[CHNOSZ-commits] r435 - in pkg/CHNOSZ: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 13 04:14:19 CEST 2019
Author: jedick
Date: 2019-04-13 04:14:18 +0200 (Sat, 13 Apr 2019)
New Revision: 435
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/add.obigt.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/affinity.Rd
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/eos.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/ionize.aa.Rd
pkg/CHNOSZ/man/makeup.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/species.Rd
pkg/CHNOSZ/man/subcrt.Rd
pkg/CHNOSZ/man/thermo.Rd
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/man/util.formula.Rd
pkg/CHNOSZ/man/util.misc.Rd
pkg/CHNOSZ/man/util.seq.Rd
pkg/CHNOSZ/man/util.water.Rd
Log:
Rd files: change thermo$ to thermo()$
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/DESCRIPTION 2019-04-13 02:14:18 UTC (rev 435)
@@ -1,6 +1,6 @@
Date: 2019-04-13
Package: CHNOSZ
-Version: 1.3.1-15
+Version: 1.3.1-16
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -87,7 +87,7 @@
\code{EOScoeffs} retrieves coefficients in the Helgeson-Kirkham-Flowers equations from the thermodynamic database (\code{\link{thermo}$obigt}) for the given aqueous \code{species}.
If the \code{property} is \samp{Cp}, the resulting data frame has column names of \samp{(Intercept)}, \samp{invTTheta2} and \samp{TX}, respectively holding the coefficients \eqn{c_1}{c1}, \eqn{c_2}{c2} and \eqn{\omega}{omega} in the equation \eqn{Cp^\circ = c_1 + c_2/(T-\Theta)^2 + {\omega}TX}{Cp = c1 + c2/(T-Theta)^2 + omega*TX}.
If the \code{property} is \samp{V}, the data frame has column names of \samp{(Intercept)}, \samp{invTTheta} and \samp{Q}, respectively holding the coefficients \eqn{\sigma}{sigma}, \eqn{\xi}{xi} and \eqn{\omega}{omega} in \eqn{V^\circ = \sigma + \xi/(T-\Theta) - {\omega}Q}{V = sigma + xi/(T-Theta) - omega*Q}.
-Here, \eqn{\sigma}{sigma} and \eqn{\xi}{xi} are calculated from a1, a2, a3 and a4 in \code{thermo$obigt} at the pressure indicated by \code{P} (default 1 bar).
+Here, \eqn{\sigma}{sigma} and \eqn{\xi}{xi} are calculated from a1, a2, a3 and a4 in \code{thermo()$obigt} at the pressure indicated by \code{P} (default 1 bar).
The original motivation for writing these functions was to explore alternatives or possible modifications to the revised Helgeson-Kirkham-Flowers equations applied to aqueous nonelectrolytes.
As pointed out by Schulte et al., 2001, the functional forms of the equations do not permit retrieving values of the solvation parameter (\eqn{\omega}{omega}) that closely represent the observed trends in both heat capacity and volume at high temperatures (above ca. 200 \degC).
Modified: pkg/CHNOSZ/man/add.obigt.Rd
===================================================================
--- pkg/CHNOSZ/man/add.obigt.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/add.obigt.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -35,7 +35,7 @@
If \code{species} is given and matches the name(s) of species in the file, only those species are added to the database.
By default, species in the file replace any existing species having the same combination of name and state.
-Set \code{force} to FALSE to avoid replacing species that are present in (\code{thermo$obigt}).
+Set \code{force} to FALSE to avoid replacing species that are present in (\code{thermo()$obigt}).
Given the default setting of \code{E.units}, the function does not perform any unit conversions.
If \code{E.units} is set to \samp{J}, then the thermodynamic parameters are converted from units of Joules to calories, as used in the CHNOSZ database.
@@ -50,11 +50,11 @@
The formula is taken from the \samp{formula} argument, or if that is missing, is taken to be the same as the \samp{name} of the species.
An error results if the formula is not valid (i.e. can not be parsed by\code{\link{makeup}}).
Additional arguments refer to the name of the property(s) to be updated and are matched to any part of compound column names in \code{\link{thermo}$obigt}, such as \samp{z} or \samp{T} in \samp{z.T}.
-Unless \samp{state} is specified as one of the properties, its value is taken from \code{thermo$opt$state}.
-When adding species, properties that are not specified become NA, except for \samp{state}, which takes a default value from \code{thermo$opt$state}, and \samp{z.T}, which for aqueous species is set to the charge calculated from the chemical formula (otherwise, NA charge for newly added species would trigger the \code{\link{AkDi}} model).
+Unless \samp{state} is specified as one of the properties, its value is taken from \code{thermo()$opt$state}.
+When adding species, properties that are not specified become NA, except for \samp{state}, which takes a default value from \code{thermo()$opt$state}, and \samp{z.T}, which for aqueous species is set to the charge calculated from the chemical formula (otherwise, NA charge for newly added species would trigger the \code{\link{AkDi}} model).
The values provided should be in the units specifed in the documentation for the \code{thermo} data object, including any order-of-magnitude scaling factors.
-\code{today} returns the current date in the format adopted for \code{thermo$obigt} (inherited from SUPCRT-format data files) e.g. \samp{13.May.12} for May 13, 2012.
+\code{today} returns the current date in the format adopted for \code{thermo()$obigt} (inherited from SUPCRT-format data files) e.g. \samp{13.May.12} for May 13, 2012.
}
\value{
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/add.protein.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -15,7 +15,7 @@
}
\arguments{
- \item{aa}{data frame, amino acid composition in the format of \code{thermo$protein}}
+ \item{aa}{data frame, amino acid composition in the format of \code{thermo()$protein}}
\item{protein}{character, name of protein; numeric, indices of proteins (rownumbers of \code{\link{thermo}$protein})}
\item{sequence}{character, protein sequence}
\item{...}{additional arguments passed to \code{\link{read.csv}}}
@@ -31,7 +31,7 @@
The purpose of the functions described here is to identify proteins and work with their amino acid compositions.
From the amino acid compositions, the thermodynamic properties of the proteins can be estimated by group additivity.
-\code{seq2aa} returns a data frame of amino acid composition, in the format of \code{thermo$protein}, corresponding to the provided \code{sequence}.
+\code{seq2aa} returns a data frame of amino acid composition, in the format of \code{thermo()$protein}, corresponding to the provided \code{sequence}.
Here, the \code{protein} argument indicates the name of the protein with an underscore (e.g. \samp{LYSC_CHICK}).
\code{aasum} returns a data frame representing the sum of amino acid compositions in the rows of the input \code{aa} data frame.
@@ -39,9 +39,9 @@
If \code{average} is TRUE the final sum is divided by the number of input compositions.
The name used in the output is taken from the first row of \code{aa} or from \code{protein} and \code{organism} if they are specified.
-Given amino acid compositions returned by the \code{*aa} functions described above, \code{add.protein} adds them to \code{thermo$protein} for use by other functions in CHNOSZ.
-The amino acid compositions of proteins in \code{aa} with the same name as one in \code{thermo$protein} are replaced.
-The value returned by this function is the rownumbers of \code{thermo$protein} that are added and/or replaced.
+Given amino acid compositions returned by the \code{*aa} functions described above, \code{add.protein} adds them to \code{thermo()$protein} for use by other functions in CHNOSZ.
+The amino acid compositions of proteins in \code{aa} with the same name as one in \code{thermo()$protein} are replaced.
+The value returned by this function is the rownumbers of \code{thermo()$protein} that are added and/or replaced.
}
\examples{
Modified: pkg/CHNOSZ/man/affinity.Rd
===================================================================
--- pkg/CHNOSZ/man/affinity.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/affinity.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -71,7 +71,7 @@
}
\seealso{
-\code{\link{ionize.aa}}, activated if proteins are among the species of interest, \samp{H+} is in the basis, and \code{thermo$opt$ionize} is TRUE.
+\code{\link{ionize.aa}}, activated if proteins are among the species of interest and \samp{H+} is in the basis.
\code{\link{equilibrate}} for using the results of \code{affinity} to calculate equilibrium activities of species, and \code{\link{diagram}} to plot the results.
}
Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/basis.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -26,7 +26,7 @@
The special names \samp{pH}, \samp{pe} and \samp{Eh} can be included in the \code{species} argument; they get translated into the names of the proton (\samp{H+}) and electron (\samp{e-}) as appropriate.
The physical states or logarithms of activities of species in the basis definition can be changed by calling \code{basis} with the formulas of species that are in the basis set, or their species indices.
-If either of the second or third arguments to \code{basis} is of type character, it refers to the name of a state (if present in \code{thermo$obigt$state}) or to the name of a chemical activity \code{\link{buffer}} (if present in \code{thermo$buffers$name}).
+If either of the second or third arguments to \code{basis} is of type character, it refers to the name of a state (if present in \code{thermo()$obigt$state}) or to the name of a chemical activity \code{\link{buffer}} (if present in \code{thermo()$buffers$name}).
If either of these arguments is numeric it specifies the logarithms of activities (or fugacities for gases) of the basis species.
In case \samp{pH}, \samp{pe} or \samp{Eh} is named, the logarithm of activity of the basis species is converted from these values.
For example, a value of 7 for pH is stored as a logarithm of activity of -7.
@@ -57,7 +57,7 @@
}
\value{
-Returns the value of \code{thermo$basis} after any modifications; or, if \code{delete} is TRUE, its value before deletion (invisibly).
+Returns the value of \code{thermo()$basis} after any modifications; or, if \code{delete} is TRUE, its value before deletion (invisibly).
}
\seealso{
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/berman.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -15,7 +15,7 @@
\item{name}{character, name of mineral}
\item{T}{numeric, temperature(s) at which to calculate properties (K)}
\item{P}{numeric, pressure(s) at which to calculate properties (bar)}
- \item{thisinfo}{dataframe, row for mineral from \code{thermo$obigt}}
+ \item{thisinfo}{dataframe, row for mineral from \code{thermo()$obigt}}
\item{check.G}{logical, check consistency of G, H, and S?}
\item{calc.transition}{logical, include calculation of polymorphic transition properties?}
\item{calc.disorder}{logical, include calculation of disordering properties?}
@@ -24,7 +24,7 @@
\details{
This function calculates the thermodynamic properties of minerals at high \P and \T using equations given by Berman (1988).
-These minerals should be listed in \code{thermo$obigt} with the state \samp{cr} and chemical formula, and optionally an abbreviation and references, but all other properties set to NA.
+These minerals should be listed in \code{thermo()$obigt} with the state \samp{cr} and chemical formula, and optionally an abbreviation and references, but all other properties set to NA.
The standard state thermodynamic properties and parameters for the calculations are stored in data files under \code{extdata/Berman}, or can be read from a user-created file (if available) named \samp{berman.csv} in the working directory.
@@ -43,7 +43,7 @@
The data files have the following 30 columns:
\tabular{lll}{
- \code{name} \tab mineral name (must match an entry with a formula but NA properties in \code{thermo$obigt})\cr
+ \code{name} \tab mineral name (must match an entry with a formula but NA properties in \code{thermo()$obigt})\cr
\code{GfPrTr} \tab standard Gibbs energy at 298.15 K and 1 bar (J mol\S{-1}) (Benson-Helgeson convention)\cr
\code{HfPrTr} \tab standard enthalpy at 298.15 K and 1 bar (J mol\S{-1})\cr
\code{SPrTr} \tab standard entropy at 298.15 K and 1 bar (J mol\S{-1} K\S{-1})\cr
@@ -69,7 +69,7 @@
If \code{check.G} is TRUE, the tabulated value of \code{GfTrPr} (Benson-Helgeson) is compared with that calculated from \code{HfPrTr} - 298.15*\code{DSPrTr} (\code{DSPrTr} is the difference between the entropies of the elements in the formula and \code{SPrTr} in the table).
A warning is produced if the absolute value of the difference between tabulated and calculated \code{GfTrPr} is greater than 1000 J/mol.
-Providing \code{thisinfo} avoids searching for the mineral in \code{thermo$obigt}, potentially saving some running time.
+Providing \code{thisinfo} avoids searching for the mineral in \code{thermo()$obigt}, potentially saving some running time.
If the function is called with missing \code{name}, the parameters for all available minerals are returned.
}
@@ -80,7 +80,7 @@
\examples{
\dontshow{reset()}
# other than the formula, the parameters aren't stored in
-# thermo$obigt, so this shows NAs
+# thermo()$obigt, so this shows NAs
info(info("quartz", "cr"))
# properties of alpha-quartz (aQz) at 298.15 K and 1 bar
berman("quartz")
@@ -167,7 +167,7 @@
# the curves cross at about 725 deg C (BA96 Fig. 8)
# (actually, in our calculation they cross closer to 800 deg C)
stopifnot(T[which.min(abs(Gex_BA96 - Gex_Ber88))] == 800)
-# reset the database (thermo$opt$E.units, thermo$obigt, and thermo$opt$Berman)
+# reset the database (thermo()$opt$E.units, thermo()$obigt, and thermo()$opt$Berman)
reset()
}
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/buffer.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -13,7 +13,7 @@
}
\arguments{
- \item{name}{character, name of buffer to add to or find in \code{thermo$buffers}.}
+ \item{name}{character, name of buffer to add to or find in \code{thermo()$buffers}.}
\item{species}{character, names or formulas of species in a buffer.}
\item{state}{character, physical states of species in buffer.}
\item{logact}{numeric, logarithms of activities of species in buffer.}
@@ -38,7 +38,7 @@
It is possible to set the logarithms of activities of the species in the buffer through the \code{logact} argument; if this is missing unit activity is assigned to crystalline species in buffer, otherwise (for aqueous species) the default value of activity is 10\eqn{^{-3}}{^-3}.
If \code{name} identifies an already defined buffer, this function modifies the logarithms of activities or states of species in that buffer, optionally restricted to only those species given in \code{species}.
-It is possible to assign different buffers to different basis species, in which case the order of their calculation depends on their order in \code{thermo$buffers}.
+It is possible to assign different buffers to different basis species, in which case the order of their calculation depends on their order in \code{thermo()$buffers}.
This function is compatible with systems of proteins, but note that for buffers \emph{made} of proteins the buffer calculations presently use whole protein formulas (instead of residue equivalents) and consider nonionized proteins only.
}
Modified: pkg/CHNOSZ/man/eos.Rd
===================================================================
--- pkg/CHNOSZ/man/eos.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/eos.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -18,7 +18,7 @@
\arguments{
\item{property}{character, name(s) of properties to calculate}
- \item{parameters}{dataframe, species parameters as one or more rows from \code{thermo$obigt}}
+ \item{parameters}{dataframe, species parameters as one or more rows from \code{thermo()$obigt}}
\item{T}{numeric, temperature(s) at which to calculate properties (K)}
\item{P}{numeric, pressure(s) at which to calculate properties (bar)}
\item{contrib}{character, which contributions to consider in the revised HKF equations equations of state: (\code{n})onsolvation, (\code{s})olvation (the \eqn{\omega}{omega} terms), or (o)rigination contributions (i.e., the property itself at 25 \degC and 1 bar). Default is \code{c("n","s","o")}, for all contributions}
@@ -34,7 +34,7 @@
\code{hkf} implements the revised HKF equations of state (Helgeson et al., 1981; Tanger and Helgeson, 1988; Shock and Helgeson, 1988).
The equations-of-state parameters are \code{a1}, \code{a2}, \code{a3}, \code{a4}, \code{c1}, \code{c2}, \code{omega} and \code{Z}; the units of these parameters are as indicated for \code{\link{thermo}$obigt}, without the order of magnitude multipliers.
-Note that the equation-of-state parameter \code{Z} (appearing in the \eqn{g}{g}-function for the temperature derivatives of the omega parameter; Shock et al., 1992) is taken from \code{thermo$obigt} and \emph{not} from the \code{\link{makeup}} of the species.
+Note that the equation-of-state parameter \code{Z} (appearing in the \eqn{g}{g}-function for the temperature derivatives of the omega parameter; Shock et al., 1992) is taken from \code{thermo()$obigt} and \emph{not} from the \code{\link{makeup}} of the species.
\code{H2O.props} is an optional argument that lists the properties of water that should be returned; it is used by \code{\link{subcrt}} so that the time-consuming water calculations are only performed once.
The temperature and pressure derivatives of the \code{omega} parameter for charged species (where \code{Z != 0}, but not for the aqueous proton, H+) are calculated using the \eqn{g}{g}- and \eqn{f}{f}-functions described by Shock et al., 1992 and Johnson et al., 1992.
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/extdata.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -93,8 +93,8 @@
Files in \code{supcrt} contain scripts for reading and comparing SUPCRT files (including slop98.dat and newer slop files from GEOPIG (http://geopig.asu.edu)) with the database in CHNOSZ:
\itemize{
\item \code{read.supcrt.R} defines the function \code{read.supcrt} that can be used to read SUPCRT files.
- \item \code{compare.R} uses \code{read.supcrt} to compare data in the SUPCRT file with that in \code{thermo$obigt}.
- \item \code{newnames.csv} maps names generated by \code{read.supcrt}, based on names present in the source SUPCRT files, to names used in \code{thermo$obigt}.
+ \item \code{compare.R} uses \code{read.supcrt} to compare data in the SUPCRT file with that in \code{thermo()$obigt}.
+ \item \code{newnames.csv} maps names generated by \code{read.supcrt}, based on names present in the source SUPCRT files, to names used in \code{thermo()$obigt}.
}
Files in \code{taxonomy} contain taxonomic data files:
@@ -108,7 +108,7 @@
\item \code{obigt_check.csv} contains the results of running \code{\link{check.obigt}} to check the internal consistency of entries in the default and optional datafiles.
\item \code{RH98_Table15.csv} Group stoichiometries for high molecular weight crystalline and liquid organic compounds taken from Table 15 of Richard and Helgeson, 1998. The first three columns have the \code{compound} name, \code{formula} and physical \code{state} (\samp{cr} or \samp{liq}). The remaining columns have the numbers of each group in the compound; the names of the groups (columns) correspond to species in \code{\link{thermo}$obigt}. The compound named \samp{5a(H),14a(H)-cholestane} in the paper has been changed to \samp{5a(H),14b(H)-cholestane} here to match the group stoichiometry given in the table. See \code{\link{RH2obigt}} for a function that uses this file.
\item \code{DLEN67.csv} Standard Gibbs energies of formation, in kcal/mol, from Dayhoff et al., 1967, for nitrogen (N2) plus 17 compounds shown in Fig. 2 of Dayhoff et al., 1964, at 300, 500, 700 and 1000 K. See \code{demo("wjd")} and the vignette \code{wjd.Rmd} for examples that use this file.
- \item \code{SK95.csv} contains thermodynamic data for alanate, glycinate, and their complexes with metals, taken from Shock and Koretsky (1995) as corrected in slop98.dat. The data are used in the package tests (\code{test-recalculate.R}) to check the recalculated values of G, H, and S in \code{thermo$obigt} using properties for alanate and glycinate from Amend and Helgeson (1997).
+ \item \code{SK95.csv} contains thermodynamic data for alanate, glycinate, and their complexes with metals, taken from Shock and Koretsky (1995) as corrected in slop98.dat. The data are used in the package tests (\code{test-recalculate.R}) to check the recalculated values of G, H, and S in \code{thermo()$obigt} using properties for alanate and glycinate from Amend and Helgeson (1997).
}
Modified: pkg/CHNOSZ/man/info.Rd
===================================================================
--- pkg/CHNOSZ/man/info.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/info.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -24,7 +24,7 @@
The searches of the indicated \code{species} are made among the names, chemical formulas, and abbreviations (in the \samp{abbrv} column) in the thermodynamic database.
If the text of the \code{species} is matched the index of that species is returned.
If there are multiple matches for the \code{species}, and \code{state} is NULL, the index of first match is returned.
-The order of entries in \code{thermo$obigt} is grouped by states in the order \samp{aq}, \samp{cr}, \samp{gas}, \samp{liq}, so for species in both aqueous and gaseous states the index of the aqueous species is returned, unless \code{state} is set to \samp{gas}.
+The order of entries in \code{thermo()$obigt} is grouped by states in the order \samp{aq}, \samp{cr}, \samp{gas}, \samp{liq}, so for species in both aqueous and gaseous states the index of the aqueous species is returned, unless \code{state} is set to \samp{gas}.
Names of species including an underscore character are indicative of proteins, e.g. \samp{LYSC_CHICK}.
If the name of a protein is provided to \code{info} and the composition of the protein can be found using \code{\link{protein}}, the thermodyamic properties and parameters of the nonionized protein (calculated using amino acid group additivity) are added to the thermodynamic database.
@@ -33,8 +33,8 @@
If no exact matches are found, \code{info} searches the database for similar names or formulas using \code{\link{agrep}}.
If any of these are found, the results are summarized on the screen, but the function always returns NA in this case.
-With a numeric argument, the rows of \code{thermo$obigt} indicated by \code{ispecies} are returned, after removing any order-of-magnitude scaling factors.
-If these species are all aqueous or are all not aqueous, the compounded column names used in \code{thermo$obigt} are replaced with names appropriate for the corresponding equations of state.
+With a numeric argument, the rows of \code{thermo()$obigt} indicated by \code{ispecies} are returned, after removing any order-of-magnitude scaling factors.
+If these species are all aqueous or are all not aqueous, the compounded column names used in \code{thermo()$obigt} are replaced with names appropriate for the corresponding equations of state.
A missing value of one of the standard molal Gibbs energy (\code{G}) or enthalpy (\code{H}) of formation from the elements or entropy (\code{S}) is calculated from the other two, if available.
If \code{check.it} is TRUE, several checks of self consistency among the thermodynamic properties and parameters are performed using \code{\link{checkGHS}} and \code{\link{checkEOS}}.
}
Modified: pkg/CHNOSZ/man/ionize.aa.Rd
===================================================================
--- pkg/CHNOSZ/man/ionize.aa.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/ionize.aa.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -12,7 +12,7 @@
}
\arguments{
- \item{aa}{data frame, amino acid composition in the format of \code{thermo$protein}}
+ \item{aa}{data frame, amino acid composition in the format of \code{thermo()$protein}}
\item{property}{character, property to calculate}
\item{T}{numeric, temperature in \degC}
\item{P}{numeric, pressure in bar, or \samp{Psat} for vapor pressure of \H2O above 100 \degC}
@@ -36,7 +36,7 @@
\examples{\dontshow{reset()}
## Charge of LYSC_CHICK as a function of pH and T
# After Fig. 10 of Dick et al., 2006
-# the rownumber of the protein in thermo$protein
+# the rownumber of the protein in thermo()$protein
ip <- pinfo("LYSC_CHICK")
# its amino acid composition
aa <- pinfo(ip)
Modified: pkg/CHNOSZ/man/makeup.Rd
===================================================================
--- pkg/CHNOSZ/man/makeup.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/makeup.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -31,7 +31,7 @@
\code{makeup} will issue a warning for elemental symbols that are not present in \code{\link{thermo}$element}.
\code{makeup} can handle numeric and length > 1 values for the \code{formula} argument.
-If the argument is numeric, it identifies row number(s) in \code{thermo$obigt} from which to take the formulas of species.
+If the argument is numeric, it identifies row number(s) in \code{thermo()$obigt} from which to take the formulas of species.
If \code{formula} has length > 1, the function returns a list containing the elemental counts in each of the formulas.
If \code{count.zero} is TRUE, the elemental counts for each formula include zeros to indicate elements that are only present in any of the other formulas.
@@ -67,8 +67,8 @@
# these all represent a single negative charge, i.e., electron
makeup("-1")
makeup("Z-1+0")
-makeup("Z0-1") # the "old" formula for the electron in thermo$obigt
-makeup("(Z-1)") # the current formula in thermo$obigt
+makeup("Z0-1") # the "old" formula for the electron in thermo()$obigt
+makeup("(Z-1)") # the current formula in thermo()$obigt
# hypothetical compounds with negative numbers of elements
makeup("C-4(O-2)") # -4 carbon, -2 oxygen
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/nonideal.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -61,8 +61,8 @@
\section{Neutral Species}{
For neutral species, the Setch{\eacute}now equation is used, as described in Shvarov and Bastrakov, 1999.
If \code{\link{thermo}$opt$Setchenow} is \samp{bgamma0} (the default), the extended term parameter is set to zero and the only non-zero term is the mole fraction to molality conversion factor (using the value of \code{m_star}).
-If \code{thermo$opt$Setchenow} is \samp{bgamma}, the extended term paramter is taken from the setting for the charged species (which can be either \samp{Bdot} or \samp{bgamma}).
-Set \code{thermo$opt$Setchenow} to any other value to disable the calculations for neutral species.
+If \code{thermo()$opt$Setchenow} is \samp{bgamma}, the extended term paramter is taken from the setting for the charged species (which can be either \samp{Bdot} or \samp{bgamma}).
+Set \code{thermo()$opt$Setchenow} to any other value to disable the calculations for neutral species.
}
\section{b_gamma}{
Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd 2019-04-13 01:34:09 UTC (rev 434)
+++ pkg/CHNOSZ/man/protein.info.Rd 2019-04-13 02:14:18 UTC (rev 435)
@@ -35,14 +35,14 @@
}
\details{
-For character \code{protein}, \code{pinfo} returns the rownumber(s) of \code{thermo$protein} that match the protein names.
+For character \code{protein}, \code{pinfo} returns the rownumber(s) of \code{thermo()$protein} that match the protein names.
The names can be supplied in the single \code{protein} argument (with an underscore, denoting protein_organism) or as pairs of \code{protein}s and \code{organism}s.
NA is returned for any unmatched proteins, including those for which no \code{organism} is given or that do not have an underscore in \code{protein}.
-Alternatively, if \code{regexp} is TRUE, the \code{protein} argument is used as a pattern (regular expression); rownumbers of all matches of \code{thermo$protein$protein} to this pattern are returned.
-When using \code{regexp}, the \code{organism} can optionally be provided to return only those entries that also match \code{thermo$protein$organism}.
+Alternatively, if \code{regexp} is TRUE, the \code{protein} argument is used as a pattern (regular expression); rownumbers of all matches of \code{thermo()$protein$protein} to this pattern are returned.
+When using \code{regexp}, the \code{organism} can optionally be provided to return only those entries that also match \code{thermo()$protein$organism}.
-For numeric \code{protein}, \code{pinfo} returns the corresponding row(s) of \code{thermo$protein}.
+For numeric \code{protein}, \code{pinfo} returns the corresponding row(s) of \code{thermo()$protein}.
Set \code{residue} to TRUE to return the per-residue composition (i.e. amino acid composition of the protein divided by total number of residues).
For dataframe \code{protein}, \code{pinfo} returns it unchanged, except for possibly the per-residue calculation.
@@ -55,21 +55,21 @@
The amino acid compositions are multiplied by the output of \code{\link{group.formulas}} to generate the result.
\code{protein.obigt} calculates the thermodynamic properties and equations-of-state parameters for the completely nonionized proteins using group additivity with parameters taken from Dick et al., 2006 (aqueous proteins) and LaRowe and Dick, 2012 (crystalline proteins and revised aqueous methionine sidechain group).
-The return value is a data frame in the same format as \code{thermo$obigt}.
+The return value is a data frame in the same format as \code{thermo()$obigt}.
\code{state} indicates the physical state for the parameters used in the calculation (\samp{aq} or \samp{cr}).
The following functions also depend on an existing definition of the basis species:
\code{protein.basis} calculates the numbers of the basis species (i.e. opposite of the coefficients in the formation reactions) that can be combined to form the composition of each of the proteins.
-The basis species must be present in \code{thermo$basis}, and if \samp{H+} is among the basis species, the ionization states of the proteins are included.
-The ionization state of the protein is calculated at the pH defined in \code{thermo$basis} and at the temperature specified by the \code{T} argument.
+The basis species must be present in \code{thermo()$basis}, and if \samp{H+} is among the basis species, the ionization states of the proteins are included.
+The ionization state of the protein is calculated at the pH defined in \code{thermo()$basis} and at the temperature specified by the \code{T} argument.
If \code{normalize} is TRUE, the coefficients on the basis species are divided by the lengths of the proteins.
- \code{protein.equil} produces a series of messages showing step-by-step a calculation of the chemical activities of proteins in metastable equilibrium. For the first protein, it shows the standard Gibbs energies of the reaction to form the nonionized protein from the basis species and of the ionization reaction of the protein (if \samp{H+} is in the basis), then the standard Gibbs energy/RT of the reaction to form the (possibly ionized) protein per residue. The per-residue values of \samp{logQstar} and \samp{Astar/RT} are also shown for the first protein. Equilibrium calculations are then performed, only if more than one protein is specified. This calculation applies the Boltzmann distribution to the calculation of the equilibrium degrees of formation of the residue equivalents of the proteins, then converts them to activities of proteins taking account of \code{loga.protein} and protein length. If the \code{protein} argument is numeric (indicating rownumbers in \code{thermo$protein}), the values of \samp{Astar/RT} are compared with the output of \code{\link{affinity}}, and those of the equilibrium degrees of formation of the residues and the chemical activities of the proteins with the output of \code{\link{diagram}}. If the values in any of these tests are are not \code{\link{all.equal}} an error is produced indicating a bug.
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 435
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