MDL: some fixes for CRAN submission

R/Rphree_ReactTrans.R

 ##  Functions for dealing with surrogate simulations
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-28 15:30:47 delucia"
+### Time-stamp: "Last modified 2021-04-28 15:54:48 delucia"
 
 
-##' Todo
+##' This function takes the current state of a chemical system in form
+##' of a matrix, a vector of concentrations representing boundary
+##' conditions (injection), the required time step (dt/s), grid spcing
+##' (dx/m) and U (Darcy velocity/m^3/s). Note that it is
+##' responsibility of user to check that the required dt does not
+##' trespass the CFL condition.
 ##'
 ##' @title Simple explicit 1D forward-Euler advection, multispecies
-##' @param conc matrix containing the chemical state
+##' @param conc either a vector or a matrix containing the chemical
+##'     state to be updated
 ##' @param inflow vector of concentrations entering the inlet
 ##' @param dx the grid spacing in m
 ##' @param dt the required time step in s
-##' @param U  Darcy velocity in m^3/s
+##' @param U Darcy velocity in m^3/s
 ##' @return a matrix containing the state after the advection
 ##' @author MDL
 ##' @export
 AdvectionPQC <- function(conc, inflow=rep(0,ncol(conc)), dx, dt, U)
 {
     if (is.matrix(conc)) {
-        ##        msg("conc is matrix")
-        ## CurrConc <<- conc
         ## actually the first iteration does not have the attributes attached
         if ( "immobile" %in% names(attributes(conc)) ) { 
             immobile <- attr(conc,"immobile")
@@ -146,8 +150,6 @@ Act2pH <- function(state){
 }
 
 
-##' TODO
-##'
 ##' @title Recompose a chemical state after reduction
 ##' @param state the state to be recomposed
 ##' @param reduced the initial reduced state containing the "index" attribute
@@ -168,13 +170,13 @@ RecomposeState <- function(state, reduced)
     return(res)
 }
 
-##' This functions requires the package \code{mgcv}
-##'
-##' TODO
+##' Applies \code{mgcv::uniquecombs} to the matrix representing the
+##' current chemical state.
 ##' @title Finds unique problems in a geochemical state
 ##' @param data the matrix
-##' @return a matrix plus an attribute containing the indeces of the
-##'     compressed matrix
+##' @return a matrix with attached attribute containing the indeces of
+##'     the compressed matrix for later restoring and the "immobile"
+##'     indices
 ##' @author MDL
 ##' @export
 ReduceState <- function(data)
@@ -187,7 +189,7 @@ ReduceState <- function(data)
 
 
 
-##' TODO
+##' Cfr \code{demo}
 ##' @title 1D Reactive transport simulations using phreeqc or a
 ##'     surrogate, equilibrium simulations
 ##' @param setup a list with several input parameters
@@ -291,11 +293,12 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
     pad <- floor(log10(maxiter+1))+1 ## to properly format the step names
     spr_string <- paste0("%0", pad,"d")
     names(saved_complete) <- paste0("step_",sprintf(spr_string,seq(0,maxiter)))
-    
-    out_inp <<- vector(mode="list",length=length(maxiter))
-    out_res <<- vector(mode="list",length=length(maxiter))
-    out_bal <<- vector(mode="list",length=length(maxiter))
-    out_of_tol <<- vector(mode="list",length=length(maxiter))
+
+    utils::globalVariables(c("out_inp","out_res","out_bal"))
+
+    out_inp <- vector(mode="list",length=length(maxiter))
+    out_res <- vector(mode="list",length=length(maxiter))
+    out_bal <- vector(mode="list",length=length(maxiter))
 
     timing <- matrix(NA,ncol=5,nrow=maxiter)
 
@@ -332,7 +335,6 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
     
     attr(state_C,"immobile") <- immobile
 
-    ## ssC <<- state_C
     index_saved <- 1
     saved_complete[[index_saved]] <- list(C=Act2pH(state_C))
     index_saved <- index_saved + 1
@@ -372,8 +374,8 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
     
     saved_complete[[index_saved]] <- list(T=Act2pH(state_T), C=Act2pH(state_C))
     index_saved <- index_saved + 1
-    out_inp[[1]] <<- inplist
-    out_res[[1]] <<- res_C
+    out_inp[[1]] <- inplist
+    out_res[[1]] <- res_C
     
     if (ebreak) {
         msg("Early break invoked, bye.")
@@ -426,7 +428,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
 
             Tm <- system.time( tmpsur <- Selected.Surrogate(reduced, model=model) )[3]
             bal <- CheckBalance(baleq,reduced,tmpsur)
-            out_bal[[iter]] <<- bal
+            out_bal[[iter]] <- bal
             totbal <- apply(bal, 1, mae)
 
             nonok <- which(totbal>tol) ### max(tol,tol2))
@@ -455,7 +457,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
             ## new input
             Ts <- system.time(inplist <- splitMultiFix(data=reduced, procs=procs, base=base, first=first,
                                                        prop=prop, minerals=immobile, nmax=maxsim))[3]
-            out_inp[[iter]] <<- inplist
+            out_inp[[iter]] <- inplist
             Tm <- system.time(res_C <- RunPQC(inplist, procs=procs))[3]
             attr(res_C,"immobile") <- immobile
         }
@@ -473,7 +475,7 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
         ## ## transform the pH/pe back into activities
         ## state_C <- pH2Act(state_C)
 
-        out_res[[iter]] <<- res_C
+        out_res[[iter]] <- res_C
 
         timing[iter,] <- c( dim(reduced)[1], procs, Tm, Tr, Ts)
         msg("done iteration", iter, "/", maxiter," CPU-time ",round(Tm,3),"[s]")
@@ -601,10 +603,12 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
     pad <- floor(log10(maxiter+1))+1 ## to properly format the step names
     spr_string <- paste0("%0", pad,"d")
     names(saved_complete) <- paste0("step_",sprintf(spr_string,seq(0,maxiter)))
+
+    utils::globalVariables(c("out_inp","out_res","out_bal"))
     
-    out_inp <<- vector(mode="list",length=length(maxiter))
-    out_res <<- vector(mode="list",length=length(maxiter))
-    out_bal <<- vector(mode="list",length=length(maxiter))
+    out_inp <- vector(mode="list",length=length(maxiter))
+    out_res <- vector(mode="list",length=length(maxiter))
+    out_bal <- vector(mode="list",length=length(maxiter))
     
     timing <- matrix(NA,ncol=5,nrow=maxiter)
     msg("Loading phreeqc db... ")
@@ -675,8 +679,8 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
     
     saved_complete[[index_saved]] <- list(T=Act2pH(state_T), C=Act2pH(state_C))
     index_saved <- index_saved + 1
-    out_inp[[1]] <<- inplist
-    out_res[[1]] <<- res_C
+    out_inp[[1]] <- inplist
+    out_res[[1]] <- res_C
     
     if (ebreak) {
         msg("Early break invoked, bye.")
@@ -730,7 +734,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
             Tm <- system.time( tmpsur <- Selected.Surrogate(reduced, model=model) )[3]
             ## print(head(tmpsur))
             bal <- CheckBalance(baleq,reduced,tmpsur)
-            out_bal[[iter]] <<- bal
+            out_bal[[iter]] <- bal
             totbal <- apply(bal, 1, mae)
             
             ## cat(":: Surrogate Balance Summary:\n")
@@ -747,7 +751,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
                     Ts <- Ts + system.time(inplist <- splitMultiKin(data=reducednonok, procs=procs, base=base, first=first, ann=ann,
                                                                     prop=prop, minerals=immobile, kin=kin, dt=dt, nmax=maxsim))[3]
                     
-                    out_inp[[iter]] <<- inplist
+                    out_inp[[iter]] <- inplist
                     if (length(nonok)==1) {
                         Tm <- Tm + system.time(tmp2 <- RunPQC(inplist, procs=1))[3]
                         pqcres_C <- tmp2[,prop]
@@ -765,7 +769,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
             ## new input
             Ts <- system.time(inplist <- splitMultiKin(data=reduced, procs=procs, base=base, first=first, ann=ann,
                                                        prop=prop, minerals=immobile, kin=kin, dt=dt, nmax=maxsim))[3]
-            out_inp[[iter]] <<- inplist
+            out_inp[[iter]] <- inplist
             Tm <- system.time(tmp3 <- RunPQC(inplist, procs=procs))[3]
             res_C <- tmp3[,prop]
             attr(res_C,"immobile") <- immobile
@@ -784,7 +788,7 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
         ## transform the pH/pe back into activities
         state_C <- pH2Act(state_C)
 
-        out_res[[iter]] <<- res_C
+        out_res[[iter]] <- res_C
      
         timing[iter,] <- c( dim(reduced)[1], procs, Tm, Tr, Ts)
         msg("done iteration", iter, "/", maxiter," CPU-time ",round(Tm,3),"[s]")

R/Rphree_SurrogateUtils.R

 ##  Functions for dealing with surrogate simulations
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-28 15:32:05 delucia"
+### Time-stamp: "Last modified 2021-04-28 15:44:10 delucia"
 
 ##' Computes the average of absolute values of a vector
 ##' @title Average of absolute values
@@ -94,9 +94,8 @@ ExtractSpecies <- function(flatlist, species) {
 ##' @param flatlist the list as input to search in
 ##' @param pphases character vector containing the names of the Pure
 ##'     Phases whose values are to be extracted
-##' @param species vector containing the names of the species to
-##'     search for
 ##' @return a matrix containing as many columns as specified pphases
+##' @export
 ##' @author MDL
 ExtractPphases <- function(flatlist, pphases) {
    tmp <- matrix(NA, len <- length(flatlist), speclen <- length(pphases))