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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,82 +1,82 @@ | ||
| #' MAgPIE-Clean | ||
| #' | ||
| #' Function cleans MAgPIE objects so that they follow some extended magpie | ||
| #' object rules (currently it makes sure that the dimnames have names and | ||
| #' removes cell numbers if it is purely regional data) | ||
| #' | ||
| #' | ||
| #' @param x MAgPIE object which should be cleaned. | ||
| #' @param what term defining what type of cleaning should be performed. Current | ||
| #' modes are "cells" (removes cell numbers if the data seems to be regional - | ||
| #' this should be used carefully as it might remove cell numbers in some cases | ||
| #' in which they should not be removed), "sets" (making sure that all | ||
| #' dimensions have names) and "all" (performing all available cleaning methods) | ||
| #' @return The eventually corrected MAgPIE object | ||
| #' @author Jan Philipp Dietrich | ||
| #' @seealso \code{"\linkS4class{magpie}"} | ||
| #' @examples | ||
| #' | ||
| #' data(population_magpie) | ||
| #' a <- clean_magpie(population_magpie) | ||
| #' | ||
| #' @export clean_magpie | ||
| clean_magpie <- function(x,what="all") { | ||
| if(!(what %in% c("all","cells","sets"))) stop('Unknown setting for argument what ("',what,'")!') | ||
| #remove cell numbers if data is actually regional | ||
| if(what=="all" | what =="cells") { | ||
| if(ncells(x)==nregions(x)) { | ||
| getCells(x) <- getRegions(x) | ||
| if(!is.null(names(dimnames(x))[[1]])) { | ||
| if(!is.na(names(dimnames(x))[[1]])) { | ||
| names(dimnames(x))[[1]] <- sub("\\..*$","",names(dimnames(x))[[1]]) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| #make sure that all dimensions have names | ||
| if(what=="all" | what =="sets") { | ||
|
|
||
| if(is.null(names(dimnames(x)))) names(dimnames(x)) <- rep(NA,3) | ||
|
|
||
| .count_subdim <- function(x,sep="\\.") { | ||
| o <- nchar(gsub(paste0("[^",sep,"]*"),"",x))+1 | ||
| if(length(o)==0) o <- 0 | ||
| return(o) | ||
| } | ||
|
|
||
| names <- names(dimnames(x)) | ||
| if(!is.na(names[1]) & (names[1]!="") & (names[1]!="NA")) { | ||
| c1 <- .count_subdim(dimnames(x)[[1]][1]) | ||
| c2 <- .count_subdim(names[1]) | ||
| if(c1!=c2) { | ||
| if(c1>2) stop("More than 2 spatial subdimensions not yet implemented") | ||
| names[1] <- paste(names[1],"cell",sep=".") | ||
| } | ||
| } else { | ||
| names[1] <- ifelse(all(grepl("\\.",dimnames(x)[[1]])),"region.cell","region") | ||
| } | ||
| if(is.na(names[2]) | names[2]=="NA" | names[2]=="") { | ||
| names[2] <- "year" | ||
| } | ||
| if(is.na(names[3]) | names[3]=="" | names[3]=="NA") { | ||
| ndim <- nchar(gsub("[^\\.]","",getNames(x)[1])) +1 | ||
| names[3] <- ifelse(length(ndim)>0,paste0("data",1:ndim,collapse="."),"data1") | ||
| } else { | ||
| c1 <- .count_subdim(dimnames(x)[[3]][1]) | ||
| c2 <- .count_subdim(names[3]) | ||
| if(c1!=c2) { | ||
| if(c1>c2) { | ||
| names[3] <- paste(c(names[3],rep("data",c1-c2)),collapse=".") | ||
| } else { | ||
| search <- paste0(c(rep("\\.[^\\.]*",c2-c1),"$"),collapse="") | ||
| names[3] <- sub(search,"",names[3]) | ||
| } | ||
| names[3] <- paste0(make.unique(strsplit(names[3],"\\.")[[1]],sep = ""),collapse=".") | ||
|
|
||
| } | ||
| } | ||
|
|
||
| names(dimnames(x)) <- names | ||
| } | ||
| return(x) | ||
| } | ||
| #' MAgPIE-Clean | ||
| #' | ||
| #' Function cleans MAgPIE objects so that they follow some extended magpie | ||
| #' object rules (currently it makes sure that the dimnames have names and | ||
| #' removes cell numbers if it is purely regional data) | ||
| #' | ||
| #' | ||
| #' @param x MAgPIE object which should be cleaned. | ||
| #' @param what term defining what type of cleaning should be performed. Current | ||
| #' modes are "cells" (removes cell numbers if the data seems to be regional - | ||
| #' this should be used carefully as it might remove cell numbers in some cases | ||
| #' in which they should not be removed), "sets" (making sure that all | ||
| #' dimensions have names) and "all" (performing all available cleaning methods) | ||
| #' @return The eventually corrected MAgPIE object | ||
| #' @author Jan Philipp Dietrich | ||
| #' @seealso \code{"\linkS4class{magpie}"} | ||
| #' @examples | ||
| #' | ||
| #' data(population_magpie) | ||
| #' a <- clean_magpie(population_magpie) | ||
| #' | ||
| #' @export clean_magpie | ||
| clean_magpie <- function(x,what="all") { | ||
| if(!(what %in% c("all","cells","sets"))) stop('Unknown setting for argument what ("',what,'")!') | ||
| #remove cell numbers if data is actually regional | ||
| if(what=="all" | what =="cells") { | ||
| if(ncells(x)==nregions(x)) { | ||
| getCells(x) <- getRegions(x) | ||
| if(!is.null(names(dimnames(x))[[1]])) { | ||
| if(!is.na(names(dimnames(x))[[1]])) { | ||
| names(dimnames(x))[[1]] <- sub("\\..*$","",names(dimnames(x))[[1]]) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| #make sure that all dimensions have names | ||
| if(what=="all" | what =="sets") { | ||
|
|
||
| if(is.null(names(dimnames(x)))) names(dimnames(x)) <- rep(NA,3) | ||
|
|
||
| .count_subdim <- function(x,sep="\\.") { | ||
| o <- nchar(gsub(paste0("[^",sep,"]*"),"",x))+1 | ||
| if(length(o)==0) o <- 0 | ||
| return(o) | ||
| } | ||
|
|
||
| names <- names(dimnames(x)) | ||
| if(!is.na(names[1]) & (names[1]!="") & (names[1]!="NA")) { | ||
| c1 <- .count_subdim(dimnames(x)[[1]][1]) | ||
| c2 <- .count_subdim(names[1]) | ||
| if(c1!=c2) { | ||
| if(c1>2) stop("More than 2 spatial subdimensions not yet implemented") | ||
| names[1] <- paste(names[1],"cell",sep=".") | ||
| } | ||
| } else { | ||
| names[1] <- ifelse(all(grepl("\\.",dimnames(x)[[1]])),"region.cell","region") | ||
| } | ||
| if(is.na(names[2]) | names[2]=="NA" | names[2]=="") { | ||
| names[2] <- "year" | ||
| } | ||
| if(is.na(names[3]) | names[3]=="" | names[3]=="NA") { | ||
| ndim <- nchar(gsub("[^\\.]","",getNames(x)[1])) +1 | ||
| names[3] <- ifelse(length(ndim)>0,paste0("data",1:ndim,collapse="."),"data1") | ||
| } else { | ||
| c1 <- .count_subdim(dimnames(x)[[3]][1]) | ||
| c2 <- .count_subdim(names[3]) | ||
| if(c1!=c2) { | ||
| if(c1>c2) { | ||
| names[3] <- paste(c(names[3],rep("data",c1-c2)),collapse=".") | ||
| } else { | ||
| search <- paste0(c(rep("\\.[^\\.]*",c2-c1),"$"),collapse="") | ||
| names[3] <- sub(search,"",names[3]) | ||
| } | ||
| names[3] <- paste0(make.unique(strsplit(names[3],"\\.")[[1]],sep = ""),collapse=".") | ||
|
|
||
| } | ||
| } | ||
|
|
||
| names(dimnames(x)) <- names | ||
| } | ||
| return(updateMetadata(x)) | ||
| } |
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