CHANGES IN CHNOSZ 1.0.0 (2013-03-28)
------------------------------------

MAJOR USER-VISIBLE CHANGE:

- 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).

OTHER CHANGES:

- 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.)


CHANGES IN CHNOSZ 0.9-9 (2013-01-01)
------------------------------------

MAJOR CHANGES:

- 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.

NEW FUNCTIONS:

- 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).

CHANGES TO ARGUMENTS:

- 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.

CHANGES TO OUTPUT:

- 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.

REFACTORING OF FUNCTIONS:

- 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.)

DATA UPDATES:

- 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.

EXTDATA UPDATES:

- 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.

DOCUMENTATION AND VIGNETTES:

- 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.

OTHER CHANGES:

- 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.

CHANGES IN CHNOSZ 0.9-7 (2011-08-23)
------------------------------------

- Restore ZipData: no in DESCRIPTION, needed for building the package
  on R < 2.13.0 on Windows.

- Remove some incorrect titles for barplots in diagram().

- Add more informative titles for plots in first example of diagram.Rd.

- In EOSvar() and EOSlab(), name the first argument 'EXPR' in calls to 
  switch() to avoid partial matching with 'E' (expansivity).

- Shorten CHNOSZ-package.Rd and clean up formatting of some examples
  in other documentation topics.

CHANGES IN CHNOSZ 0.9-6 (2011-08-18)
------------------------------------

SIGNIFICANT CHANGES TO FUNCTIONS:

- 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.

DATA UPDATES:

- 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.

EXTDATA UPDATES:

- 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.

DOCUMENTATION AND VIGNETTES:

- 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.

OTHER CHANGES:

- 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().