks to Evgeniy Bastrakov for the bug report.
Fix a bug where berman() returned NA values for K-feldspar below 298.15 K, due to improperly initialized values for the disorder properties. Thanks to Kaustubh Hakim for the bug report.
Use inherits() instead of class() for checking try() errors (don't use conditions of length > 1 in if() statements – fix for R-devel).
Fix a bug in affinity() with calculations in IS-T (but not T-IS) space. This involves a workaround for the limitation in subcrt() that only IS (if present) can be the 'grid' variable.
The csv data files in OBIGT now have a column named "E_units", which is used to specify the energy units for each species (cal or J).
The messages produced by info() (and checkGHS() and checkEOS()) use cal or J depending on the units in the database.
All properties returned by info() reflect the units in the database for each species (no conversion is done).
All properties returned by subcrt() continue to follow the user's units setting (from E.units(), default cal). The messages from subcrt() now include the units used for the output.
For backward compatibility, add.obigt() allows reading data from a user-supplied file with no "E_units" column. In this case, the units are set to cal.
convert() now handles the output from solubility(), for converting calculated concentrations to ppm or ppb.
diagram() has a new argument 'levels' for specifying the levels at which to draw solubility contours.
demo/contour.R has been updated to show the 1, 10, 100, 1000 ppb contours for Au solubility.
Add demo/sphalerite.R for calculations of solubility of sphalerite, converted to log ppm (after Akinfiev and Tagirov, 2014).
diagram(): add 'lty.cr' argument to specify line type for boundaries between minerals (two crystalline phases). Setting lty.cr = 0 suppresses the lines, which is useful for plotting only the activities of aqueous species (can be used to make solubility diagrams for some systems).
Also add 'lty.aq' to specify the line type between aqueous species.
The 'names' argument of diagram() recognizes more values, making it easier to use in scripts. A value of NULL or TRUE plots the names, and NA or FALSE hides the names.
Add functions lNaCl(), lS(), lT(), lP(), lTP(), and lex() for making legend text to describe system conditions.
In mosaic(), constant activities were used for each changing basis species, leading to an artificial inflation of the affinities of species around the transitions where the basis species become equally abundant. Now, affinities of formation of species are calculated using activities of basis species that are adjusted (i.e. lowered) according to their relative abundances.
The 'mixing' argument of mosaic() has been removed; it is no longer needed with the improved handling of activities of basis species.
Using the "Alberty" method, nonideal() calculated incorrect values of adjusted H, S, and Cp at given ionic strength. The correct equations are now used (taken from Alberty, 2001), and checks of the self- consistency of the calculated values and comparisons with the Debye-Hückel limiting slopes for G, H, and Cp have been added to test-nonideal.R.
For improved calculation of the Debye-Hückel limiting slopes, the equation for the Debye-Hückel constant was changed to use the equation given by Clarke and Glew, 1980 (valid to 150 °C).
In mosaic(), groups of changing basis species are equilibrated for a total activity given by the activity of the starting basis species in the incoming basis() definition. This provides a means to specify the the amount of a conserved element in the basis species.
equilibrate(): make it possible to process the output of mosaic(). This feature combines the equilibrium activities of the formed species with those of the changing basis species to make an object that can be plotted with diagram(). This can be useful for conserving two elements in a system: one in the basis species, the other in the formed species. Thanks to Kirt Robinson for the feature request and test system for acetamide, which has been added to ?equilibrate.
Add tests to test-mosaic.R to check that activitives produced by mosaic() - equilibrate() and mosaic() - solubility() really are equilibrium activities, i.e. that the affinities of reactions between species are zero everywhere, in particular near the transitions of basis species.
In mosaic(), include the relative abundances in each group of basis species in the output ('E.bases').
Correct the value of a1 for acetamide (Shock, 1993). Thanks to Kirt Robinson.
Add properties of aqueous species (dimethylamine, trimethylamine, resorcinol, phloroglucinol, cyclohexane carboxylate, and cyclohexane carboxylic acid) from LaRowe and Amend, 2019 and HKF parameters for dimethylammonium chloride from Shvedov and Tremaine, 1997.
Add data for zoisite, clinozoisite, and epidote from Gottschalk, 2004. Thanks to Evgeniy Bastrakov for contributing the data file.
Move some carbonates from SUPCRT92 back into default database: huntite, hydromagnesite, malachite, nesquehonite.
Add trisulfur radical ion (S3-) from Pokrovski and Dubessy, 2015.
Correct entries for aqueous phenanthrene and methylphenanthrene isomers to use Joules (Dick et al., 2013).
demo/aluminum.R: add calculations using Si(OH)4 from the Akinfiev- Diamond model (SiO2 in these reactions is replaced by Si(OH)4 - 2 H2O).
Modify demo/saturation.R to use the argument recall feature of affinity().
In anintro.Rmd, include an example of using mod.obigt() to add a solid (magnesiochromite, with data from Klemme et al., 2000). Thanks to Alan Boudreau for the suggestion.
In anintro.Rmd, add description of add.obigt("AkDi") and change mod.obigt() example for aqueous species to use CoCl4-2 (Liu et al., 2011).
Add function moles(), to calculate the total number of moles of elements in the output from equilibrate().
subcrt(): stop with an error if length(logact) is not the same as the number of species.
Add 'transect' argument to affinity(), to allow forcing transect mode for any number of values of the variables.
solubility() has a new argument 'codeanal' that when set to TRUE indicates the printing of additional diagnostic messages.
check.obigt(): add 'E_units' column and fix a bug, also involving makeup() and entropy(), where many species with differences between database and computed values of Gibbs energy were not listed.
Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a precalculated stochiometric matrix for the default database, to speed up retrieve().
retrieve() now updates the stoichiometric matrix when the database changes, instead of performing a full recalculation.
Add 'ligands' argument to retrieve(), for getting metal-bearing species with a range of possible elements in the ligands.
diagram(): Starting with R version 3.6.0, 'fill' can be the name of any available HCL-based color palette (see hcl.pals() for a list).
Add demo/contour.R for gold solubility contours on logfO2-pH diagram.
In the output of affinity(), the list of 'vals' (the values of the input variables) now has names corresponding to the variables.
In diagram(), a background grid corresponding to major and/or minor tick marks can be added using the 'grid' argument. Or, use thermo.axis() after diagram() to overlay a grid.
Add demo/arsenic.R (Eh-pH diagram after Lu and Zhu, 2011).
Rename demo/go-IU.R to aluminum.R, and add plots from Tutolo et al., 2014.
Add argument 'plot.box' (default TRUE) to thermo.plot.new() and 'plot.line' (default FALSE) to thermo.axis() to prevent unnecessary plotting of axis lines. thermo.axis() also avoids plotting tick marks at the plot limits.
OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014.
OBIGT: Move H4SiO4 (Stefánsson, 2001) to AS04.csv (optional data).
Berman: rename .csv files to include whole year. berman() now uses the years in the filenames to assemble the data in reverse chronological order, and keeps only the most recent data for any duplicated minerals.
Berman: Add data for sudoite, daphnite, Mg-amesite, and Fe-amesite (Vidal et al., 1992, 2001, 2005).
Berman: make "albite" identical to "albite,low", not "albite,high".
Move transuranic actinide complexes to optional data (SLOP98), as entropies of the elements at 298.15 K are not available to check the self-consistency of the GHS values for the complexes.
obigt.Rmd: Use Zenodo DOI for citations of slop98.dat, slop07.dat, and slop16.dat.
Because data(thermo) and data(OBIGT) did not actually create said objects in the user's workspace (the expected behavior for data()), the package's data are now loaded by two new functions, reset() and obigt(). reset() is automatically run upon loading the package, so that existing scripts beginning with data(thermo) still work (this command now has no effect other than producing a warning).
Add thermo() as a convenience function to access or modify the package's data, especially various computational options.
Add retrieve() to retrieve all the species having given elements, or all species in a given chemical system. Thanks to Evgeniy Bastrakov for the suggestion.
Add AkDi() to calculate thermodynamic properties of aqueous nonelectrolytes using the Akinfiev-Diamond model. Thanks to Evgeniy Bastrakov for guidance.
Revert to using SiO2(aq) from SUPCRT92 (i.e. Shock et al., 1989) in the default database.
Move SiO2(aq) from Apps and Spycher, 2004 and recalculated HSiO3- to new optional data file, OBIGT/AS04.csv.
Move H2AsO3- from OBIGT/SLOP98.csv to OBIGT/SUPCRT92.csv.
Add OBIGT/AkDi.csv as optional data file for aqueous species from Akinfiev and Diamond, 2003 and Akinfiev and Plyasunov, 2014.
Add gaseous HF and HCl to as requirements for the Akinfiev-Diamond model for dissolved gases.
Move Au+3, AuCl3-2, and AuCl4-3 back into default database.
Add/replace data for Ag+ and Cu+ and their complexes from Akinfiev and Zotov, 2001 and 2010.
Update HCl(aq) with data from Tagirov et al., 1997.
Update Pd+2 and complexes with data from Tagirov et al., 2013.
Update Pt+2 and complexes with data from Tagirov et al., 2015.
Update Zn+2 and complexes with data from Akinfiev and Tagirov, 2015.
In demo/NaCl.R, indicate region not considered by Shock et al., 1992 in developing the "g function" applicable to electrolytes in the revised HKF model, and note presence of resulting discontinuities (see man/examples.Rd).
Add demo/AkDi.R showing calculations of Henry's constant of dissolved gases, after Figure 1 of Akinfiev and Diamond, 2003.
In describe.reaction(), change equals sign to reaction double arrow.
water() and water.SUPCRT92(): add 'P1' argument to choose whether to output 1 bar for Psat at temperatures less than 100 degrees C (default is TRUE).
diagram(): 'xlim' and 'ylim' arguments now apply to 2-variable diagrams. Thanks to Evgeniy Bastrakov for the suggestion.
Fix bug in nonideal() where "Zn" in formula was identified as charge. Thanks to Feng Lai for the bug report.
Fix a bug where subcrt()$reaction$coeffs was incorrect for reactions involving minerals with phase transitions. Also ensure that the output reaction stoichiometry is correct for duplicated species in reactions. Thanks to Grayson Boyer for the bug report.
For species in the revised HKF model, subcrt() now sets properties to NA where the density of H2O is less than 0.35 g/cm3, avoiding the output of bogus values in this region. Thanks to Evgeniy Bastrakov.
For systems where no basis species is present in all formation reactions, and the user hasn't provided balance coefficients, stop with an error instead of setting the balance cofficients to 1. Thanks to Shuang Kong for an example calculation and Tucker Ely for a previous suggestion to produce an error here. The affected code is in balance(), an unexported function used in equilibrate() and diagram() (and now also solubility()).
Add solubility(). Run this after affinity() to calculate the solubility of a solid or gas defined as the conserved basis species, which is involved in the formation of one or more dissolved species.
Features include automatic detection of dissociation reactions and finding the final ionic strength for dissolution of a mineral into pure water (find.IS argument).
find.IS depends on the new argument recall feature of affinity() (or mosaic() if that is used instead). This allows a calculation to be re-run with the same settings except for particular additions or modifications, in this case modified values of ionic strength.
Revise demo/solubility.R to show solubility calculations for CO2(gas) and calcite as a function of T and pH.
Reorganize and expand options for activity coefficient calculations (set in thermo$opt$nonideal: Bdot, Bdot0, bgamma, bgamma0, or Alberty). The previous default, which corresponds to 'bgamma' (T- and P-dependent extended term parameter with single ion-size parameter), has been replaced by 'Bdot' (T-dependent extended term parameter and species-dependent ion-size parameter; see below).
nonideal() with the 'Bdot' or 'Bdot0' equation uses specific ion-size parameters for different ions, in accord with the HCh package (Shvarov and Bastrakov, 1999). Parameters are from Table 2.7 of Garrels and Christ, 1965.
nonideal() now calulates activity coefficients of neutral species, using the Setchénow equation. Whether the extended-term parameter in this equation is taken to be zero or is taken from the value for charged species (see above) is controlled by setting 'thermo$opt$Setchenow' to bgamma0 (default) or bgamma.
Add NaCl(), implementing a first-order calculation of the speciation of NaCl in water, taking account of activity coefficients and the reaction Na+ + Cl- = NaCl(aq).
Add dumpdata() for returning/writing all packaged thermodynamic data (including default database and optional data files). The file is also available on the website (chnosz.net/download/alldata.csv).
mosaic() has been rewritten to handle more than two changing groups of basis species.
mosaic() gets a new argument 'mixing' (default TRUE), indicating whether the Gibbs energy of ideal mixing should be included in the calculations with blend = TRUE. As a test of this change, an example using mosaic() to calculate the pH-dependent solubility of calcite has been added to solubility.Rd.
Add demo/gold.R for calculations of Au solubility in hydrothermal chloride and sulfide solutions (based on diagrams from Akinfiev and Zotov, 2001, Stefánsson and Seward, 2004, and Williams-Jones et al., 2009). This depends on the revised nonideal() and new NaCl() functions described above.
anintro.Rmd: add section on solubility calculations. Add cuprite to mosaic diagram example, and note about implications of changing balance coefficients to 1. Add 'mklinks.sh' script for adding links to CHNOSZ and R documentation.
Add demo/bison.R (average oxidation state of carbon of metagenome- derived proteins in different microbial phyla at Bison Pool)
demo/saturation.R replaces the previous activity_ratios.R, and includes not only activity ratios on the axes but also saturation limits for calcite, dolomite, magnesite, and brucite in the H2O-CO2-CaO-MgO-SiO2 system.
Add demo/glycinate.R showing logK of complexation of glycinate with divalent and monovalent metals.
Remove vignette wjd.Rnw (Winding journey down in Gibbs energy).
The Berman data (Berman, 1988 and later additions) have replaced the SUPCRT92 data (based on Helgeson et al., 1978) for most minerals in the default database (i.e. the one loaded by data(thermo)). Only native elements, sulfides, halides, sulfates, and selected carbonates and oxides from SUPCRT92 that do not duplicate any in the Berman dataset are loaded by default.
The superseded SUPCRT92 minerals (primarily the silicates and Al-bearing minerals, as well as calcite, dolomite, hematite, and magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be loaded with add.obigt("SUPCRT92"). This is used in some examples for comparing the datasets (see ?berman and demo("go-IU")), but should not be needed by most users.
In thermo$obigt, the minerals using the Berman equations are identified as those having NA values for all thermodynamic properties (columns 8-20). These minerals have the state of "cr" (not "cr_Berman" as before).
The heat capacity equation in berman() has been expanded to Cp = k0 + k1T-1/2 + k2T-2 + k3T-3 + k4T-1 + k5T + k6T2 (as used in winTWQ).
Multipliers on values in the Berman data files (extdata/Berman/*.csv) have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4, to be consistent with the winTWQ data format.
berman() now reads data from a user-supplied file specified in thermo$opt$Berman.
Add mineral data from Berman and Aranovich, 1996 to extdata/Berman/testing and an example of loading these data via add.obigt() and thermo$opt$Berman (see ?berman).
Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
To reduce confusion that "d5" might be a coefficient in the same equation as d0 .. d4, rename "d5" (constant that scales disordering enthalpy to volume) to "Vad" (notation used in Theriak-Domino manual).
Change abbreviation of grossular to Grs.
Make names for dicarboxylic acid anions from Shock, 1995 (in organic_aq.csv) consistent with those used in later papers, e.g. H-succinate and succinate-2 for the -1 and -2 charged ions. Remove duplicated entries for H-succinate and succinate-2 from biotic_aq.csv.
Update G, H, and S of celestite using properties of the dissolution reaction given by Reardon and Armstrong, 1987.
Add scheelite (CaWO4) and ferberite (FeWO4) using data adopted by Wood and Samson, 2000.
Update aqueous Au species with data from Akinfiev and Zotov, 2001 and 2010, and Pokrovski et al., 2014.
Move SUPCRTBL updates (As and Al minerals and aqueous species and SiO2(aq)) into default database.
Values for SiO2(aq) are taken from Apps and Spycher, 2004. Thanks to John Apps for providing the document.
Recalculate GHS for HSiO3- by adding difference from SiO2(aq) (Sverjensky et al., 1997) to updated values for SiO2(aq).
Add test-recalculate.R to check that recalculated values are correctly entered in OBIGT.
Move superseded data for aqueous Au, As, and Al species, SiO2 and HSiO3- to OBIGT/SLOP98.csv.
Add or update glycine, diglycine, and triglycine (zwitterions and ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai, 2014.
Add data for metal-glycinate complexes from Azadi et al., 2019, superseding Shock and Koretsky, 1995.
For reproducing previous calculations, superseded data for [Gly] and [UPBB], as well as [Met] (earlier superseded by LaRowe and Dick, 2012), and metal-glycinate complexes have been moved to OBIGT/OldAA.csv.
Lines in 1-D diagram()s can optionally be drawn as splines using the method for splinefun() given in the 'spline.method' argument (the default of NULL means no splines).
Add 'srt' argument to diagram() (rotation of line labels).
Export thermo.axis(), as it is useful for adding major and minor tick marks after (above) other plot elements such as legends.
diagram(): rename 'what' argument to 'type'.
diagram(): add new type of diagram, 'saturation', which is used to plot saturation lines for minerals (where their affinity equals zero).
thermo.plot.new() and, by extension, diagram(), now "listen" to the setting of par("mar"). However, if a new plot is being made, or the device has the default setting of mar from par(), mar is (re)set to the default value in thermo.plot.new().
diagram(): numeric 'names' now indicates subset of species names to include as labels on the plot.
diagram(): new argument 'family' to select the font family for species names (labels on the plot). New arguments 'bold' and 'italic' apply to formatted names (e.g. chemical formulas), and 'font' applies to those without formatting.
'lines' is added to the return list of diagram(), giving the coordinates of lines (field boundaries) on 2-D diagrams (these are taken from the output of contourLines()).
Add 'exceed.rhomin' argument to subcrt() and affinity() to enable output of properties for species in the revised HKF model below 0.35 g/cm3.
In equilibrate(), accept a length > 1 'normalize' argument to normalize the chemical formulas of only the selected species.
Add thermo$opt$maxcores (default 2) to specify maximum number of cores for parallel calculations with palply().
Keywords in basis(): Change 'CHNOPS+' to use O2 instead of e-, and add 'CHNOPSe' and 'MgCHNOPSe' for sets of basis species that have e-.
Add 'keep.duplicates' argument to thermo.refs(). Set it to TRUE to output a single primary reference for each species, keeping any duplicated references (but not including any secondary references in thermo$obigt$ref2). Thanks to Evgeniy Bastrakov for the suggestion.
To provide better diagnostics for other apps using CHNOSZ, warning messages produced by subcrt() are now available in the output of affinity(), under 'sout$warnings'.
Change internal variable names in subcrt() for better readability (sinfo -> ispecies, inpho -> iphases, sinph -> phasespecies).
info(): display mineral names instead of just "cr" in messages (e.g. for info("SiO2")).
info(): species with no matches in default database are also searched in optional data files.
Add C implementation of counting occurrences of all letters in a string (src/count_letters.c) to speed up operation of count.aa().
read.fasta(): add support for file connections created using archive::archive_read (https://github.com/jimhester/archive).
The arguments in expr.species() have been reorganized for more flexible and concise usage.
Reduce message clutter for diagrams showing water stability limits.
In subcrt(), improve error message for invalid property names.
In affinity(), make invalid variable names an error.
Add 'return.sout' argument to affinity(), to return just the values calculated with subcrt().
Add berman() function and extdata/Berman/*.csv files for calculating thermodynamic properties of minerals using equations of Berman, 1988.
Calculations related to Berman's (1988) Figs. 1 and 2 for the lambda transition of quartz are available in the new demo lambda.R.
Add functions implementing the Deep Earth Water (DEW) model (Sverjensky et al., 2014): water.DEW() and its supporting functions calculateDensity(), calculateGibbsofWater(), calculateEpsilon(), calculateQ().
The computational setting for water (thermo$opt$water) can now be set using water("DEW"), water("IAPWS"), etc.
Usage of the DEW model is shown in the new demo DEW.R. This demo also depends on the Berman equations (above) and, for the last diagram in the demo, the following *four* NEWS items:
In equilibrate(), it is now possible to combine affinity calculations with variable activity of the balancing basis species (loga.balance). For example, in the last plot of the DEW demo, the calculation involves simultaneously varying temperature and logfO2 (given as arguments to affinity()) as well as total concentration of carbon (given by the loga.balance argument in equilibrate()).
The 'alpha' argument of diagram() can be set to 'balance' to scale the values by the balancing component. This is useful for making "percent carbon" plots for systems where the species have different carbon numbers.
nonideal() now has three methods for calculating activity coefficients: 'Helgeson' and 'Helgeson0', which utilize the Debye-Huckel equation with parameters as described by Helgeson, 1969, and 'Alberty' (the only method previously available). The 'Helgeson' method depends on the following *two* NEWS items (but the 'Helgeson0' method omits the B-dot term):
All three water options (SUPCRT92, IAPWS95, DEW) can be used to calculate 'A_DH' and 'B_DH', i.e. A and B coefficients in the extended Debye-Huckel equation as described by Helgeson, 1969.
Add Bdot() to calculate the "B-dot" (or b_gamma) extended term parameter for activity coefficients in NaCl solutions at high temperature and pressure (Helgeson et al., 1981), including very high pressures (> 10 kbar) based on extrapolations from Manning et al., 2013.
For minerals with phase transitions (states 'cr2' 'cr3' etc.) in thermo$obigt (i.e. the Helgeson minerals), it is now possible to use the minerals in basis(), species(), affinity() with proper accounting for transition effects. Just set the state to 'cr' or omit it, e.g. species("quartz").
Implement SUPCRT92's handling of variable volume for quartz and coesite. Calculations for other minerals still assume constant volume of each phase.
Calculations of the g function are now enabled for DEW (with pressure derivative) and IAPWS-95 (no derivatives included).
water.lines() now works for diagrams of Eh, pe, logfO2, logaO2, logfH2, or logaH2 vs pH, T, or P. It is possible to have T or P on either the x- or y-axis.
Variables that are in the aguments to affinity() now override any buffers previously specified using basis().
Add data(OBIGT) command to reset only the thermodynamic database (OBIGT) to its default. data(thermo) is still used to reset *everything* (the database and all computational and system settings).
In add.obigt(), using 'file' without a file suffix now can be used to locate corresponding files (such as DEW_aq.csv or SUPCRTBL.csv) in the extdata/OBIGT package directory.
add.obigt() gets new argument 'species' for selecting species to add.
Add Berman_cr.csv with names and formulas for minerals whose thermodynamic properties are calculated using the Berman, 1988 equations. The state "cr_Berman" is used to distinguish these minerals from the Helgeson data. The parameters themselves are stored in extdata/Berman/*.csv.
Add DEW_aq.csv with aqueous species data from the DEW spreadsheet (May 2017 version). Species with data that do not differ from the default database in CHNOSZ are not included. Currently, detailed reference keys and descriptions (in thermo$refs) are given for selected species only. [Optional Data; not loaded by data(thermo)]
Add SUPCRTBL.csv with mineral and aqueous species data compiled by Zimmer et al., 2016. Data were taken from original references or from spronsbl.dat (http://www.indiana.edu/~hydrogeo/supcrtbl.html). The new demo/go-IU.R uses these data. [Optional Data]
Update HKF parameters of adenine based on experimental heat capacity and volume data (Lowe et al., 2017). Add demo/adenine.R comparing the updates with the previous data (LaRowe and Helgeson, 2006).
Remove H2O(gas) from the database (taken from SUPCRT92), as it gives inconsistent results for metastable steam (Zavarin et al., 2016, LLNL-TR-701407, doi: 10.2172/1325873).
Change the formula of the electron from "Z0-1" (parsed as "zero Z with minus one charge") to the equivalent but nicer-to-read "(Z-1)" (parsed as "minus one Z"; the parentheses cause "-1" to be interpreted as the coefficient on Z instead of the charge in the formula).
Add data for hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite from Delgado Martin and Soler i Gil, 2010 (using the Berman equations).
Add test-logmolality.R to demonstrate transformation of variables from activity to molality in the main workflow; refer to this test and describe these transformations in anintro.Rmd; remove "experimental" labeling of activity coefficient calculations in CHNOSZ-package.Rd.
Add 'use.molality' argument to axis.label() and supporting functions. So that the labels on diagrams are changed from activity (a) to molality (m), this argument is set to TRUE by diagram() when IS is supplied as an argument to affinity().
Add demo TCA.R for standard Gibbs energies of steps of the citric acid cycle (Canovas and Shock, 2016).
Components of subcrt() output indicating the stable polymorph of minerals with phase transitions are now named 'polymorph', not 'state'.
Add maxdiff() and expect_maxdiff() for calculating and testing the maximum absolute pairwise difference between two objects. expect_maxdiff() is used in tests/testthat/*.R as a more straightforward alternative for checking differences than using 'tolerance' in expect_equal().
Add 'tol' argument to equil.reaction() (convergence tolerance for uniroot()).
Add thermo$opt$Berman to signal info(), subcrt(), etc. to prefer minerals in Berman dataset over Helgeson dataset (default: FALSE).
In hkf() and cgl(), combine 'ghs' and 'eos' arguments into single argument named 'parameters'.
Remove 'H2O.PrTr' and 'domega' arguments from hkf(). Properties of water at Pr and Tr and the logic for when to find derivatives of omega are now calculated within the function, thereby simplifying the function call from subcrt().
Add 'H2O.props' argument to hkf(). This lists the properties of water to calculate (at P, T); these are now included in the results, in order to avoid duplicating the calculations in subcrt().
In water.* functions, rename the "diel" variable to "epsilon".
To save space, taxid_names.csv has been trimmed to hold only those taxids listed in extdata/bison/gi.taxid.txt.
Remove Eco.csv.xz and rename more.aa() to yeast.aa().
Remove transfer() and associated functions draw.transfer(), apc(), and feldspar().
Remove read.expr() and extdata/abundance/ISR+08.csv (protein abundance in E. coli).
Reduce the size of obigt.html by ~450 KB. This was done by 1) using rmarkdown with files in rmd/h/bootstrap-3.3.5/fonts/ replaced with empty files (291 KB), and 2) changing the theme from "cosmo" to "default" (151 KB).
Remove extdata/OBIGT/CHNOSZ_aq.csv and move the entry for pseudo-H4SiO4 to inorganic_aq.csv.
Reorganize concept index entries in Rd files: Main workflow, Extended workflow, Thermodynamic data, Thermodynamic calculations, Water properties, Protein properties, Other tools, Utility functions.
Remove anim.TCA() and anim.carboxylase(); move the latter code to demo/carboxylase.R.
Replace anintro.Rnw (Sweave) with rewritten anintro.Rmd (using knitr with Tufte style).
Add obigt.Rmd (Thermodynamic data in CHNOSZ).
Add eos-regress.Rmd (Regressing thermodynamic data), including section on Making a pseudospecies: H4SiO4.
New demos: bugstab.R (potential diagrams for microbial proteins in colorectal cancer), activity_ratios.R (mineral stability diagrams with activity ratios on the axes), Shh.R (affinities of transcription factors relative to Sonic hedgehog).
Converted demos: move examples from help pages to protein.equil.R, add.obigt.R, and affinity.R.
Updated and removed demos: update buffer.R (logfH2 set by mineral buffers and aqueous species) and rename old buffer.R to protbuff.R (proteins as buffers); remove nucleobase.R.
The NAMESPACE now exports selected functions, instead of all of them.
The following functions are no longer exported, nor documented in the Rd files: thermo.axis, optimal.index, extremes, caller.name, lsub, lsum, pprod, energy, energy.args, A.ionization, can.be.numeric, s2c, c2s, eos.args, TP.args, state.args, info.approx, info.character, info.text, info.numeric, count.charge, count.formulas, buffer, mod.basis, put.basis, preset.basis, preset.logact, species.basis, envert, outvert, which.balance, gfun, IAPWS95.residual, IAPWS95.idealgas, obigt2eos, group.formulas, get.formula, get.objfun, balance.
For the 'groups' argument, activities are multiplied by the balance coefficients before the summation.
Draw smoother boundary lines (with contour(); 'lty' is usable), at the expense of not being precisely aligned with the grid used for plotting colors. For the old behavior, use 'dotted=0'.
Default of 'legend.x' changed to NA (instead of making a legend, put labels near the lines).
Field labels: apply formatting (subscripts and superscripts) to names that parse as chemical formulas; use 'format.names=FALSE' to disable.
Chemical formulas that are part of the axis labels (log activity or fugacity) now have formatting applied.
Add arguments 'adj' and 'dy' for x-alignment and y-offset of line labels.
Add arguments 'fill.NA' (color of empty areas) and 'limit.water' (assign NA to areas beyond water stability limits on Eh-pH and pe-pH diagrams).
Add ZC.col() for generating a red-grey-blue color scale from numeric values.
Add "QEC" as a keyword for preset species in basis() (glutamine, glutamic acid, cysteine, H2O, O2).
More flexible parsing of chemical formulas for ZC() and other functions; e.g. 'ZC(colMeans(protein.formula(1:4)))' now works.
read.fasta() extracts information from UniProt FASTA headers (accession, name, organism) into columns of the output data frame (protein, abbrv, organism).
Add '...' argument to thermo.plot.new() (additional arguments for par()).
With new default arguments, thermo.axis() only plots the axis tick marks and lines; this is used in diagram() to redraw the axes on filled diagrams.
seq2aa() removes newlines and whitespace before counting the letters in the sequence.
read.fasta(): change argument 'i' to 'iseq'; this is used to select particular sequences to read from the file.
Add syslab() and ratlab() to make formatted expressions for sets of thermodynamic components and activity ratios.
Add GHS_Tr() to calculate G, H, and S at Tr (298.15 K) of phases stable at high temperature, using provided enthalpies of transition and database values of transition temperatures and heat capacity parameters, and GHS at Tr of the low-temperature phase.
Add extdata/supcrt/ directory with files read.supcrt.R, compare.R, newnames.csv; used to compare data in SUPCRT and slop files (http://geopig.asu.edu/?q=tools) to data in thermo$obigt.
Split OBIGT.csv and OBIGT-2.csv into multiple files according to type of substance (inorganic, organic, or biotic). All files are now under extdata/OBIGT/. Conflicting data from OBIGT-2.csv were removed (see below).
Citations in OBIGT now have a suffix (e.g. [S92] or [S98]) if the data were first present in sprons92.dat from SUPCRT, slop98.dat, or later versions of the slop data files (http://geopig.asu.edu/?q=tools).
biotic_aq.csv: Add data for citric acid cycle metabolites from Canovas and Shock, 2016.
CHNOSZ_aq.csv: Add H4SiO4 pseudospecies (pseudo-H4SiO4); see calculations in eos-regress.Rmd.
organic_aq.csv: Add data for aqueous phenanthrene and methylphenanthrene from Dick et al., 2013.
Remove superseded data previously in OBIGT-2.csv: citric acid cycle metabolites from Dalla-Betta and Schulte, 2009.
Remove superseded data previously in OBIGT-2.csv: methionine and [Met] from Dick et al., 2006. Examples that require the old group additivity parameters can modify the database using: 'mod.obigt("[Met]", G=-35245, H=-59310)'.
Move two datasets that conflict with the primary database, but are used in tests, examples, or vignettes, from OBIGT-2.csv to extdata/thermo (Ste01.csv and BZA10.csv).
Remove other conflicting datasets (i.e. that provide different data for a species already in the database) previously listed in OBIGT-2.csv (21 sources).
Replace GHS for iron (c2, c3) calculated in CHNOSZ with values derived from sprons92.dat.
Replace data for sulfur (cr) from Gurrieri, 1996, personal communication with that "as used by" McCollom and Shock, 1997 (from slop98.dat).
Update selected nonelectrolytes with data from Plyasunov and Shock, 2001, as listed in slop07.dat (http://geopig.asu.edu/?q=tools).
extdata: Add fasta/rubisco.fasta and cpetc/*.csv files SS98_Fig5a, SS98_Fig5b, PM90 (all used in anintro.Rmd).
Correct charge (-2) of NAD(red)-2 in biotic_aq.csv. Thanks to Peter Canovas.
Correct charge (-2) of MgATP-2.
subcrt() returns 'loggam' using the common logarithm; add test-nonideal.R to check for consistency between loggam and logK values returned by subcrt(). This also fixes the issue previously noted for the first example in ?nonideal. Thanks to David T. Wang for the bug report and test.
NaN values from equilibrate() are now preserved by diagram(), producing empty (NA) fields rather than being mistakenly labeled with the first species. Thanks to Grayson Boyer for the bug report.
Remove msgout(), and replace previous calls to that function with message() from base R. As a result, the messages don't appear in Sweave vignettes, but can be turned on or off in knitr vignettes.
Remove HTCC1062.faa.xz.
Remove the bold formatting for "A" in expr.property(); "A" is italicized like most other uppercase letters.
Rename browse.refs() to thermo.refs(); remove URL browsing (except for summary table).
New function pinfo() merges functionality of old iprotein() and ip2aa(). Add 'regexp' argument to control whether matches are made using a regular expression.
Rename aa2eos() to protein.obigt().
Remove anim.plasma() and AA03.csv.
Remove stress() and stress.csv; move data from Tai et al., 2005 (used in an example in ?read.expr) to TBD+05.csv.
Remove read.aa() - replaced by read.csv() with as.is=TRUE.
Remove grep.file().
Remove sideeffects.Rd (functions with side effects are now identified with red color in anintro.Rmd).
Add mosaic() function for affinity calculations with changing basis species. See also new 'mosaic.R' demo.
Add thermo$opt$varP option for subcrt() to calculate Gibbs energies of gases using a variable-pressure standard state. Thanks to Kirt Robinson for the submitting the problem that led to this change.
Add 'solubility.R' demo, and add calcite solubility plot to anintro.Rnw.
Move aqueous Ti(OH)4 and H4SiO4 to OBIGT-2.csv.
Add warning about data consistency and use of examples to CHNOSZ-package.Rd and anintro.Rnw.
When making filled color diagrams, diagram() calls image() with useRaster=TRUE. This speeds up plotting, eliminates artifacts (i.e. blank lines) at some resolutions, and greatly reduces the size of PDF files.
diagram() returns 'lx', 'ly' and 'is' for calculated positions of labels and indices of those species in predominance diagrams, including when the labels aren't plotted (by setting names=FALSE).
In energy(), add missing 'IS' argument in call to subcrt(). Thanks to Grayson Boyer for the bug report.
In nonideal(), skip proton and electron. Add test for calculations at constant and variable IS to test-util.affinity.R.
Modify hotspring.Rnw to use knitr, and add example calculations of relative abundances of microbial phyla from Dick and Shock, 2013.
Add files with average amino acid compositions of proteins from Bison Pool hot spring grouped according to annotation keyword (DS11.csv) (moved here from protein.csv) or phylum assignment (DS13.csv).
water.lines() gets 'O2state' argument to specify state of O2.
Add 'as.residue' argument to diagram(), to divide reactions by balance coefficients without rescaling to whole species formulas (cf. 'normalize' argument which uses rescaling).
In equilibrate(), change name of 'stay.normal' argument to 'as.residue'.
In test-diagram.R, test that same diagrams are produced using 'normalize' in equilibrate() or diagram().
In test-diagram.R, test that same diagrams are produced using 'as.residue' in equilibrate() or diagram().
Add 'tplot' argument to diagram() (change to FALSE to use R's default plot set-up).
R version dependency changed to (>= 3.0.0).
On attaching the package, the user is asked to load the 'thermo' object, containing thermodynamic data and system settings, using data(thermo). This is required because packages are not permitted to alter the search path (but the user may).
Fix calculation of free energy derivative in wjd().
Add 'stay.normal' argument to equilibrate().
If obigt$G is available, hkf() returns this value, not NA, at Tr, Pr.
mod.obigt() defaults to taking chemical formula from the species name, and checks for validity of formula.
Add example for LYSC_CHICK to protein.info.Rd.
Enable DGtr in findit(), 1-D DGtr plot in revisit().
Disable a check in valTP function of H2O92D.f to allow properties of H2O to be calculated below 0.01 degrees C, to -20 degrees C.
Remove thermo$water and thermo$water2 storage of previous results; they gave no significant speed gain in running examples.
Split IAPWS95.Rd out of water.Rd.
expr.* functions now do not wrap their values in as.expression() (makes compounding expressions, e.g. with substitute(), easier).
Rename dl.aa() to uniprot.aa().
Add start and stop arguments to count.aa(), read.fasta(), uniprot.aa().
add.protein() replaces amino acid compositions for existing proteins with the same name.
Examples of calculation of affinity of formation of CSG_METVO (following Dick and Shock, 2011) added to protein.info.Rd.
Use consistent names for water properties (Speed, diel, QBorn, ...).
Add water.props() to get names of properties of water.
Remove 'isat' argument from water.SUPCRT92(); function now accepts 'Psat' as value for 'P' argument.
Separate rho.IAPWS95() from water.IAPWS95().
In addition to the original regression variables, EOSvar() recognizes names for available properties in water(), or can use the name to get a user-defined function of temperature and pressure.
Simplify EOSplot() somewhat (don't group data by pressure ranges).
EOSlab() gets label from attribute (if present) of user-defined function.
Modify test-util.data.R and wjd.Rd to pass R CMD check using R configured with –disable-long-double .
The name of the environment affected by data(thermo), and used in many functions, is changed from CHNOSZ:thermo to CHNOSZ.
Remove read.supcrt() and write.supcrt().
guess() now defaults to "stoich" method, not "central". (Needed since limSolve package is not found during R-Forge checks on Windows.)
Split the functionality of diagram() into equilibrate() and diagram(). Old workflow: a <- affinity(); d <- diagram(a) . New workflow: a <- affinity(); e <- equilibrate(a); d <- diagram(e) . Old workflow is still usable for plotting the values of affinity, or for making predominance diagrams using the maximum affinity method.
The 'thermo' object, which holds the thermodynamic database, and system definitions (made by the user), is now placed in an environment named 'CHNOSZ:thermo' on loading the package. Therefore, instances of '<<-' in the code now refer to this environment instead of the global environment.
Create a set of tests in 'inst/tests', particularly for functions that have been modified during this development cycle, and add a Suggests dependency on 'testthat'.
Move the code for the temperature and pressure derivatives of the "g" function (related to the solvation parameter omega) to a new function gfun(); incorporate some fixes and a series of test_that() tests. There is some impact on the calculated Gibbs energies of charged species.
Add wjd() implementing the steepest descent algorithm for free energy minimization described by White et al., 1958. Also add supporting functions element.potentials(), invertible.combs() for finding linearly independent combinations of rows of a matrix, is.near.equil(), and run.wjd().
Add guess() as another supporting function for wjd(), to produce initial guesses of moles of species satisfying a given elemental bulk composition, and a Suggests dependency on 'limSolve'.
New function i2A() for generating a stoichiometric matrix from indices of species in the thermodynamic database.
Add protein.equil() for step-by-step calculation of chemical activities of proteins in metastable equilibrium.
Add an objective function DGtr() for calculating the Gibbs energy of transformation of a system at constant temperature, pressure and chemical activities of basis species.
Add msgout(), which is a modification of message() from base R. Now used instead of cat(), to allow suppressing messages (e.g. during testing with test_that).
In equilibrate(), the argument 'logact' (inherited from diagram()), specifying the logarithm of activity of the balanced quantity, has been renamed to 'loga.balance'. In the result, rename 'logact' to 'loga.equil', containing the equilibrium logarithms of activities of the species of interest.
The 'residue' argument of diagram() has been changed to 'normalize' in diagram() and equilibrate(). normalize=FALSE is always the default, including for systems of proteins.
In balance(), the value of 'balance' used to indicate protein length has been changed from 'PBB' to 'length'.
Everywhere it appeared, the logical argument 'do.plot' has been renamed to 'plot.it' (diagram(), revisit(), findit(), transfer()). (This scheme is more consistent with e.g. qqplot().)
'do.phases' argument in subcrt() and affinity() has been renamed to 'exceed.Ttr'. When that argument is FALSE (the default for subcrt()), the Gibbs energies of mineral phases at temperatures beyond their transition temperature are set to NA, instead of 999999 used previously.
ZC() now accepts a numeric argument, referring to one or more species indices in the thermodynamic database.
subcrt() now only outputs T (temperature), P (pressure) and rho (density) columns if there is more than one T-P point ... makes unlist()ing the results easier (used in element.mu() and basis.logact()).
subcrt() now outputs NA values for properties at temperatures above the critical temperature of H2O, when Psat is being used.
read.blast() accepts NA for 'similarity', 'evalue' and 'max.hits' options. Descriptive column names are now assigned to the data frame returned by the function.
energy.args() (called by affinity()) shows units in messages about limits of variables.
EOSvar() has new variables invPPsi and invPPsiTTheta, used for temperature- and pressure-dependent regressions in the revised HKF equations of state.
thermo.plot.new() now saves the graphics device parameters (par(no.readonly=TRUE)) to thermo$opar the first time the function is called, allowing the parameters to be restored after running examples that change them.
Rewrite mod.obigt() (it's now used by info() when adding proteins) and add today() for returning today's date in the format used in SUPCRT files.
Split the primary functionality of makeup(), parsing of chemical formulas, into a smaller makeup() function and supporting functions count.charge(), count.formulas(), and count.elements(). The new functions make extensive use of regular expressions, and no data frames. Running makeup() over the ca. 3000 formulas in thermo$obigt drops from ~35 to ~5 seconds on one machine.
New function as.chemical.formula() to replace the previous functionality of makeup() for making string representations of chemical formulas.
Replace element() with two separate functions, mass() and entropy().
Units setting interface is now split between three separate functions: P.units(), T.units() and E.units().
Replace describe() with describe.basis(), describe.property(), describe.reaction(). It is now fairly easy to make legends showing temperature, pressure and chemical activities with italic symbols, subscripts, and units.
Reorganize axis.label() and its supporting functions (now expr.species(), expr.property() and expr.units()). Add an example showing a plot annotated with chemical formulas and reactions.
The functionality of info() is split into info(), info.character(), info.approx(), info.numeric() and info.text(). For ease of use, single approximate matches are accepted by info(), and searches for 'H2O' in the 'aq' state now return H2O(liq).
The basis definition functionality of basis() is split into basis(), is.basis(), put.basis(), mod.basis(), preset.basis() and preset.logact().
The basis swapping functionality of basis() is split into basis.matrix(), element.mu(), basis.logact() and swap.basis(). Rename basis.comp() to species.basis(), and remove expand.formulas().
Split aminoacids() into aminoacids() and count.aa().
The monolithic protein() function no longer exists; it has been superseded by iprotein(), ip2aa(), get.aa(), dl.aa(), read.aa(), sum.aa(), and aa2eos(). The user shouldn't notice significant changes (other than in the composition of messages) when including proteins in functions like subcrt() and affinity().
Functionality of get.protein() is split into more.aa() (amino acid compositions from model organisms) and stress() (proteins identified in stress response experiments).
get.expr(), for reading abundances or expression levels of proteins from variously formatted data files, is renamed to read.expr(), with retrieval of amino acid compositions of proteins moved to more.aa().
Replace ionize() with a completely rewritten and much easier to use ionize.aa() for calculating the additive ionization properties of proteins; also add A.ionization(), usually invoked by affinity()
residue.info() mostly replaced by protein.basis().
Rename equil.react() to equil.reaction(), and give it parallel potential (via palply) and a more efficient algorithm for determining limits of the uniroot search. Also remove a redundant argument; arguments are now identical to those of equil.boltzmann() (and that function was renamed from equil.boltz()).
Objective functions used in revisit() and findit() now each have their own definitions, with an attribute indicating whether the function is minimized or maximized.
Separate idealgas.IAPWS95() and residual.IAPWS95() from water.IAPWS95() (in order to write some test_that tests.)
Add 148 liquid and 148 crystalline acyclic isoprenoids, polycyclic alkanes, polynuclear aromatic hydrocarbons (PAH) and 62 crystalline double ether-bonded or ester-bonded n-alkanes from Tables 16-23 of Richard and Helgeson, 1998. The properties of the following crystalline and liquid compounds, taken from those tables, replace the previously entered values from the "reference model compound" tables appearing earlier in that paper: biphenyl, naphthalene, 1-methylnaphthalene, 1,8-dimethylnaphthalene, 2,3-dimethylnaphthalene (cr only), anthracene, pyrene.
Add 13 crystalline, 29 liquid and 39 gaseous organic iodine compounds from Richard and Gaona, 2011.
Add crystalline peptide sidechain and [AABB] and [PBB] groups and dipeptide model compounds and revised equations of state parameters for crystalline leucine and revised standard Gibbs energies of crystalline and aqueous methionine and its aqueous sidechain group [Met], from LaRowe and Dick, 2012. Also, use revised volumes of all other crystalline amino acids given in that paper together with those of Lys:HCl and His:HCl calculated using an effective volume of HCl(cr) equal to 33.8 cm3/mol (difference between Arg and Arg:HCl).
Add 6 aqueous chloroethylenes from Haas and Shock, 1999.
Move superseded aqueous methionine sidechain group [Met] to OBIGT-2.csv so that its properties are available for reproduction of published results (relevant to some examples in the package).
As revised makeup() function now strictly interprets a signed value at the end of a chemical formula as charge, the formula of the electron in thermo$obigt is changed from "Z-1" to "Z0-1".
In thermo$obigt, change the value for standard Gibbs energy of H2O from -56688 to -56687.711481 cal mol-1, to be consistent with the value generated by the fortran code from SUPCRT92 (H2O92D.f). Although the latter is the source of the properties of H2O for many functions in the package, there is an occasional function that accesses the tabulated value at 25 degrees C (e.g., element.mu() and basis.logact()).
In protein.csv, change organism code BACST (Bacillus stearothermophilus) to GEOSE (Geobacillus stearothermophilus) for SLAP and DPO1 proteins, and also apply changes in vignettes and examples.
In stress.csv, change ECO to Eco and SGD to Sce.
In extdata/refseq, scripts and data files were updated for NCBI Reference Sequence (RefSeq) release 55 (2012-09-17).
In extdata/bison, sample BLAST output files for Bison Pool metagenome use target database generated from RefSeq release 55.
Add P(ressure) column to extdata/cpetc/SOJSH.csv and a stopifnot() test for similarity to the experimental data to the example in water.Rd.
In extdata/protein rename ECO.csv.xz to Eco.csv.xz and SGD.csv.xz to Sce.csv.xz.
In extdata/thermo add RH98_Table15.csv; this file together with new function RH2obigt() is used to calculate thermodynamic properties of organic compounds using group contributions from Richard and Helgeson, 1998.
Add a Known Bugs section to the package help page.
Move 'extra' examples previously available in longex() to individual demos, and add a function demos() to run them all.
All examples now run without any warnings (at least, as intended).
Add an example based on Shock and Canovas, 2010 for the 'transect' mode of affinity().
ionize.aa() has examples of contour plots as a function of temperature and pH.
Group residue.formula(), protein.formula(), protein.name(), protein.length() into new documentation topic (util.protein.Rd).
Add 'sideeffects.Rd' to document some of the side effects of functions.
Add 'objective.Rd' for the objective functions.
To make output of examples reproducible, change mod.obigt() and protein() to not include current date/time for new data entries (remains an option for mod.obigt()).
Move vignette sources to 'vignettes' directory.
Remove vignettes formation.Rnw and xadditivity.Rnw (and, for the latter, the package Suggests dependency on xtable).
Rename protactive.Rnw to equilibrium.Rnw, with some changes.
Add vignette wjd.Rnw to accompany the new function wjd().
Add a release CHECKLIST to the installation directory of the package.
Replace "degrees" with UTF-8 degree symbol in second argument of
\eqn{}{}; add \encoding{UTF-8} to affected Rd files.
A matrix is now returned by makeup(), GHS() and some other functions to avoid the performace penalty associated with data frames.
Add parallel as a Suggests dependency and replace mylapply() (based on 'multicore') with palply(), as a wrapper for parLapply and lapply. palply() now invokes parLapply for length(X) > 10000 instead of 100.
Comment out lines containing WRITE and STOP statements in src/H2O92D.f since they are discouraged by CRAN guidelines (and calls to them are unlikely to be encountered while using the package).
Remove thermo$opt$verbose and thermo$opt$online.
In c2s(), use 'collapse' argument of paste() instead of a for loop.
Change R dependency to R >= 2.12.0, required for useDynLib in NAMESPACE to find the shared library on Windows.
New function browse.refs() for listing references for thermodynamic data and opening associated URLs. Supported by extdata/js/sorttable.js for sorting table of references in browser.
Add EOSregress(), EOSvar(), EOSlab(), EOSplot(), EOScoeffs() for regressing and comparing equations-of-state parameters from heat capacity and volume data for aqueous species.
Add anim.plasma() and anim.carboxylase() for making animated GIFs of equilibrium activity diagrams. All anim.* functions now also work on Windows (with ImageMagick installed).
New functions checkEOS(), checkGHS() for checking self-consistency of individual database entries. check.obigt() replaces 'check' argument of info().
New argument 'chains' for protein() can be used to specify the number of polypeptide chains in group additivity calculations.
protein() now looks for protein backbone group named '[PBB]' for group additivity of crystalline proteins.
Remove count.taxa(), splitting its functionality into read.blast() and id.blast(); new function write.blast().
eqdata() can now also extract results for solids, saturation states of minerals, and major speciation of basis species from EQ6 output files.
Rename 'source.csv' to 'refs.csv'. Add URLs for most references.
Column names 'source1' and 'source2' in OBIGT.csv, changed to 'ref1' and 'ref2'.
In protein.csv, add amino acid compositions of 105 model proteins derived from metagenomic sequences at Bison Pool (Dick and Shock, 2011). protein: overall, transferase, transport, dehydrogenase, ...; organism: bisonN, bisonS, bisonR, bisonQ, bisonP
Add properties for aqueous bromine (Br2) and iodine (I2) from Wagman et al., 1982.
Add properties of crystalline and liquid groups from Helgeson et al., 1998 and Richard and Helgeson, 1998.
Reorganize the 'extdata' directory, putting all files into one of nine subdirectories (abundance, bison, cpetc, fasta, js, protein, refseq, taxonomy, thermo).
To reduce installed package size, compress many data files in extdata using xz.
In extdata/bison, update partial protein BLAST output files for five Bison Pool sites to use target database made up of microbial protein sequences in NCBI Reference Sequence database version 47.
In extdata/cpetc, new files 'Cp.CH4.HW97.csv' and 'V.CH4.HWM96.csv' contain experimental heat capacity and volume data for aqueous methane from Hnedkovsky and Wood, 1997 and Hnedkovsky et al., 1996.
In extdata/refseq, rename 'taxid_phylum.csv' to 'taxid_names.csv'.
In extdata/thermo/OBIGT-2.csv, fix incorrectly entered values of c1 from Dalla-Betta and Schulte, 2010. Also apply corrected values of c1 and c2 and minor corrections for delta-H and S from Marini and Accornero, 2010.
Change vignette file names and titles to be in the same alphabetical order to achieve the desired sorting in browseVignettes().
Add .Rinstignore to inst/doc to exclude figure, bibliography and LyX files from the installation directory.
Adapted 'formation.Rnw' to work with pdflatex, and remove Makefile in inst/doc.
Add 'hs-chemistry.Rnw' with calculations of relative stabilities of model proteins in a hot spring (Dick and Shock, 2011).
Add 'protactiv.Rnw' with detailed information on calculating equilibrium activities of proteins, and comparisons with experimental abundances in human blood plasma and E. coli.
Add 'xadditivity.Rnw' with examples of group contribution calculations (using qr.solve()) and comparison of two group contribution schemes.
In DESCRIPTION, change Depends to a more recent R (>= 2.10.0), required for reading of compressed (including .xz) files.
Add Suggests: xtable in DESCRIPTION (used for 'xadditivity' vignette).
In DESCRIPTION, change "ZipData" to "BuildResaveData", keeping the setting at "no". Resaving data as compressed files reduces the installed package size by about 200Kb, but complicates showing the file formats to new users.
Loading of shared object for calculating properties of H2O now done by useDynLib in NAMESPACE.
Change .First.lib() to .onAttach(). In .onAttach, use packageStartupMessage() instead of cat().