NEWS in package ‘CHNOSZ’

Changes in version 0.9-7

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.

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().