NEWS in package ‘CHNOSZ’
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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.
Changes in version 0.9-6
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().