CHNOSZ_0.9-5 (2011-04-05) Minor updates in consideration of upcoming R-2.13.0:
change Makefile in inst/doc to be compatible with a parallel make; move *.csv
files not used in construction of 'thermo' object to 'inst/extdata' (and adjust
paths in examples and in argument defaults of 'add.obigt' accordingly).

CHNOSZ_0.9-4 (2011-02-22) Add 'cex.names' argument to strip(). Rewrite s2c() to
use strsplit(). diagram() now accepts a 'group' argument without names. Update
read.supcrt() to be able to import SLOP07.dat (fixes some problems with
strangely formatted header and data fields). Add cyclohexane,aq data from
Plyasunov and Shock, 2001. Add scripts in 'refseq' directory for processing
NCBI RefSeq data, and add 'protein_refseq.csv' datafile with computed amino
acid compositions for each taxon ID (taxid). Move code from danger() to
add.obigt() (used to activate supplementary thermodynamic data). Add anim.TCA()
for making animated stability diagrams for reactants in tricarboxylic acid
cycle. New function slice.affinity() for extracting results from affinity()
along a particular dimension. Move data files with non-standard file types to
new 'extdata' directory.

CHNOSZ_0.9-3 (2010-12-21) diagram() by default does not plot legends on 1D
diagrams if there are more than 10 species, and now handles activity
calculations in more than two dimensions (still only up to two are plotted).
Change 'title' argument to 'main' and 'property' to 'what'; if latter is set to
the name of a basis species the function calculates its equilibrium activity.
get.protein() now searches the "AC" column in ECO.csv. Add HUM.csv for human
proteins. Merge draw.diversity() into revisit(); add new targets (qqr, rmsd,
cvrmsd, ratio) and plots (scatterplots with legend and LOESS fit). affinity()
now returns x- and y-values used for calculations.  Change argument 'x' to
'pattern' in grep.file() and implement search for multiple patterns.  Add
vignettes on energy of rotein formation, getting started with CHNOSZ, and
growth temperature and relative stabilities of proteins. 

CHNOSZ_0.9-2 (2010-08-25) Add missing aliases in help files for data sets
'SOJSH' and 'check'.

CHNOSZ_0.9-1 (2010-07-20) Add expansivity (E) and compressibility (kT) to water
(SUPCRT92) calculations.  Use double quotes to system calls to grep in
grep.file() and read.fasta() so filenames with special characters can be
processed.  The 'values' element of the list returned by affinity() now has
dimensions equal to the number of variables. Use extendrange() to automatically
get the y-limits of line (1-D) plots made by diagram(). Separate the utility
functions in thermo.R into a number of util.* files, and also reorganize the
corresponding documentation files. Add functions mtitle(), count.taxa(),
is.fasta(), splitline(), trimfas(), protein.formula(), residue.formula(),
species.label().  Add functions getnodes(), getrank(), parent(), allparents(),
getnames() and sciname() for working with NCBI taxonomy files. Add function
danger() for loading alternative entries to the thermodynamic database (this
supersedes the functionality provided by the 'level' setting in thermo$opt,
which is no longer supported). Move some of the longer examples from the
documentation to longex(). Parts of the examples in the documentation that
should not be run during e.g. the CRAN package checks are now protected by
'\donttest'.

CHNOSZ_0.9 (2009-11-30) Fix .First.lib so package date correctly displays when
a CRAN-built package is loaded. Add URL to DESCRIPTION. In protein(), fix
UniProt search and add colClasses to read.csv function call so names of
proteins and organisms are always read as character. Add DNA polymerases and
mammalian aquaporin-1, myoglobin and p53 to protein.csv to support examples.
Fix issue in supcrt() where balancing reactions with charged species didn't
work correctly.  affinity() now handles transects along multiple variables
(useful for specifying nonuniform increments), invoked by specifying variables
with length > 3. Modifications to diagram(): Add 'group' argument to treat
groups of species as single composite species; implement 'alpha' option for 0-D
diagrams; add 'bg' argument for specifying background color of legend; speed up
plotting of predominance field labels and boundary lines. Change system
function call in grep.file() from grep to egrep (for extended regular
expressions). read.fasta() now has options to return the sequences and the
lines from the file. Add functions residue.comp() for calculating the
per-residue compositions of proteins, nucleicacids() for counting the bases and
computing the formulas of DNA and RNA, unitize() for scaling activities of
proteins so total activity of residues is unity (or other user-specified
value), strip() to plot relative abundances as variable-width color bars,
longex() to run additional examples. Add ability to select from duplicated
species in database using new 'level' option in thermo$opt.  Update yeast
examples in get.protein() to be consistent with Dick, 2009. Add URLs to
reference lists in documentation.

CHNOSZ_0.8 (2009-04-22) New functions extremes, where.extreme, diversity,
richness, plot.diversity, abundance, abundance.old (extracted from diagram),
protein.residue, grep.file, read.fasta, energy (extracted from affinity),
mylapply transfer. Affinity calculations using new 'energy' function can be
performed in more than two dimensions. Using Boltzmann distribution equation,
new 'abundance' function performs faster calculations of relative abundance of
species than 'abundance.old'. Files SGD.csv, ECO.csv and yeastgfp.csv are now
included in the CHNOSZ package. Protein sequences in FASTA files can be
searched and loaded using 'grep.file' and 'read.fasta'. Parallel processing
implemented for some calculations -- new utility function mylapply calls
lapply, or mclapply if multicore package is loaded; mylapply used in functions
abundance, affinity (iprotein option), protein.length, aminoacids. New argument
iprotein in 'affinity' to designate proteins for which to calculate affinities
of formation reactions using speed-optimized approach (calculate those of the
amino acid residues, then sum them together appropriately). Replaced 'proteome'
with 'get.protein' and fixed bug in calculating compositions of proteologs from
abundance data. Add residues, yeast cell-cycle proteins and carboxylases to
protein datafile. Introduce transfer function for reaction path simulations for
minerals and proteins. Documentation includes new examples of stress response
and diversity calculations.

CHNOSZ_0.7-2 (2008-11-12) New functions 'add.protein' and 'add.obigt' to read
local data files. In 'diagram' fix calculation of predominant proteins in
residue formation reactions.

CHNOSZ_0.7-1 (2008-09-19) Minor update. Add SLAP_BACLI to protein composition
data file. Fix some issues with the online search of Swiss-Prot.

CHNOSZ_0.7 (2008-09-14) More work on calculations of the partial derivatives of
omega; NaCl dissociation example is closer to but still not quite matching
SOJ+92.  Increase speed of 'water' in SUPCRT92 mode (handle intermediate
results in matrix instead of dataframe) and of 'diagram' when drawing
boundaries on predominance diagrams (pass coordinates of line segments in a
single call to 'line'). Add 'do.plot' argument to 'diagram' to enable figure
calculations without actually making a plot. Fix labels for charged species
generated by 'axis.label'.  Add 'return.approx' argument to 'info' for getting
indicies of approximately matching species.

CHNOSZ_0.6 (2008-03-08) Incorporate Debye-Huckel equation from Alberty, 2003 in
function 'nonideal' and add corresponding argument (IS - ionic strength) to
'subcrt', 'affinity'. Rename thermo$par (annoying conflict when trying to get
help on the 'par' in graphics package) to thermo$opt. Add code for (but mask
it) "f" term in the "g" function (Shock et al., 1992) for partial derivatives
of omega parameter. Extensive testing and modification of speciation code in
'diagram' for residue = TRUE.  New function 'change' wrapping 'mod.buffer' and
'mod.obigt'. Add yline and xrange arguments to 'diagram'. Add minor tick marks
to axes drawn using 'thermo.plot.new'. First release on chnosz.net.

CHNOSZ_0.0.5 (2007-12-21) Change name of package, rename 'supcrt' to 'subcrt',
link to H2O92D.F from SUPCRT92 (much faster than IAPWS calculations in R code),
add 'examples' function and add more examples of buffers and protein
calculations, update 'buffer' to be able to handle certain situations (e.g.,
fayalite- magnetite-quartz, where no basis species in Fe-SiO2-O2 is in common
to all species), add functions 'axis.label', 'describe', 'mod.obigt' and
'mod.buffer', upload supporting proteomic (ECO.csv, SGD.csv, yeastgfp.csv) and
thermodynamic data file (slop98.edit.dat) to webfiles.berkeley.edu. OBIGT.csv
now has 3001 entries.

speciate_0.04 (2007-08-08) Add support for phase transitions of minerals in
'supcrt'. A new function 'proteome' retrieves amino acid compositions of
proteins in yeast and E. coli and interacts with YeastGFP data to calculate the
compositions of subproteomes (assemblages of proteins in compartments),
requires external files. Change default style of axis labels (no longer e.g. O2
(log f)). New function 'water.lines' adds oxidation- reduction stability limits
of water to Eh-pH and related diagrams.

speciate_0.03 (2006-12-06) Add license file, and make minor updates to code and
data files. Extend the precision of values of G of the protein groups tabulated
in OBIGT.csv to the units place (calculated from H and S), to prevent warnings
caused by propagated rounding errors. Also recalculate the tabulated values of
Cp and V of these groups to greater precision (hundredths place, thousandths
for [UPBB]). Give the aqueous electron a value of standard molal entropy
consistent with that of Z. Correct guanosine to guanine in nucleobase-amino
acid example. Make single-species basis definition possible.

speciate_0.02 (2006-11-10) Major update. Incorporates IAPWS-95 equations for
water; additivity and ionization functions for proteins; and functions
'affinity', 'buffer' and 'diagram'. Thermodynamic data are now retrieved from
the OBIGT.csv data file (of 2006-11-07; 2928 entries); a function called 'info'
is added as a user and programming interface to the data. 'protein' function
can access the compositions of 115 proteins provided in the package, or
retrieve compositions from SGD or Swiss-Prot. Includes R documentation and now
passes R CMD check.

speciate-0.01 (2006-08-17) Limited release. Primary functions include equations
of state ('hkf', 'cgl'), 'makeup', 'supcrt'. ('basis', 'species' and 'info' are
present but not working). Properties of liquid water are calculated from
tabulated values on a P-T grid using 'interp' from the akima package. Separate
data files for aqueous species (1548), and crystalline,gas,liquid species
(242).
