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().