[CHNOSZ-commits] r545 - in pkg/CHNOSZ: . R demo inst tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 5 10:04:45 CEST 2020
Author: jedick
Date: 2020-07-05 10:04:45 +0200 (Sun, 05 Jul 2020)
New Revision: 545
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/add.OBIGT.R
pkg/CHNOSZ/R/add.protein.R
pkg/CHNOSZ/R/affinity.R
pkg/CHNOSZ/R/basis.R
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/R/equilibrate.R
pkg/CHNOSZ/R/hkf.R
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/ionize.aa.R
pkg/CHNOSZ/R/makeup.R
pkg/CHNOSZ/R/nonideal.R
pkg/CHNOSZ/R/palply.R
pkg/CHNOSZ/R/protein.info.R
pkg/CHNOSZ/R/species.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/swap.basis.R
pkg/CHNOSZ/R/util.affinity.R
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/R/util.expression.R
pkg/CHNOSZ/R/util.fasta.R
pkg/CHNOSZ/R/util.formula.R
pkg/CHNOSZ/R/util.plot.R
pkg/CHNOSZ/R/util.seq.R
pkg/CHNOSZ/R/util.units.R
pkg/CHNOSZ/demo/copper.R
pkg/CHNOSZ/demo/density.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/tests/testthat/test-add.protein.R
pkg/CHNOSZ/tests/testthat/test-affinity.R
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/tests/testthat/test-info.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
pkg/CHNOSZ/tests/testthat/test-makeup.R
pkg/CHNOSZ/tests/testthat/test-species.R
pkg/CHNOSZ/tests/testthat/test-thermo.R
pkg/CHNOSZ/tests/testthat/test-util.R
pkg/CHNOSZ/tests/testthat/test-util.data.R
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
Log:
Change thermo$... to thermo()$... in messages and comments
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-05 08:04:45 UTC (rev 545)
@@ -1,6 +1,6 @@
-Date: 2020-07-04
+Date: 2020-07-05
Package: CHNOSZ
-Version: 1.3.6-19
+Version: 1.3.6-20
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/R/add.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/add.OBIGT.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/add.OBIGT.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -18,7 +18,7 @@
}
mod.OBIGT <- function(...) {
- # add or modify species in thermo$OBIGT
+ # add or modify species in thermo()$OBIGT
thermo <- get("thermo", CHNOSZ)
# the names and values are in the arguments
# this works for providing arguments via do.call
@@ -41,7 +41,7 @@
else ispecies <- suppressMessages(mapply(info.character,
species=args$name, check.protein=FALSE, SIMPLIFY=TRUE, USE.NAMES=FALSE))
}
- # the column names of thermo$OBIGT, split at the "."
+ # the column names of thermo()$OBIGT, split at the "."
cnames <- c(do.call(rbind, strsplit(colnames(thermo$OBIGT), ".", fixed=TRUE)), colnames(thermo$OBIGT))
# the columns we are updating
icol <- match(names(args), cnames)
@@ -55,7 +55,7 @@
# the arguments as data frame
args <- data.frame(args, stringsAsFactors=FALSE)
if(length(inew) > 0) {
- # the right number of blank rows of thermo$OBIGT
+ # the right number of blank rows of thermo()$OBIGT
newrows <- thermo$OBIGT[1:length(inew), ]
# if we don't know something it's NA
newrows[] <- NA
@@ -83,7 +83,7 @@
Z[is.na(Z)] <- 0
newrows$z.T[isaq] <- Z[isaq]
}
- # assign to thermo$OBIGT
+ # assign to thermo()$OBIGT
thermo$OBIGT <- rbind(thermo$OBIGT, newrows)
rownames(thermo$OBIGT) <- NULL
assign("thermo", thermo, CHNOSZ)
Modified: pkg/CHNOSZ/R/add.protein.R
===================================================================
--- pkg/CHNOSZ/R/add.protein.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/add.protein.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -2,7 +2,7 @@
# calculate properties of proteins 20061109 jmd
# reorganize protein functions 20120513
-# add.protein - add amino acid counts to thermo$protein (returns iprotein)
+# add.protein - add amino acid counts to thermo()$protein (returns iprotein)
# seq2aa - calculate amino acid counts from a sequence
# aasum - combine amino acid counts (sum, average, or weighted sum by abundance)
@@ -56,10 +56,10 @@
add.protein <- function(aa) {
# add a properly constructed data frame of
- # amino acid counts to thermo$protein
+ # amino acid counts to thermo()$protein
thermo <- get("thermo", CHNOSZ)
if(!identical(colnames(aa), colnames(thermo$protein)))
- stop("'aa' does not have the same columns as thermo$protein")
+ stop("'aa' does not have the same columns as thermo()$protein")
# find any protein IDs that are duplicated
po <- paste(aa$protein, aa$organism, sep="_")
ip <- pinfo(po)
@@ -74,7 +74,7 @@
# return the new rownumbers
ip <- pinfo(po)
# make some noise
- if(!all(ipdup)) message("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo$protein")
- if(any(ipdup)) message("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo$protein")
+ if(!all(ipdup)) message("add.protein: added ", nrow(aa)-sum(ipdup), " new protein(s) to thermo()$protein")
+ if(any(ipdup)) message("add.protein: replaced ", sum(ipdup), " existing protein(s) in thermo()$protein")
return(ip)
}
Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/affinity.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -75,7 +75,7 @@
if(!is.null(iprotein)) {
# check all proteins are available
if(any(is.na(iprotein))) stop("`iprotein` has some NA values")
- if(!all(iprotein %in% 1:nrow(thermo$protein))) stop("some value(s) of `iprotein` are not rownumbers of thermo$protein")
+ if(!all(iprotein %in% 1:nrow(thermo$protein))) stop("some value(s) of `iprotein` are not rownumbers of thermo()$protein")
# add protein residues to the species list
resnames <- c("H2O",aminoacids(3))
# residue activities set to zero;
Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/basis.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -89,7 +89,7 @@
### unexported functions ###
-# to add the basis to thermo$OBIGT
+# to add the basis to thermo()$OBIGT
put.basis <- function(ispecies, logact = rep(NA, length(ispecies))) {
thermo <- get("thermo", CHNOSZ)
state <- thermo$OBIGT$state[ispecies]
@@ -120,7 +120,7 @@
# the second test: matrix is invertible
if(inherits(tryCatch(solve(comp), error = identity), "error"))
stop("singular stoichiometric matrix")
- # store the basis definition in thermo$basis, including
+ # store the basis definition in thermo()$basis, including
# both numeric and character data, so we need to use a data frame
comp <- cbind(as.data.frame(comp), ispecies, logact, state, stringsAsFactors=FALSE)
# ready to assign to the global thermo object
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/berman.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -31,7 +31,7 @@
userfileexists <- TRUE
BDat_user <- read.csv(userfile, as.is=TRUE)
dat <- rbind(BDat_user, dat)
- } else stop("the file named in thermo$opt$Berman (", userfile, ") does not exist")
+ } else stop("the file named in thermo()$opt$Berman (", userfile, ") does not exist")
}
}
# remove duplicates (only the first, i.e. most recent entry is kept)
@@ -46,7 +46,7 @@
irow <- which(dat$name == name)
if(length(irow)==0) {
if(userfileexists) stop("Data for ", name, " not available. Please add it to ", userfile)
- if(!userfileexists) stop("Data for ", name, " not available. Please add it to your_data_file.csv and run thermo$OBIGT$Berman <<- 'path/to/your_data_file.csv'")
+ if(!userfileexists) stop("Data for ", name, " not available. Please add it to your_data_file.csv and run thermo('opt$Berman' = 'path/to/your_data_file.csv')")
}
# the function works fine with just the following assign() call,
# but an explicit dummy assignment here is used to avoid "Undefined global functions or variables" in R CMD check
@@ -55,7 +55,7 @@
k4 <- k5 <- k6 <- l1 <- l2 <- v1 <- v2 <- v3 <- v4 <- NA
# assign values to the variables used below
for(i in 1:ncol(dat)) assign(colnames(dat)[i], dat[irow, i])
- # get the entropy of the elements using the chemical formula in thermo$OBIGT
+ # get the entropy of the elements using the chemical formula in thermo()$OBIGT
if(is.null(thisinfo)) thisinfo <- info(info(name, "cr", check.it=FALSE))
SPrTr_elements <- convert(entropy(thisinfo$formula), "J")
# check that G in data file is the G of formation from the elements --> Benson-Helgeson convention (DG = DH - T*DS)
Modified: pkg/CHNOSZ/R/cgl.R
===================================================================
--- pkg/CHNOSZ/R/cgl.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/cgl.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -15,7 +15,7 @@
# the parameters for *this* species
PAR <- parameters[k, ]
if(all(is.na(PAR[9:21]))) {
- # use Berman equations (parameters not in thermo$OBIGT)
+ # use Berman equations (parameters not in thermo()$OBIGT)
properties <- berman(PAR$name, T=T, P=P, thisinfo=PAR)
iprop <- match(property, colnames(properties))
values <- properties[, iprop, drop=FALSE]
@@ -28,7 +28,7 @@
values <- data.frame(matrix(NA, ncol = length(property), nrow=ncond))
colnames(values) <- property
# a test for availability of heat capacity coefficients (a, b, c, d, e, f)
- # based on the column assignments in thermo$OBIGT
+ # based on the column assignments in thermo()$OBIGT
if(any(!is.na(PAR[, 14:19]))) {
# we have at least one of the heat capacity coefficients;
# zero out any NA's in the rest (leave lambda and T of transition (columns 19-20) alone)
@@ -85,7 +85,7 @@
if(property[i] == "H") values[, i] <- PAR$H + intCpdT + intVdP - T*intdVdTdP
if(property[i] == "S") values[, i] <- PAR$S + intCpdlnT - intdVdTdP
}
- } # end calculations using parameters from thermo$OBIGT
+ } # end calculations using parameters from thermo()$OBIGT
out[[k]] <- values
} # end loop over species
return(out)
Modified: pkg/CHNOSZ/R/equilibrate.R
===================================================================
--- pkg/CHNOSZ/R/equilibrate.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/equilibrate.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -349,7 +349,7 @@
# (default if balance is missing and all species are proteins)
# 1 - balanced on one mole of species
# numeric vector - user-defined n.balance
- # "volume" - standard-state volume listed in thermo$OBIGT
+ # "volume" - standard-state volume listed in thermo()$OBIGT
# the index of the basis species that might be balanced
ibalance <- numeric()
# deal with proteins
Modified: pkg/CHNOSZ/R/hkf.R
===================================================================
--- pkg/CHNOSZ/R/hkf.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/hkf.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -52,7 +52,7 @@
# loop over each species
PAR <- parameters[k, ]
# substitute Cp and V for missing EoS parameters
- # here we assume that the parameters are in the same position as in thermo$OBIGT
+ # here we assume that the parameters are in the same position as in thermo()$OBIGT
# we don't need this if we're just looking at solvation properties (Cp_s_var, V_s_var)
if("n" %in% contrib) {
# put the heat capacity in for c1 if both c1 and c2 are missing
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/info.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -10,7 +10,7 @@
#source("util.data.R")
info <- function(species=NULL, state=NULL, check.it=TRUE) {
- ## return information for one or more species in thermo$OBIGT
+ ## return information for one or more species in thermo()$OBIGT
thermo <- get("thermo", CHNOSZ)
# that should give us the data, not the thermo() function 20190928
if(is.function(thermo)) stop("CHNOSZ package data is not available; use reset() or library(CHNOSZ) to load it")
@@ -17,11 +17,11 @@
## if no species are requested, summarize the available data 20101129
if(is.null(species)) {
message("info: 'species' is NULL; summarizing information about thermodynamic data...")
- message(paste("thermo$OBIGT has", nrow(thermo$OBIGT[thermo$OBIGT$state=="aq", ]), "aqueous,",
+ message(paste("thermo()$OBIGT has", nrow(thermo$OBIGT[thermo$OBIGT$state=="aq", ]), "aqueous,",
nrow(thermo$OBIGT), "total species"))
message(paste("number of literature sources: ", nrow(thermo$refs), ", elements: ",
nrow(thermo$element), ", buffers: ", length(unique(thermo$buffers$name)), sep=""))
- message(paste("number of proteins in thermo$protein is", nrow(thermo$protein), "from",
+ message(paste("number of proteins in thermo()$protein is", nrow(thermo$protein), "from",
length(unique(thermo$protein$organism)), "organisms"))
return()
}
@@ -77,14 +77,14 @@
}
info.character <- function(species, state=NULL, check.protein=TRUE) {
- # returns the rownumbers of thermo$OBIGT having an exact match of 'species' to
- # thermo$OBIGT$[species|abbrv|formula] or NA otherwise
- # a match to thermo$OBIGT$state is also required if 'state' is not NULL
+ # returns the rownumbers of thermo()$OBIGT having an exact match of 'species' to
+ # thermo()$OBIGT$[species|abbrv|formula] or NA otherwise
+ # a match to thermo()$OBIGT$state is also required if 'state' is not NULL
# (first occurence of a match to species is returned otherwise)
thermo <- get("thermo", CHNOSZ)
# find matches for species name, abbreviation or formula
matches.species <- thermo$OBIGT$name==species | thermo$OBIGT$abbrv==species | thermo$OBIGT$formula==species
- # since thermo$OBIGT$abbrv contains NAs, convert NA results to FALSE
+ # since thermo()$OBIGT$abbrv contains NAs, convert NA results to FALSE
matches.species[is.na(matches.species)] <- FALSE
# turn it in to no match if it's a protein in the wrong state
ip <- pinfo(species)
@@ -98,7 +98,7 @@
if(check.protein) {
# did we find a protein? add its properties to OBIGT
if(!is.na(ip)) {
- # here we use a default state from thermo$opt$state
+ # here we use a default state from thermo()$opt$state
if(is.null(state)) state <- thermo$opt$state
# add up protein properties
eos <- protein.OBIGT(ip, state=state)
@@ -182,7 +182,7 @@
# species indices must be in range
ispeciesmax <- nrow(thermo$OBIGT)
if(ispecies > ispeciesmax | ispecies < 1)
- stop(paste("species index", ispecies, "not found in thermo$OBIGT\n"))
+ stop(paste("species index", ispecies, "not found in thermo()$OBIGT\n"))
# remove scaling factors on EOS parameters depending on state
# use new OBIGT2eos function here
this <- OBIGT2eos(this, this$state)
Modified: pkg/CHNOSZ/R/ionize.aa.R
===================================================================
--- pkg/CHNOSZ/R/ionize.aa.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/ionize.aa.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -17,7 +17,7 @@
# turn charges into a matrix with as many rows as T,P,pH conditions
charges <- c(-1, -1, -1, 1, 1, 1, -1, 1, -1)
charges <- matrix(rep(charges, lmax), nrow=lmax, byrow=TRUE)
- # the rownumbers of the ionizable groups in thermo$OBIGT
+ # the rownumbers of the ionizable groups in thermo()$OBIGT
neutral <- c("[Cys]", "[Asp]", "[Glu]", "[His]", "[Lys]", "[Arg]", "[Tyr]", "[AABB]", "[AABB]")
charged <- c("[Cys-]","[Asp-]","[Glu-]","[His+]","[Lys+]","[Arg+]","[Tyr-]","[AABB+]","[AABB-]")
ineutral <- info(neutral, "aq")
Modified: pkg/CHNOSZ/R/makeup.R
===================================================================
--- pkg/CHNOSZ/R/makeup.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/makeup.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -58,7 +58,7 @@
}
# if the formula argument is numeric,
# and if the thermo object is available,
- # get the formula of that numbered species from thermo$OBIGT
+ # get the formula of that numbered species from thermo()$OBIGT
if(exists("CHNOSZ")) {
thermo <- get("thermo", CHNOSZ)
if(is.numeric(formula)) formula <- thermo$OBIGT$formula[formula]
@@ -89,7 +89,7 @@
# complain if there are any elements that look strange
if(exists("CHNOSZ")) {
are.elements <- names(out) %in% thermo$element$element
- if(!all(are.elements)) warning(paste("element(s) not in thermo$element:",
+ if(!all(are.elements)) warning(paste("element(s) not in thermo()$element:",
paste(names(out)[!are.elements], collapse=" ") ))
}
# done!
Modified: pkg/CHNOSZ/R/nonideal.R
===================================================================
--- pkg/CHNOSZ/R/nonideal.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/nonideal.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -30,7 +30,7 @@
# check if we have a valid method setting
if(!method %in% c("Alberty", "Bdot", "Bdot0", "bgamma", "bgamma0")) {
- if(missing(method)) stop("invalid setting (", thermo$opt$nonideal, ") in thermo$opt$nonideal")
+ if(missing(method)) stop("invalid setting (", thermo$opt$nonideal, ") in thermo()$opt$nonideal")
else stop("invalid method (", thermo$opt$nonideal, ")")
}
Modified: pkg/CHNOSZ/R/palply.R
===================================================================
--- pkg/CHNOSZ/R/palply.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/palply.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -1,7 +1,7 @@
# CHNOSZ/palply.R
palply <- function(varlist, X, FUN, ...) {
- # a wrapper function to run parLapply if length(X) >= thermo$opt$paramin
+ # a wrapper function to run parLapply if length(X) >= thermo()$opt$paramin
# and package 'parallel' is available, otherwise run lapply
if(length(X) >= get("thermo", CHNOSZ)$opt$paramin) {
# Use option mc.cores to choose an appropriate cluster size.
Modified: pkg/CHNOSZ/R/protein.info.R
===================================================================
--- pkg/CHNOSZ/R/protein.info.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/protein.info.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -1,7 +1,7 @@
# CHNOSZ/protein.info.R
# calculate formulas and summarize properties of proteins
-# pinfo: find rownumber in thermo$protein
+# pinfo: find rownumber in thermo()$protein
# protein.length: lengths of the indicated proteins
# protein.formula: chemical makeup of the indicated proteins
# protein.OBIGT: perform group additivity calculations
@@ -11,15 +11,15 @@
pinfo <- function(protein, organism=NULL, residue=FALSE, regexp=FALSE) {
# return the `protein` (possibly per residue) for:
# dataframe `protein`
- # return the rownumber(s) of thermo$protein for:
+ # return the rownumber(s) of thermo()$protein for:
# character `protein`, e.g. LYSC_CHICK
# character `protein` and `organism`, e.g. 'LYSC', 'CHICK'
- # return the row(s) of thermo$protein (possibly per residue) for:
+ # return the row(s) of thermo()$protein (possibly per residue) for:
# numeric `protein` (the rownumber itself)
if(is.data.frame(protein)) out <- protein
if(is.numeric(protein)) {
t_p <- get("thermo", CHNOSZ)$protein
- # drop NA matches to thermo$protein
+ # drop NA matches to thermo()$protein
iproteins <- 1:nrow(t_p)
protein[!protein %in% iproteins] <- NA
# get amino acid counts
@@ -37,7 +37,7 @@
if(!is.null(organism)) iorganism <- grepl(organism, t_p$organism)
iprotein <- which(iprotein & iorganism)
} else {
- # search for protein or protein_organism in thermo$protein
+ # search for protein or protein_organism in thermo()$protein
t_p_names <- paste(t_p$protein, t_p$organism, sep="_")
if(is.null(organism)) my_names <- protein
else my_names <- paste(protein, organism, sep="_")
@@ -77,12 +77,12 @@
groups <- c("AABB", colnames(aa)[6:25], bbgroup)
# put brackets around the group names
groups <- paste("[", groups, "]", sep="")
- # the rownumbers of the groups in thermo$OBIGT
+ # the rownumbers of the groups in thermo()$OBIGT
groups_state <- paste(groups, state)
OBIGT <- get("thermo", CHNOSZ)$OBIGT
OBIGT_state <- paste(OBIGT$name, OBIGT$state)
igroup <- match(groups_state, OBIGT_state)
- # the properties are in columns 9-21 of thermo$OBIGT
+ # the properties are in columns 9-21 of thermo()$OBIGT
groupprops <- OBIGT[igroup, 9:21]
# the elements in each of the groups
groupelements <- i2A(igroup)
@@ -163,7 +163,7 @@
# get some general information about the proteins
pname <- paste(aa$protein, aa$organism, sep="_")
plength <- protein.length(aa)
- # use thermo$basis to decide whether to ionize the proteins
+ # use thermo()$basis to decide whether to ionize the proteins
thermo <- get("thermo", CHNOSZ)
ionize.it <- FALSE
iword <- "nonionized"
Modified: pkg/CHNOSZ/R/species.R
===================================================================
--- pkg/CHNOSZ/R/species.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/species.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -5,7 +5,7 @@
species <- function(species=NULL, state=NULL, delete=FALSE, index.return=FALSE) {
# 20080925 default quiet=TRUE 20101003 default quiet=FALSE
# 20120128 remove 'quiet' argument (messages can be hidden with suppressMessages())
- # 20120523 return thermo$species instead of rownumbers therein, and remove message showing thermo$species
+ # 20120523 return thermo()$species instead of rownumbers therein, and remove message showing thermo()$species
thermo <- get("thermo", CHNOSZ)
## argument processing
# we can't deal with NA species
@@ -72,15 +72,15 @@
ispecies <- match(species, thermo$species$name)
# if all species names match, and logact is given, re-call the function with the species indices
if(!any(is.na(ispecies)) & !is.null(logact)) return(species(ispecies, state=logact, index.return=index.return))
- # look for species in thermo$OBIGT
+ # look for species in thermo()$OBIGT
iOBIGT <- suppressMessages(info(species, state))
- # since that could have updated thermo$OBIGT (with proteins), re-read thermo
+ # since that could have updated thermo()$OBIGT (with proteins), re-read thermo
thermo <- get("thermo", CHNOSZ)
# check if we got all the species
ina <- is.na(iOBIGT)
if(any(ina)) stop(paste("species not available:", paste(species[ina], collapse=" ")))
} else {
- # if species is numeric and low number it refers to the index of existing species, else to thermo$OBIGT
+ # if species is numeric and low number it refers to the index of existing species, else to thermo()$OBIGT
nspecies <- nrow(thermo$species)
if(is.null(thermo$species)) nspecies <- 0
if(max(species) > nspecies) iOBIGT <- species
@@ -117,7 +117,7 @@
rownames(thermo$species) <- seq(nrow(thermo$species))
} else {
# update activities or states of existing species
- # first get the rownumbers in thermo$species
+ # first get the rownumbers in thermo()$species
if(is.numeric(species[1])) {
ispecies <- species
# if state and logact are both NULL we don't do anything but return the selected species
Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/subcrt.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -135,9 +135,9 @@
# get the species index for a named species
if(!can.be.numeric(species[i])) si <- info.character(species[i], state[i])
else {
- # check that a numeric argument is a rownumber of thermo$OBIGT
+ # check that a numeric argument is a rownumber of thermo()$OBIGT
si <- as.numeric(species[i])
- if(!si %in% 1:nrow(thermo$OBIGT)) stop(paste(species[i], "is not a row number of thermo$OBIGT"))
+ if(!si %in% 1:nrow(thermo$OBIGT)) stop(paste(species[i], "is not a row number of thermo()$OBIGT"))
}
# that could have the side-effect of adding a protein; re-read thermo
thermo <- get("thermo", CHNOSZ)
@@ -351,7 +351,7 @@
# if we are considering multiple phases, and if this phase is cr2 or higher, check if we're below the transition temperature
if(length(iphases) > length(ispecies) & i > 1) {
if(!(reaction$state[i] %in% c('liq','cr','gas')) & reaction$name[i-1] == reaction$name[i]) {
- # after add.OBIGT("SUPCRT92"), quartz cr and cr2 are not next to each other in thermo$OBIGT,
+ # after add.OBIGT("SUPCRT92"), quartz cr and cr2 are not next to each other in thermo()$OBIGT,
# so use iphases[i-1] here, not iphases[i]-1 20181107
Ttr <- Ttr(iphases[i-1], iphases[i], P=P, dPdT = dPdTtr(iphases[i-1], iphases[i]))
if(all(is.na(Ttr))) next
Modified: pkg/CHNOSZ/R/swap.basis.R
===================================================================
--- pkg/CHNOSZ/R/swap.basis.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/swap.basis.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -16,7 +16,7 @@
# matrix part of the basis definition
basis.mat <- basis.elements(basis)
# the standard Gibbs energies of the basis species
- # don't take it from thermo$OBIGT, even at 25 degC, because G for H2O is NA there
+ # don't take it from thermo()$OBIGT, even at 25 degC, because G for H2O is NA there
# the sapply(..., "[", 1) is needed to get the first value, in case subcrt appends a polymorph column (i.e. for S(cr)) 20171105
G <- unlist(sapply(subcrt(basis$ispecies, T=T, property="G")$out, "[", 1))
# chemical potentials of the basis species
@@ -39,7 +39,7 @@
# check that elements of basis.mat and emu are identical
if(any(is.na(ielem))) stop(paste("element(s)", paste(names(emu)[is.na(ielem)], collapse=" "), "not found in basis"))
# the standard Gibbs energies of the basis species
- # don't take it from thermo$OBIGT, even at 25 degC, because G for H2O is NA there
+ # don't take it from thermo()$OBIGT, even at 25 degC, because G for H2O is NA there
# the sapply(..., "[", 1) is needed to get the first value, in case subcrt appends a polymorph column (i.e. for S(cr)) 20171105
G <- unlist(sapply(subcrt(basis$ispecies, T=T, property="G")$out, "[", 1))
# the chemical potentials of the basis species in equilibrium
@@ -89,7 +89,7 @@
if(is.numeric(species2)) ispecies2 <- species2
else ispecies2 <- suppressMessages(info(species2))
if(is.na(ispecies2) | is.list(ispecies2))
- stop(paste("a species matching '",species2,"' is not available in thermo$OBIGT",sep=""))
+ stop(paste("a species matching '",species2,"' is not available in thermo()$OBIGT",sep=""))
# try to load the new basis species
ispecies <- oldbasis$ispecies
ispecies[ib] <- ispecies2
Modified: pkg/CHNOSZ/R/util.affinity.R
===================================================================
--- pkg/CHNOSZ/R/util.affinity.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.affinity.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -207,7 +207,7 @@
# which species are proteins
isprotein <- grepl("_", myspecies$name)
if(any(isprotein)) {
- # the rownumbers in thermo$protein
+ # the rownumbers in thermo()$protein
ip <- pinfo(myspecies$name[isprotein])
# get the affinity of ionization
iHplus <- match("H+", rownames(mybasis))
Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.data.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -28,7 +28,7 @@
# remove the last (URL) component
#x$URL <- NULL
x <- x[1:5]
- # count the number of times each source is cited in thermo$OBIGT
+ # count the number of times each source is cited in thermo()$OBIGT
# e.g. if key is "Kel60" we match "Kel60 [S92]" but not "Kel60.1 [S92]"
# http://stackoverflow.com/questions/6713310/how-to-specify-space-or-end-of-string-and-space-or-start-of-string
# we also have to escape keys with "+" signs
@@ -394,7 +394,7 @@
### unexported functions ###
-# Take a data frame in the format of thermo$OBIGT of one or more rows,
+# Take a data frame in the format of thermo()$OBIGT of one or more rows,
# remove scaling factors from equations-of-state parameters,
# and apply new column names depending on the state.
# And convert energy units from J to cal (used by subcrt()) 20190530
Modified: pkg/CHNOSZ/R/util.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.expression.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -15,7 +15,7 @@
if(use.makeup) {
# the counts of elements in the species:
# here we don't care too much if an "element" is a real element
- # (listed in thermo$element), so we suppress warnings
+ # (listed in thermo()$element), so we suppress warnings
elements <- suppressWarnings(try(makeup(species), TRUE))
} else elements <- split.formula(species)
# if species can't be parsed as a chemical formula, we don't do the formula formatting
Modified: pkg/CHNOSZ/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.fasta.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -8,7 +8,7 @@
# read.fasta in package seqinR
# value of 'iseq' is what sequences to read (default is all)
# value of 'ret' determines format of return value:
- # count: amino acid composition (same columns as thermo$protein, can be used by add.protein)
+ # count: amino acid composition (same columns as thermo()$protein, can be used by add.protein)
# or nucleic acid base composition (A-C-G-T)
# seq: amino acid sequence
# fas: fasta entry
@@ -155,7 +155,7 @@
else if(type=="DNA") letts <- c("A", "C", "G", "T")
else if(type=="RNA") letts <- c("A", "C", "G", "U")
else stop(paste("unknown sequence type", type))
- # the numerical positions of the letters in alphabetical order (i.e. for amino acids, same order as in thermo$protein)
+ # the numerical positions of the letters in alphabetical order (i.e. for amino acids, same order as in thermo()$protein)
ilett <- match(letts, LETTERS)
# the letters A-Z represented by raw values
rawAZ <- charToRaw("ABCDEFGHIJKLMNOPQRSTUVWXYZ")
Modified: pkg/CHNOSZ/R/util.formula.R
===================================================================
--- pkg/CHNOSZ/R/util.formula.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.formula.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -17,7 +17,7 @@
# convert formulas into a stoichiometric matrix with elements on the columns
A <- t(sapply(msz, c))
# add names from character argument
- # or from thermo$OBIGT for numeric argument
+ # or from thermo()$OBIGT for numeric argument
if(is.numeric(formula[1])) rownames(A) <- get("thermo", CHNOSZ)$OBIGT$name[formula]
else rownames(A) <- formula
}
@@ -64,7 +64,7 @@
formula <- i2A(get.formula(formula))
ielem <- match(colnames(formula), thermo$element$element)
if(any(is.na(ielem))) stop(paste("element(s)",
- colnames(formula)[is.na(ielem)], "not available in thermo$element"))
+ colnames(formula)[is.na(ielem)], "not available in thermo()$element"))
mass <- as.numeric(formula %*% thermo$element$mass[ielem])
return(mass)
}
@@ -75,7 +75,7 @@
formula <- i2A(get.formula(formula))
ielem <- match(colnames(formula), thermo$element$element)
if(any(is.na(ielem))) warning(paste("element(s)",
- paste(colnames(formula)[is.na(ielem)], collapse=" "), "not available in thermo$element"))
+ paste(colnames(formula)[is.na(ielem)], collapse=" "), "not available in thermo()$element"))
# entropy per atom
Sn <- thermo$element$s[ielem] / thermo$element$n[ielem]
# if there are any NA values of entropy, put NA in the matrix, then set the value to zero
@@ -157,7 +157,7 @@
# Accept a numeric or character argument; the character argument can be mixed
# (i.e. include quoted numbers). as.numeric is tested on every value; numeric values
-# are then interpreted as species indices in the thermodynamic database (rownumbers of thermo$OBIGT),
+# are then interpreted as species indices in the thermodynamic database (rownumbers of thermo()$OBIGT),
# and the chemical formulas for those species are returned.
# Values that can not be converted to numeric are returned as-is.
get.formula <- function(formula) {
@@ -168,17 +168,17 @@
if(is.data.frame(formula)) return(as.matrix(formula))
# return the values in the argument, or chemical formula(s)
# for values that are species indices
- # for numeric values, get the formulas from those rownumbers of thermo$OBIGT
+ # for numeric values, get the formulas from those rownumbers of thermo()$OBIGT
i <- as.integer.nowarn(formula)
- # we can't have more than the number of rows in thermo$OBIGT
+ # we can't have more than the number of rows in thermo()$OBIGT
thermo <- get("thermo", CHNOSZ)
iover <- i > nrow(thermo$OBIGT)
iover[is.na(iover)] <- FALSE
if(any(iover)) stop(paste("species number(s)",paste(i[iover],collapse=" "),
- "not available in thermo$OBIGT"))
+ "not available in thermo()$OBIGT"))
# we let negative numbers pass as formulas
i[i < 0] <- NA
- # replace any species indices with formulas from thermo$OBIGT
+ # replace any species indices with formulas from thermo()$OBIGT
formula[!is.na(i)] <- thermo$OBIGT$formula[i[!is.na(i)]]
return(formula)
}
Modified: pkg/CHNOSZ/R/util.plot.R
===================================================================
--- pkg/CHNOSZ/R/util.plot.R 2020-07-04 09:22:47 UTC (rev 544)
+++ pkg/CHNOSZ/R/util.plot.R 2020-07-05 08:04:45 UTC (rev 545)
@@ -6,7 +6,7 @@
las=1,xline=NULL, grid = "", col.grid = "gray", ...) {
# start a new plot with some customized settings
thermo <- get("thermo", CHNOSZ)
- # 20120523 store the old par in thermo$opar
+ # 20120523 store the old par in thermo()$opar
if(is.null(thermo$opar)) {
thermo$opar <- par(no.readonly=TRUE)
assign("thermo", thermo, CHNOSZ)
Modified: pkg/CHNOSZ/R/util.seq.R
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 545
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