[CHNOSZ-commits] r32 - in pkg/CHNOSZ: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Dec 16 14:22:51 CET 2012
Author: jedick
Date: 2012-12-16 14:22:50 +0100 (Sun, 16 Dec 2012)
New Revision: 32
Added:
pkg/CHNOSZ/inst/NEWS
Removed:
pkg/CHNOSZ/inst/NEWS
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/sideeffects.Rd
Log:
change R dependency to R >= 2.12.0
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2012-12-09 14:09:44 UTC (rev 31)
+++ pkg/CHNOSZ/DESCRIPTION 2012-12-16 13:22:50 UTC (rev 32)
@@ -1,10 +1,10 @@
-Date: 2012-12-09
+Date: 2012-12-16
Package: CHNOSZ
-Version: 0.9.8-6
+Version: 0.9.8-7
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick <jmdick at asu.edu>
-Depends: R (>= 2.10.0), utils
+Depends: R (>= 2.12.0), utils
Suggests: testthat, parallel, limSolve
Description: This package includes functions and data sets to support chemical thermodynamic
modeling in biochemistry and low-temperature geochemistry. The features include calculation
Deleted: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2012-12-09 14:09:44 UTC (rev 31)
+++ pkg/CHNOSZ/inst/NEWS 2012-12-16 13:22:50 UTC (rev 32)
@@ -1,433 +0,0 @@
-CHANGES IN CHNOSZ 0.9.8-6 (2012-12-09)
---------------------------------------
-
-SIGNIFICANT USER-VISIBLE CHANGES:
-
-- diagram() split 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 certain diagrams.)
-
-- 'residue' argument of diagram() changed to 'normalize' in diagram()
- and equilibrate(). normalize=FALSE is always the default, including
- for systems of proteins.
-
-- 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 elemental bulk
- composition, and a Suggests dependency on 'limSolve'.
-
-- Create 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.
-
-- 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.
-
-NEW FUNCTIONS:
-
-- 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).
-
-- 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.
-
-- New function i2A() for generating a stoichiometric matrix from indices
- of species in the thermodynamic database.
-
-- 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 split into 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()
-
-- Add protein.equil() for step-by-step calculation of chemical
- activities of proteins in metastable equilibrium.
-
-- Objective functions used in revisit() and findit() now each have
- their own definitions, with an attribute indicating whether the
- function is minimized or maximized.
-
-- 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.
-
-OTHER CHANGES TO FUNCTIONS:
-
-- In equilibrate(), the argument 'logact' (inherited from diagram()),
- specifying the logarithm of
- activity of the balanced quantity, has been renamed to 'loga.balance'.
- The function now has 'loga.equil' in its result, containing the
- equilibrium logarithms of activities of the species of interest.
-
-- 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.
-
-- 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.
-
-- ZC() now accepts a numeric argument, referring to one or more species
- indices in the thermodynamic database.
-
-- 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()).
-
-- 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.
-
-- residue.info() mostly replaced by protein.basis().
-
-- 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.
-
-- EOSvar() has new variables invPPsi and invPPsiTTheta, used for
- temperature- and pressure-dependent regressions in the revised HKF
- equations of state.
-
-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 TODO and CHECKLIST to the installation directory of the package.
-
-- Use UTF-8 degree symbol in second argument of \eqn{}{}.
-
-PERFORMANCE AND CODE CLEAN-UPS:
-
-- 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" package 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.
-
-
-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().
Added: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS (rev 0)
+++ pkg/CHNOSZ/inst/NEWS 2012-12-16 13:22:50 UTC (rev 32)
@@ -0,0 +1,440 @@
+CHANGES IN CHNOSZ 0.9.8-7 (2012-12-16)
+--------------------------------------
+
+SIGNIFICANT USER-VISIBLE 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.
+
+- 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 elemental bulk
+ composition, and a Suggests dependency on 'limSolve'.
+
+NEW FUNCTIONS:
+
+- 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'. The function now has 'loga.equil'
+ in its result, 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 split into 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.
+
+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 TODO and CHECKLIST to the installation directory of the package.
+
+- Use UTF-8 degree symbol in second argument of \eqn{}{}.
+
+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, 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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 32
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