tidy up stuff

NAMESPACE

@@ -4,6 +4,7 @@ export(addMapping)
 export(cacheCleanup)
 export(cacheCopy)
 export(calcOutput)
+export(calcOutputWrapper)
 export(compareData)
 export(compareMadratOutputs)
 export(downloadSource)
@@ -28,7 +29,6 @@ export(metadataGFZ)
 export(pucAggregate)
 export(putMadratMessage)
 export(readSource)
-export(readSourceAlternative)
 export(readSourceWrapper)
 export(redirectSource)
 export(regionscode)

R/convertTau.R

@@ -1,44 +1,43 @@
 #' Convert Tau
-#' 
+#'
 #' Convert landuse intensity data (tau) to data on ISO country level.
-#' 
-#' 
+#'
+#'
 #' @param x MAgPIE object containing tau values and corresponding weights xref
 #' at 0.5deg cellular level.
 #' @return Tau data and weights as MAgPIE object aggregated to country level
 #' @author Jan Philipp Dietrich
 #' @importFrom magclass ncells getCells<- collapseNames getCells
 
 convertTau <- function(x) {
-  
+
   "!# @monitor madrat:::sysdata$iso_cell magclass:::ncells"
   "!# @ignore  madrat:::toolAggregate"
-  
-  tau  <- x[,,"tau"]
-  xref <- x[,,"xref"]
-  
+
+  tau  <- x[, , "tau"]
+  xref <- x[, , "xref"]
+
   # clean data
   # make sure that the weight for nonexisting tau values is 10^-10
-  xref[is.na(tau) | is.nan(tau)] <- 10^-10
-  #fill gaps within tau factors with 1 (the global mean)
-  tau[ is.na(tau) | is.nan(tau)] <- 1  
-
-  #calculate numbers on country level if they are provided on cellular level
-  if (ncells(x) == 59199) {
+  xref[is.na(tau)] <- 10^-10
+  # fill gaps within tau factors with 1 (the global mean)
+  tau[is.na(tau)] <- 1
 
+  # calculate numbers on country level if they are provided on cellular level
+  if (ncells(x) == 59199) {
     # read mapping cells -> iso countries
-    iso_cell <- sysdata$iso_cell
-    iso_cell[,2] <- getCells(x)
+    isoCell <- sysdata$iso_cell
+    isoCell[, 2] <- getCells(x)
 
-    # aggregate data        
-    tau  <- toolAggregate(tau,  rel=iso_cell, weight = collapseNames(xref))
-    xref <- toolAggregate(xref, rel=iso_cell)
+    # aggregate data
+    tau  <- toolAggregate(tau,  rel = isoCell, weight = collapseNames(xref))
+    xref <- toolAggregate(xref, rel = isoCell)
   }
-  
-  #check whether the country list agrees with the list of countries in the madrat package
-  #remove unrequired data, add missing data  
-  tau  <- toolCountryFill(tau,fill=1,TLS="IDN",HKG="CHN",SGP="CHN",BHR="QAT")
-  xref <- toolCountryFill(xref, fill=0, verbosity=2)
-
-  return(mbind(tau,xref))
-}  
+
+  # check whether the country list agrees with the list of countries in the madrat package
+  # remove unrequired data, add missing data
+  tau  <- toolCountryFill(tau, fill = 1, TLS = "IDN", HKG = "CHN", SGP = "CHN", BHR = "QAT")
+  xref <- toolCountryFill(xref, fill = 0, verbosity = 2)
+
+  return(mbind(tau, xref))
+}

R/readSource.R

@@ -27,7 +27,7 @@
 #' if the convert argument is set to TRUE, should be on ISO code country level.
 #' @author Jan Philipp Dietrich, Anastasis Giannousakis, Lavinia Baumstark, Pascal Sauer
 #' @seealso \code{\link{setConfig}}, \code{\link{downloadSource}}, \code{\link{readTau}}
-#' #' @note The underlying read-functions can return a magpie object or a list of information
+#' @note The underlying read-functions can return a magpie object or a list of information
 #' (preferred) back to \code{readSource}. In list format the object should have the following
 #' structure:
 #' \itemize{

R/readSourceWrapper.R

@@ -18,7 +18,7 @@
 #' @export
 readSourceWrapper <- function(read, correct = NULL, convert = NULL, subtype = NULL, subset = NULL) {
 
-  #' get string/bool from function(s) for use in readSource
+  # get string/bool from function(s) for use in readSource
   .getConvert <- function(convert, correct) {
     if (!is.null(convert)) {do_convert <- TRUE}
     else if (!is.null(correct)) {do_convert <- "onlycorrect"}