[CHNOSZ-commits] r793 - in pkg/CHNOSZ: . R inst inst/extdata/adds man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jun 24 02:59:45 CEST 2023
Author: jedick
Date: 2023-06-24 02:59:45 +0200 (Sat, 24 Jun 2023)
New Revision: 793
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/Berman.R
pkg/CHNOSZ/R/DEW.R
pkg/CHNOSZ/R/IAPWS95.R
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/buffer.R
pkg/CHNOSZ/R/cgl.R
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/equilibrate.R
pkg/CHNOSZ/R/examples.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/mix.R
pkg/CHNOSZ/R/mosaic.R
pkg/CHNOSZ/R/nonideal.R
pkg/CHNOSZ/R/palply.R
pkg/CHNOSZ/R/protein.info.R
pkg/CHNOSZ/R/retrieve.R
pkg/CHNOSZ/R/solubility.R
pkg/CHNOSZ/R/species.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/R/swap.basis.R
pkg/CHNOSZ/R/taxonomy.R
pkg/CHNOSZ/R/thermo.R
pkg/CHNOSZ/R/util.affinity.R
pkg/CHNOSZ/R/util.args.R
pkg/CHNOSZ/R/util.array.R
pkg/CHNOSZ/R/util.character.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.misc.R
pkg/CHNOSZ/R/util.plot.R
pkg/CHNOSZ/R/util.protein.R
pkg/CHNOSZ/R/util.seq.R
pkg/CHNOSZ/R/util.units.R
pkg/CHNOSZ/R/water.R
pkg/CHNOSZ/R/zzz.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/man/util.data.Rd
pkg/CHNOSZ/vignettes/FAQ.Rmd
Log:
Add spaces around equals signs
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/DESCRIPTION 2023-06-24 00:59:45 UTC (rev 793)
@@ -1,6 +1,6 @@
-Date: 2023-06-23
+Date: 2023-06-24
Package: CHNOSZ
-Version: 2.0.0-12
+Version: 2.0.0-13
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/Berman.R
===================================================================
--- pkg/CHNOSZ/R/Berman.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/Berman.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -4,14 +4,14 @@
# in the system Na2O-K2O-CaO-MgO-FeO-Fe2O3-Al2O3-SiO2-TiO2-H2O-CO2.
# J. Petrol. 29, 445-522. https://doi.org/10.1093/petrology/29.2.445
-Berman <- function(name, T = 298.15, P = 1, check.G=FALSE, calc.transition=TRUE, calc.disorder=TRUE) {
+Berman <- function(name, T = 298.15, P = 1, check.G = FALSE, calc.transition = TRUE, calc.disorder = TRUE) {
# Reference temperature and pressure
Pr <- 1
Tr <- 298.15
# Make T and P the same length
ncond <- max(length(T), length(P))
- T <- rep(T, length.out=ncond)
- P <- rep(P, length.out=ncond)
+ T <- rep(T, length.out = ncond)
+ P <- rep(P, length.out = ncond)
# Get parameters in the Berman equations
# Start with thermodynamic parameters provided with CHNOSZ
@@ -20,10 +20,10 @@
userfile <- get("thermo", CHNOSZ)$opt$Berman
userfileexists <- FALSE
if(!is.na(userfile)) {
- if(userfile!="") {
+ if(userfile != "") {
if(file.exists(userfile)) {
userfileexists <- TRUE
- BDat_user <- read.csv(userfile, as.is=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")
}
@@ -38,7 +38,7 @@
if(missing(name)) return(dat) else {
# Which row has data for this mineral?
irow <- which(dat$name == name)
- if(length(irow)==0) {
+ if(length(irow) == 0) {
if(userfileexists) stop("Data for ", name, " not available. Please add it to ", userfile)
if(!userfileexists) stop("Data for ", name, " not available. Please add it to your_data_file.csv and run thermo('opt$Berman' = 'path/to/your_data_file.csv')")
}
@@ -62,7 +62,7 @@
Gdiff <- GfPrTr_calc - GfPrTr
#if(is.na(GfPrTr)) warning(paste0(name, ": GfPrTr(table) is NA"), call.=FALSE)
if(!is.na(GfPrTr)) if(abs(Gdiff) >= 1000) warning(paste0(name, ": GfPrTr(calc) - GfPrTr(table) is too big! == ",
- round(GfPrTr_calc - GfPrTr), " J/mol"), call.=FALSE)
+ round(GfPrTr_calc - GfPrTr), " J/mol"), call. = FALSE)
# (the tabulated GfPrTr is unused below)
}
Modified: pkg/CHNOSZ/R/DEW.R
===================================================================
--- pkg/CHNOSZ/R/DEW.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/DEW.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -47,8 +47,8 @@
calculateDensity
}
# Make input pressure and temperature the same length
- if(length(pressure) < length(temperature)) pressure <- rep(pressure, length.out=length(temperature))
- if(length(temperature) < length(pressure)) temperature <- rep(temperature, length.out=length(pressure))
+ if(length(pressure) < length(temperature)) pressure <- rep(pressure, length.out = length(temperature))
+ if(length(temperature) < length(pressure)) temperature <- rep(temperature, length.out = length(pressure))
# Use a loop to process vectorized input
sapply(1:length(pressure), function(i) myfunction(pressure[i], temperature[i]))
}
@@ -88,8 +88,8 @@
GAtOneKb + integral
}
# Make input pressure and temperature the same length
- if(length(pressure) < length(temperature)) pressure <- rep(pressure, length.out=length(temperature))
- if(length(temperature) < length(pressure)) temperature <- rep(temperature, length.out=length(pressure))
+ if(length(pressure) < length(temperature)) pressure <- rep(pressure, length.out = length(temperature))
+ if(length(temperature) < length(pressure)) temperature <- rep(temperature, length.out = length(pressure))
# Use a loop to process vectorized input
sapply(1:length(pressure), function(i) myfunction(pressure[i], temperature[i]))
}
@@ -223,7 +223,7 @@
omega <- eta * (Z * Z / re - Z / (3.082 + g))
# 'If species is hydrogen, the species is neutral, or the pressure is above 6 kb,
# 'this equation is not necessary because omega is very close to wref.
- if(Z==0) omega[] <- wref
+ if(Z == 0) omega[] <- wref
omega[pressure > 6000] <- wref
}
Modified: pkg/CHNOSZ/R/IAPWS95.R
===================================================================
--- pkg/CHNOSZ/R/IAPWS95.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/IAPWS95.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -1,6 +1,6 @@
# Calculate properties of water using the IAPWS-95 formulation (Wagner and Pruss, 2002)
-IAPWS95 <- function(property,T=298.15,rho=1000) {
+IAPWS95 <- function(property,T = 298.15,rho = 1000) {
property <- tolower(property)
# Triple point
T.triple <- 273.16 # K
@@ -95,7 +95,7 @@
t <- c(t,get(property[j])())
}
t <- data.frame(t)
- if(j==1) ww <- t else ww <- cbind(ww,t)
+ if(j == 1) ww <- t else ww <- cbind(ww,t)
}
colnames(ww) <- property
return(ww)
Modified: pkg/CHNOSZ/R/add.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/add.OBIGT.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/add.OBIGT.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -15,7 +15,7 @@
if(is.list(args[[1]])) args <- args[[1]]
if(length(args) < 2) stop("please supply at least a species name and a property to update")
if(is.null(names(args))) stop("all arguments after the first should be named")
- if(any(tail(nchar(names(args)), -1)==0)) stop("all arguments after the first should be named")
+ if(any(tail(nchar(names(args)), -1) == 0)) stop("all arguments after the first should be named")
# If the first argument is numeric, it's the species index
if(is.numeric(args[[1]][1])) {
ispecies <- args[[1]]
@@ -23,7 +23,7 @@
speciesname <- info(ispecies, check.it = FALSE)$name
} else {
# If the name of the first argument is missing, assume it's the species name
- if(names(args)[1]=="") names(args)[1] <- "name"
+ if(names(args)[1] == "") names(args)[1] <- "name"
speciesname <- args$name
# Search for this species, use check.protein = FALSE to avoid infinite loop when adding proteins
# and suppressMessages to not show messages about matches of this name to other states
@@ -33,10 +33,10 @@
species = args$name, check.protein = FALSE, SIMPLIFY = TRUE, USE.NAMES = FALSE))
}
# The column names of thermo()$OBIGT, split at the "."
- cnames <- c(do.call(rbind, strsplit(colnames(thermo$OBIGT), ".", fixed=TRUE)), colnames(thermo$OBIGT))
+ cnames <- c(do.call(rbind, strsplit(colnames(thermo$OBIGT), ".", fixed = TRUE)), colnames(thermo$OBIGT))
# The columns we are updating
icol <- match(names(args), cnames)
- if(any(is.na(icol))) stop(paste("properties not in thermo$OBIGT:", paste(names(args)[is.na(icol)], collapse=" ")) )
+ if(any(is.na(icol))) stop(paste("properties not in thermo$OBIGT:", paste(names(args)[is.na(icol)], collapse = " ")) )
# The column numbers for properties that matched after the split
icol[icol > 44] <- icol[icol > 44] - 44
icol[icol > 22] <- icol[icol > 22] - 22
@@ -44,7 +44,7 @@
inew <- which(is.na(ispecies))
iold <- which(!is.na(ispecies))
# The arguments as data frame
- args <- data.frame(args, stringsAsFactors=FALSE)
+ args <- data.frame(args, stringsAsFactors = FALSE)
if(length(inew) > 0) {
# The right number of blank rows of thermo()$OBIGT
newrows <- thermo$OBIGT[1:length(inew), ]
@@ -62,7 +62,7 @@
namodel <- is.na(newrows$model)
if(any(namodel)) newrows$model[namodel] <- ifelse(newrows$state[namodel] == "aq", "HKF", "CGL")
# Now check the formulas
- e <- tryCatch(makeup(newrows$formula), error=function(e) e)
+ e <- tryCatch(makeup(newrows$formula), error = function(e) e)
if(inherits(e, "error")) {
warning("please supply a valid chemical formula as the species name or in the 'formula' argument")
# Transmit the error from makeup
@@ -76,7 +76,8 @@
ntotal <- nrow(thermo$OBIGT)
ispecies[inew] <- (ntotal-length(inew)+1):ntotal
# Inform user
- message(paste("mod.OBIGT: added ", newrows$name, "(", newrows$state, ")", " with ", newrows$model, " model and energy units of ", newrows$E_units, sep="", collapse="\n"))
+ message(paste("mod.OBIGT: added ", newrows$name, "(", newrows$state, ")", " with ", newrows$model,
+ " model and energy units of ", newrows$E_units, sep = "", collapse = "\n"))
}
if(length(iold) > 0) {
# Loop over species
@@ -108,19 +109,19 @@
return(ispecies)
}
-add.OBIGT <- function(file, species=NULL, force=TRUE) {
+add.OBIGT <- function(file, species = NULL, force = TRUE) {
# Add/replace entries in thermo$OBIGT from values saved in a file
- # Only replace if force==TRUE
+ # Only replace if force == TRUE
thermo <- get("thermo", CHNOSZ)
to1 <- thermo$OBIGT
id1 <- paste(to1$name,to1$state)
# We match system files with the file suffixes (.csv) removed
- sysfiles <- dir(system.file("extdata/OBIGT/", package="CHNOSZ"))
+ sysfiles <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ"))
sysnosuffix <- sapply(strsplit(sysfiles, "\\."), "[", 1)
isys <- match(file, sysnosuffix)
- if(!is.na(isys)) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package="CHNOSZ")
+ if(!is.na(isys)) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package = "CHNOSZ")
# Read data from the file
- to2 <- read.csv(file, as.is=TRUE)
+ to2 <- read.csv(file, as.is = TRUE)
Etxt <- paste(unique(to2$E_units), collapse = " and ")
# Load only selected species if requested
if(!is.null(species)) {
@@ -127,7 +128,7 @@
idat <- match(species, to2$name)
ina <- is.na(idat)
if(!any(ina)) to2 <- to2[idat, ]
- else stop(paste("file", file, "doesn't have", paste(species[ina], collapse=", ")))
+ else stop(paste("file", file, "doesn't have", paste(species[ina], collapse = ", ")))
}
id2 <- paste(to2$name,to2$state)
# Check if the data table is compatible with thermo$OBIGT
Modified: pkg/CHNOSZ/R/add.protein.R
===================================================================
--- pkg/CHNOSZ/R/add.protein.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/add.protein.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -56,7 +56,7 @@
aasum <- function(aa, abundance = 1, average = FALSE, protein = NULL, organism = NULL) {
# Returns the sum of the amino acid counts in aa,
# multiplied by the abundances of the proteins
- abundance <- rep(abundance, length.out=nrow(aa))
+ abundance <- rep(abundance, length.out = nrow(aa))
# Drop any NA rows or abundances
ina.aa <- is.na(aa$chains)
ina.ab <- is.na(abundance)
Modified: pkg/CHNOSZ/R/affinity.R
===================================================================
--- pkg/CHNOSZ/R/affinity.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/affinity.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -12,8 +12,8 @@
#source("util.data.R")
#source("species.R")
-affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rhomin=FALSE,
- return.buffer=FALSE, return.sout=FALSE, balance="PBB", iprotein=NULL, loga.protein=0, transect = NULL) {
+affinity <- function(..., property = NULL, sout = NULL, exceed.Ttr = FALSE, exceed.rhomin = FALSE,
+ return.buffer = FALSE, return.sout = FALSE, balance = "PBB", iprotein = NULL, loga.protein = 0, transect = NULL) {
# ...: variables over which to calculate
# property: what type of energy
# (G.basis,G.species,logact.basis,logK,logQ,A)
@@ -34,7 +34,7 @@
args.orig <- list(...)
# We can only do anything with at least one argument
if(length(args.orig) > 0) {
- if(identical(args.orig[[1]][1], list(fun="affinity"))) {
+ if(identical(args.orig[[1]][1], list(fun = "affinity"))) {
aargs <- args.orig[[1]]$args
# We can only update arguments given after the first argument
if(length(args.orig) > 1) {
@@ -49,7 +49,7 @@
# The argument list
args <- energy.args(args.orig, transect = transect)
- args <- c(args, list(sout=sout, exceed.Ttr=exceed.Ttr, exceed.rhomin=exceed.rhomin))
+ args <- c(args, list(sout = sout, exceed.Ttr = exceed.Ttr, exceed.rhomin = exceed.rhomin))
# The species we're given
thermo <- get("thermo", CHNOSZ)
@@ -77,7 +77,7 @@
# Add protein residues to the species list
resnames <- c("H2O",aminoacids(3))
# Residue activities set to zero; account for protein activities later
- resprot <- paste(resnames,"RESIDUE",sep="_")
+ resprot <- paste(resnames,"RESIDUE",sep = "_")
species(resprot, 0)
thermo <- get("thermo", CHNOSZ)
ires <- match(resprot, thermo$species$name)
@@ -93,7 +93,7 @@
buffer <- TRUE
message('affinity: loading buffer species')
if(!is.null(thermo$species)) is.species <- 1:nrow(thermo$species) else is.species <- numeric()
- is.buffer <- buffer(logK=NULL)
+ is.buffer <- buffer(logK = NULL)
thermo <- get("thermo", CHNOSZ)
is.buff <- numeric()
for(i in 1:length(is.buffer)) is.buff <- c(is.buff,as.numeric(is.buffer[[i]]))
@@ -117,7 +117,7 @@
logact.basis.new <- logact.basis <- do.call("energy",args)$a
ibasis.new <- numeric()
for(k in 1:length(buffers)) {
- ibasis <- which(as.character(mybasis$logact)==buffers[k])
+ ibasis <- which(as.character(mybasis$logact) == buffers[k])
# Calculate the logKs from the affinities
logK <- a
for(i in 1:length(logK)) {
@@ -126,8 +126,8 @@
logK[[i]] <- logK[[i]] - logact.basis.new[[j]] * thermo$species[i,j]
}
}
- lbn <- buffer(logK=logK,ibasis=ibasis,logact.basis=logact.basis.new,
- is.buffer=as.numeric(is.buffer[[which(names(is.buffer)==buffers[k])]]),balance=balance)
+ lbn <- buffer(logK = logK,ibasis = ibasis,logact.basis = logact.basis.new,
+ is.buffer = as.numeric(is.buffer[[which(names(is.buffer) == buffers[k])]]),balance = balance)
for(j in 1:length(logact.basis.new)) if(j %in% ibasis) logact.basis.new[[j]] <- lbn[[2]][[j]]
# Calculation of the buffered activities' effect on chemical affinities
is.only.buffer.new <- is.only.buffer[is.only.buffer %in% is.buffer[[k]]]
@@ -143,12 +143,12 @@
#if(!identical(a[[i]],aa)) print(paste(i,j))
}
}
- if(k==length(buffers) & return.buffer) {
+ if(k == length(buffers) & return.buffer) {
logact.basis.new <- lbn[[2]]
ibasis.new <- c(ibasis.new,lbn[[1]])
} else ibasis.new <- c(ibasis.new,ibasis)
}
- species(is.only.buffer,delete=TRUE)
+ species(is.only.buffer,delete = TRUE)
if(length(is.only.buffer) > 0) a <- a[-is.only.buffer]
# To return the activities of buffered basis species
tb <- logact.basis.new[unique(ibasis.new)]
@@ -159,9 +159,9 @@
for(i in 1:length(tb)) {
#tb[[i]] <- as.data.frame(tb[[i]])
if(nd > 0) rownames(tb[[i]]) <-
- seq(args$lims[[1]][1],args$lims[[1]][2],length.out=args$lims[[1]][3])
+ seq(args$lims[[1]][1],args$lims[[1]][2],length.out = args$lims[[1]][3])
if(nd > 1) colnames(tb[[i]]) <-
- seq(args$lims[[2]][1],args$lims[[2]][2],length.out=args$lims[[2]][3])
+ seq(args$lims[[2]][1],args$lims[[2]][2],length.out = args$lims[[2]][3])
}
}
}
@@ -171,7 +171,7 @@
if(!is.null(iprotein)) {
# Fast protein calculations 20090331
# Function to calculate affinity of formation reactions from those of residues
- loga.protein <- rep(loga.protein,length.out=length(iprotein))
+ loga.protein <- rep(loga.protein,length.out = length(iprotein))
protein.fun <- function(ip) {
tpext <- as.numeric(thermo$protein[iprotein[ip],5:25])
return(Reduce("+", pprod(a[ires],tpext)) - loga.protein[ip])
@@ -186,14 +186,14 @@
# The current species list, containing the residues
resspecies <- thermo$species
# Now we can delete the residues from the species list
- species(ires,delete=TRUE)
+ species(ires,delete = TRUE)
# State and protein names
state <- resspecies$state[1]
- name <- paste(thermo$protein$protein[iprotein],thermo$protein$organism[iprotein],sep="_")
+ name <- paste(thermo$protein$protein[iprotein],thermo$protein$organism[iprotein],sep = "_")
# The numbers of basis species in formation reactions of the proteins
protbasis <- t(t((resspecies[ires,1:nrow(mybasis)])) %*% t((thermo$protein[iprotein,5:25])))
# Put them together
- protspecies <- cbind(protbasis,data.frame(ispecies=ispecies,logact=loga.protein,state=state,name=name))
+ protspecies <- cbind(protbasis,data.frame(ispecies = ispecies,logact = loga.protein,state = state,name = name))
myspecies <- rbind(myspecies,protspecies)
rownames(myspecies) <- 1:nrow(myspecies)
## Update the affinity values
@@ -231,8 +231,8 @@
# they got converted to log_a(e-) at an unknown temperature
Eharg <- args.orig[[iEh]]
if(length(Eharg) > 3) Ehvals <- Eharg
- else if(length(Eharg) == 3) Ehvals <- seq(Eharg[1], Eharg[2], length.out=Eharg[3])
- else if(length(Eharg) == 2) Ehvals <- seq(Eharg[1], Eharg[2], length.out=256)
+ else if(length(Eharg) == 3) Ehvals <- seq(Eharg[1], Eharg[2], length.out = Eharg[3])
+ else if(length(Eharg) == 2) Ehvals <- seq(Eharg[1], Eharg[2], length.out = 256)
vals[[iEh]] <- Ehvals
}
# Get pe and pH
@@ -252,18 +252,18 @@
names(vals) <- vars
# Content of return value depends on buffer request
- if(return.buffer) return(c(tb, list(vars=vars, vals=vals)))
+ if(return.buffer) return(c(tb, list(vars = vars, vals = vals)))
# For argument recall, include all arguments (except sout) in output 20190117
- allargs <- c(args.orig, list(property=property, exceed.Ttr=exceed.Ttr, exceed.rhomin=exceed.rhomin,
- return.buffer=return.buffer, balance=balance, iprotein=iprotein, loga.protein=loga.protein))
+ allargs <- c(args.orig, list(property = property, exceed.Ttr = exceed.Ttr, exceed.rhomin = exceed.rhomin,
+ return.buffer = return.buffer, balance = balance, iprotein = iprotein, loga.protein = loga.protein))
# Add IS value only if it given as an argument 20171101
# (even if its value is 0, the presence of IS will trigger diagram() to use "m" instead of "a" in axis labels)
iIS <- match("IS", names(args.orig))
- if(!is.na(iIS)) a <- list(fun="affinity", args=allargs, sout=sout, property=property,
- basis=mybasis, species=myspecies, T=T, P=P, IS=args$IS, vars=vars, vals=vals, values=a)
- else a <- list(fun="affinity", args=allargs, sout=sout, property=property,
- basis=mybasis, species=myspecies, T=T, P=P, vars=vars, vals=vals, values=a)
- if(buffer) a <- c(a, list(buffer=tb))
+ if(!is.na(iIS)) a <- list(fun = "affinity", args = allargs, sout = sout, property = property,
+ basis = mybasis, species = myspecies, T = T, P = P, IS = args$IS, vars = vars, vals = vals, values = a)
+ else a <- list(fun = "affinity", args = allargs, sout = sout, property = property,
+ basis = mybasis, species = myspecies, T = T, P = P, vars = vars, vals = vals, values = a)
+ if(buffer) a <- c(a, list(buffer = tb))
return(a)
}
Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/basis.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -137,7 +137,7 @@
newbasis
}
-### unexported functions ###
+### Unexported functions ###
# To add the basis to thermo()$OBIGT
put.basis <- function(ispecies, logact = rep(NA, length(ispecies))) {
@@ -146,17 +146,17 @@
# Make the basis matrix, revised 20120114
# Get the elemental makeup of each species,
# counting zero for any element that only appears in other species in the set
- comp <- makeup(ispecies, count.zero=TRUE)
+ comp <- makeup(ispecies, count.zero = TRUE)
# Turn the list into a matrix
comp <- sapply(comp, c)
# Transpose to get put basis species on the rows
comp <- t(comp)
- # Note, makeup(count.zero=TRUE) above gave elements (colnames) sorted alphabetically
+ # Note, makeup(count.zero = TRUE) above gave elements (colnames) sorted alphabetically
# rownames identify the species
rownames(comp) <- as.character(thermo$OBIGT$formula[ispecies])
# FIXME: the electron doesn't look like a chemical formula
# This is needed for affinity() to understand a 'pe' or 'Eh' variable
- if("(Z-1)" %in% rownames(comp)) rownames(comp)[rownames(comp)=="(Z-1)"] <- "e-"
+ if("(Z-1)" %in% rownames(comp)) rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
# Now check it for validity of basis species
# The first test: matrix is square
if( nrow(comp) > ncol(comp) ) {
@@ -172,7 +172,7 @@
stop("singular stoichiometric matrix")
# Store the basis definition in thermo()$basis, including
# both numeric and character data, so we need to use a data frame
- comp <- cbind(as.data.frame(comp), ispecies, logact, state, stringsAsFactors=FALSE)
+ comp <- cbind(as.data.frame(comp), ispecies, logact, state, stringsAsFactors = FALSE)
# Ready to assign to the global thermo object
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
@@ -179,7 +179,7 @@
}
# Modify the states or logact values in the existing basis definition
-mod.basis <- function(species, state=NULL, logact=NULL) {
+mod.basis <- function(species, state = NULL, logact = NULL) {
thermo <- get("thermo", CHNOSZ)
# The basis must be defined
if(is.null(thermo$basis)) stop("basis is not defined")
@@ -197,7 +197,7 @@
if(!is.null(state)) {
if(state[i] %in% thermo$buffer$name) {
# This is the name of a buffer
- ibuff <- which(as.character(thermo$buffer$name)==state[i])
+ ibuff <- which(as.character(thermo$buffer$name) == state[i])
# Check that each species in the buffer is compositionally compatible with the basis definition
for(k in 1:length(ibuff)) {
ispecies <- suppressMessages(info(as.character(thermo$buffer$species)[ibuff[k]],
@@ -207,7 +207,7 @@
if(FALSE %in% inbasis) {
stop(paste("the elements '",c2s(names(bufmakeup)[!inbasis]),
"' of species '",thermo$buffer$species[ibuff[k]],"' in buffer '",state[i],
- "' are not in the basis\n",sep=""))
+ "' are not in the basis\n",sep = ""))
}
}
thermo$basis$logact[ib] <- state[i]
@@ -221,7 +221,7 @@
ispecies <- suppressMessages(info(myformula, state[i]))
if(is.na(ispecies) | is.list(ispecies)) {
# If that failed, we're out of luck
- if(myname==myformula) nametxt <- myname else nametxt <- paste(myname, "or", myformula)
+ if(myname == myformula) nametxt <- myname else nametxt <- paste(myname, "or", myformula)
stop(paste0("state or buffer '", state[i], "' not found for ", nametxt, "\n"))
}
}
@@ -242,7 +242,7 @@
}
# To load a preset basis definition by keyword
-preset.basis <- function(key=NULL) {
+preset.basis <- function(key = NULL) {
# The available keywords
basis.key <- c("CHNOS", "CHNOS+", "CHNOSe", "CHNOPS+", "CHNOPSe", "MgCHNOPS+", "MgCHNOPSe", "FeCHNOS", "FeCHNOS+", "QEC4", "QEC", "QEC+", "QCa", "QCa+")
# Just list the keywords if none is specified
@@ -252,23 +252,23 @@
# Match the keyword to the available ones
ibase <- match(key, basis.key)
if(is.na(ibase)) stop(paste(key, "is not a keyword for preset basis species"))
- if(ibase==1) species <- c("CO2", "H2O", "NH3", "H2S", "oxygen")
- else if(ibase==2) species <- c("CO2", "H2O", "NH3", "H2S", "oxygen", "H+")
- else if(ibase==3) species <- c("CO2", "H2O", "NH3", "H2S", "e-", "H+")
- else if(ibase==4) species <- c("CO2", "H2O", "NH3", "H3PO4", "H2S", "oxygen", "H+")
- else if(ibase==5) species <- c("CO2", "H2O", "NH3", "H3PO4", "H2S", "e-", "H+")
- else if(ibase==6) species <- c("Mg+2", "CO2", "H2O", "NH3", "H3PO4", "H2S", "oxygen", "H+")
- else if(ibase==7) species <- c("Mg+2", "CO2", "H2O", "NH3", "H3PO4", "H2S", "e-", "H+")
- else if(ibase==8) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen")
- else if(ibase==9) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen", "H+")
+ if(ibase == 1) species <- c("CO2", "H2O", "NH3", "H2S", "oxygen")
+ else if(ibase == 2) species <- c("CO2", "H2O", "NH3", "H2S", "oxygen", "H+")
+ else if(ibase == 3) species <- c("CO2", "H2O", "NH3", "H2S", "e-", "H+")
+ else if(ibase == 4) species <- c("CO2", "H2O", "NH3", "H3PO4", "H2S", "oxygen", "H+")
+ else if(ibase == 5) species <- c("CO2", "H2O", "NH3", "H3PO4", "H2S", "e-", "H+")
+ else if(ibase == 6) species <- c("Mg+2", "CO2", "H2O", "NH3", "H3PO4", "H2S", "oxygen", "H+")
+ else if(ibase == 7) species <- c("Mg+2", "CO2", "H2O", "NH3", "H3PO4", "H2S", "e-", "H+")
+ else if(ibase == 8) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen")
+ else if(ibase == 9) species <- c("Fe2O3", "CO2", "H2O", "NH3", "H2S", "oxygen", "H+")
else if(ibase %in% c(10, 11)) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen")
- else if(ibase==12) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen", "H+")
- else if(ibase==13) species <- c("glutamine", "cysteine", "acetic acid", "H2O", "oxygen")
- else if(ibase==14) species <- c("glutamine", "cysteine", "acetic acid", "H2O", "oxygen", "H+")
+ else if(ibase == 12) species <- c("glutamine", "glutamic acid", "cysteine", "H2O", "oxygen", "H+")
+ else if(ibase == 13) species <- c("glutamine", "cysteine", "acetic acid", "H2O", "oxygen")
+ else if(ibase == 14) species <- c("glutamine", "cysteine", "acetic acid", "H2O", "oxygen", "H+")
# Get the preset logact
logact <- preset.logact(species)
# For QEC4, we use logact = -4 for the amino acids
- if(key=="QEC4") logact[1:3] <- -4
+ if(key == "QEC4") logact[1:3] <- -4
# Load the species and return the result
return(basis(species, logact))
}
Modified: pkg/CHNOSZ/R/buffer.R
===================================================================
--- pkg/CHNOSZ/R/buffer.R 2023-06-23 14:00:30 UTC (rev 792)
+++ pkg/CHNOSZ/R/buffer.R 2023-06-24 00:59:45 UTC (rev 793)
@@ -6,7 +6,7 @@
# 20071102 add or change a buffer system
thermo <- get("thermo", CHNOSZ)
if(is.null(species)) {
- iname <- which(name==thermo$buffer$name)
+ iname <- which(name == thermo$buffer$name)
if(length(iname)>0) species <- thermo$buffer$species[iname]
else species <- character()
}
@@ -13,22 +13,22 @@
ls <- length(species)
if(ls < length(name) | ls < length(state) | ls < length(logact))
stop('species must be at least as long as the other arguments')
- if(length(name)!=ls) name <- rep(name,length.out=ls)
+ if(length(name) != ls) name <- rep(name,length.out = ls)
add <- TRUE
if(TRUE %in% (name %in% thermo$buffer$name)) {
add <- FALSE
imod <- which(thermo$buffer$name %in% name & thermo$buffer$species %in% species)
if(length(imod)>0) {
- if(state[1]=='') {
+ if(state[1] == '') {
thermo$buffer <- thermo$buffer[-imod,]
assign("thermo", thermo, CHNOSZ)
message(paste('mod.buffer: removed ',c2s(species),' in ',
- c2s(unique(name)),' buffer',sep=''))
+ c2s(unique(name)),' buffer',sep = ''))
} else {
if(missing(state)) state <- thermo$buffer$state[imod]
if(missing(logact)) logact <- thermo$buffer$logact[imod]
- if(length(state)!=ls) state <- rep(state,length.out=ls)
- if(length(logact)!=ls) logact <- rep(logact,length.out=ls)
+ if(length(state) != ls) state <- rep(state,length.out = ls)
+ if(length(logact) != ls) logact <- rep(logact,length.out = ls)
state.old <- thermo$buffer$state[imod]
logact.old <- thermo$buffer$logact[imod]
thermo$buffer$state[imod] <- state
@@ -36,10 +36,10 @@
assign("thermo", thermo, CHNOSZ)
if(identical(state.old,state) & identical(logact.old,logact)) {
message(paste('mod.buffer: nothing changed for ',
- c2s(species),' in ',c2s(unique(name)),' buffer',sep=''))
+ c2s(species),' in ',c2s(unique(name)),' buffer',sep = ''))
} else {
message(paste('mod.buffer: changed state and/or logact of ',
- c2s(species),' in ',c2s(unique(name)),' buffer',sep=''))
+ c2s(species),' in ',c2s(unique(name)),' buffer',sep = ''))
}
}
} else {
@@ -47,8 +47,8 @@
}
}
if(add) {
- if(state[1]=='') state <- rep(thermo$opt$state,length.out=ls)
- t <- data.frame(name=name,species=species,state=state,logact=logact)
+ if(state[1] == '') state <- rep(thermo$opt$state,length.out = ls)
+ t <- data.frame(name = name,species = species,state = state,logact = logact)
thermo$buffer <- rbind(thermo$buffer,t)
assign("thermo", thermo, CHNOSZ)
message(paste('mod.buffer: added',c2s(unique(name))))
@@ -58,7 +58,7 @@
### Unexported functions ###
-buffer <- function(logK=NULL,ibasis=NULL,logact.basis=NULL,is.buffer=NULL,balance='PBB') {
+buffer <- function(logK = NULL,ibasis = NULL,logact.basis = NULL,is.buffer = NULL,balance = 'PBB') {
thermo <- get("thermo", CHNOSZ)
# If logK is NULL load the buffer species,
# otherwise perform buffer calculations
@@ -67,14 +67,14 @@
buffers <- unique(as.character(thermo$basis$logact)[!can.be.numeric(as.character(thermo$basis$logact))])
ispecies.new <- list()
for(k in 1:length(buffers)) {
- ibasis <- which(thermo$basis$logact==buffers[k])
+ ibasis <- which(thermo$basis$logact == buffers[k])
ispecies <- numeric()
for(i in 1:length(ibasis)) {
- ib <- as.character(thermo$buffer$name)==as.character(thermo$basis$logact[ibasis[i]])
+ ib <- as.character(thermo$buffer$name) == as.character(thermo$basis$logact[ibasis[i]])
species <- as.character(thermo$buffer$species)[ib]
state <- as.character(thermo$buffer$state)[ib]
- #ibuff <- info(species,state,quiet=TRUE)
- ispecies <- c(ispecies, species(species, state, index.return=TRUE, add = TRUE))
+ #ibuff <- info(species,state,quiet = TRUE)
+ ispecies <- c(ispecies, species(species, state, index.return = TRUE, add = TRUE))
}
ispecies.new <- c(ispecies.new,list(ispecies))
# Make sure to set the activities
@@ -92,16 +92,16 @@
bufname <- thermo$basis$logact[ibasis[1]]
basisnames <- rownames(thermo$basis)
are.proteins <- grep('_',as.character(thermo$species$name[is.buffer]))
- if((length(are.proteins)>0 & balance=='PBB') | balance==1) {
- if(balance==1) {
+ if((length(are.proteins)>0 & balance == 'PBB') | balance == 1) {
+ if(balance == 1) {
basisnames <- c('product',basisnames)
nb <- rep(1,nrow(bufbasis))
- bufbasis <- cbind(data.frame(product=nb),bufbasis)
+ bufbasis <- cbind(data.frame(product = nb),bufbasis)
} else {
basisnames <- c('PBB',basisnames)
# Prepend a PBB column to bufbasis and increment ibasis by 1
nb <- as.numeric(protein.length(thermo$species$name[is.buffer]))
- bufbasis <- cbind(data.frame(PBB=nb),bufbasis)
+ bufbasis <- cbind(data.frame(PBB = nb),bufbasis)
}
ibasis <- ibasis + 1
# Make logact.basis long enough
@@ -112,7 +112,7 @@
logact.basis <- logact.basis[ilb]
}
# Say hello
- #message(paste("buffer: '",bufname,"', of ",length(is.buffer),' species, ',length(ibasis),' activity(s) requested.',sep=''))
+ #message(paste("buffer: '",bufname,"', of ",length(is.buffer),' species, ',length(ibasis),' activity(s) requested.',sep = ''))
ibasisrequested <- ibasis
# Check and maybe add to the number of buffered activities
ibasisadded <- numeric()
@@ -125,7 +125,7 @@
# look for additional activities to buffer ... do columns in reverse
for(j in ncol(bufbasis):1) {
if(j %in% ibasis) next
- if(FALSE %in% (bufbasis[,j]==0)) {
+ if(FALSE %in% (bufbasis[,j] == 0)) {
newbasis <- j
break
}
@@ -134,7 +134,7 @@
ibasis <- c(ibasis,newbasis)
ibasisadded <- c(ibasisadded,newbasis)
} else {
- stop('can not find enough buffered basis species for ',thermo$basis$logact[ibasis[1]],'.',sep='')
+ stop('can not find enough buffered basis species for ',thermo$basis$logact[ibasis[1]],'.',sep = '')
}
}
}
@@ -146,28 +146,28 @@
# First try to get one that is present in all species
for(i in ncol(bufbasis):1) {
if(i %in% ibasis) next
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 793
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