Add spaces around equals signs

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@793 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
jedick · Jun 24, 2023 · aa13309 · aa13309
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -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@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

diff --git a/R/Berman.R b/R/Berman.R
@@ -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 @@ Berman <- function(name, T = 298.15, P = 1, check.G=FALSE, calc.transition=TRUE,
   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 @@ Berman <- function(name, T = 298.15, P = 1, check.G=FALSE, calc.transition=TRUE,
   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 @@ Berman <- function(name, T = 298.15, P = 1, check.G=FALSE, calc.transition=TRUE,
     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)
   }
 

diff --git a/R/DEW.R b/R/DEW.R
@@ -47,8 +47,8 @@ calculateDensity <- function(pressure, temperature, error = 0.01) {
     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 @@ calculateGibbsOfWater <- function(pressure, temperature) {
     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 @@ calculateOmega <- function(pressure, temperature, density, wref, Z) {
   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
 }
 

diff --git a/R/IAPWS95.R b/R/IAPWS95.R
@@ -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 @@ IAPWS95 <- function(property,T=298.15,rho=1000) {
       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)

diff --git a/R/add.OBIGT.R b/R/add.OBIGT.R
@@ -15,15 +15,15 @@ mod.OBIGT <- function(..., zap = FALSE) {
   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]]
     args <- args[-1]
     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
@@ -33,18 +33,18 @@ mod.OBIGT <- function(..., zap = FALSE) {
       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
   # Which species are new and which are old
   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 @@ mod.OBIGT <- function(..., zap = FALSE) {
     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$formula), error = function(e) e)
     if(inherits(e, "error")) {
       warning("please supply a valid chemical formula as the species name or in the 'formula' argument")
       # Transmit the error from makeup
@@ -76,7 +76,8 @@ mod.OBIGT <- function(..., zap = FALSE) {
     ntotal <- nrow(thermo$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
@@ -108,26 +109,26 @@ mod.OBIGT <- function(..., zap = FALSE) {
   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$E_units), collapse = " and ")
   # Load only selected species if requested
   if(!is.null(species)) {
     idat <- match(species, to2$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

diff --git a/R/add.protein.R b/R/add.protein.R
@@ -56,7 +56,7 @@ add.protein <- function(aa, as.residue = FALSE) {
 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)

diff --git a/R/affinity.R b/R/affinity.R
@@ -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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
   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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
 
   # 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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
       # 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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
       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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
       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$logact) == buffers[k])
         # Calculate the logKs from the affinities
         logK <- a
         for(i in 1:length(logK)) {
@@ -126,8 +126,8 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
             logK[[i]] <- logK[[i]] - logact.basis.new[[j]] * thermo$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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
             #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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
           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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
     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$protein[iprotein[ip],5:25])
         return(Reduce("+", pprod(a[ires],tpext)) - loga.protein[ip])
@@ -186,14 +186,14 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
       # The current species list, containing the residues
       resspecies <- thermo$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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
     # 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 @@ affinity <- function(..., property=NULL, sout=NULL, exceed.Ttr=FALSE, exceed.rho
   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)
 }