diff --git a/R/challengeR.R b/R/challengeR.R index c30253e..06fc8fd 100644 --- a/R/challengeR.R +++ b/R/challengeR.R @@ -1,150 +1,150 @@ #' Title #' #' @param object #' @param value #' @param algorithm #' @param case #' @param taskName Optional for single-task data set that does not contain a task column. #' @param by The name of the column that contains the task identifiers. Required for multi-task data set. #' @param annotator #' @param smallBetter #' @param na.treat #' @param check #' #' @return #' @export #' #' @examples as.challenge=function(object, + case, + algorithm, value, - algorithm , - case=NULL, - taskName=NULL, by=NULL, + taskName=NULL, annotator=NULL, smallBetter=FALSE, na.treat=NULL, # optional check=TRUE) { object=as.data.frame(object[,c(value, algorithm, case, by, annotator)]) # sanity checks if (check) { if (!is.null(by) && !is.null(taskName)) { warning("Argument 'taskName' is ignored for multi-task data set.") } # Add task column for data set without task column by using the specified task name. if (is.null(by) && !is.null(taskName)) { taskName <- trimws(taskName) if (taskName == "") { stop("Argument 'taskName' is empty.") } object <- cbind(task=taskName, object) by = "task" } # Add task column for data set without task column by using a dummy task name. if (is.null(by) && is.null(taskName)) { object <- cbind(task="dummyTask", object) by = "task" } object=splitby(object,by=by) object=lapply(object,droplevels) missingData = n.missing = list() for (task in names(object)) { if (!all(is.numeric(object[[task]][[value]]))) stop("Performance values must be numeric.") n.missing[[task]] <- sum(is.na(object[[task]][[value]])) # already missing before na.treat; for report if (n.missing[[task]]>0) message("Note: ", n.missing, " missing cases have been found in the data set.") # check for missing cases missingData[[task]]=object[[task]] %>% expand(!!as.symbol(algorithm), !!as.symbol(case))%>% anti_join(object[[task]], by=c( algorithm,case)) if (nrow(missingData[[task]])>0) { if (length(object) == 1 ) { # single task message("Performance of not all algorithms has been observed for all cases. Therefore, missings have been inserted in the following cases:") } else { # multi task message("Performance of not all algorithms has been observed for all cases in task '", task, "'. Therefore, missings have been inserted in the following cases:") } print(as.data.frame(missingData[[task]])) object[[task]]=as.data.frame(object[[task]] %>% complete(task, !!as.symbol(algorithm), !!as.symbol(case))) } # check duplicate cases all1=apply(table(object[[task]][[algorithm]], object[[task]][[case]]), 2, function(x) all(x==1)) if (!all(all1)) { n.duplicated <- sum(all1!=1) if (length(object) == 1 ) { # single task if (n.duplicated/length(all1) >= 1/5) { # at least a quarter of the cases is duplicated stop ("The following case(s) appear(s) more than once for the same algorithm. Please revise. ", "Or are you considering a multi-task challenge and forgot to specify argument 'by'?\n", "Case(s): ", paste(names(which(all1!=1)), collapse=", ") ) } else { stop ("The following case(s) appear(s) more than once for the same algorithm. Please revise.\n", "Case(s): ", paste(names(which(all1!=1)), collapse=", ") ) } } else { # multi task stop ("The following case(s) appear(s) more than once for the same algorithm in task '", task, "'. Please revise.\n", "Case(s): ", paste(names(which(all1!=1)), collapse=", ") ) } } if (!is.null(na.treat)) { if (is.numeric(na.treat)) object[[task]][,value][is.na(object[[task]][,value])]=na.treat else if (is.function(na.treat)) object[[task]][,value][is.na(object[[task]][,value])]=na.treat(object[[task]][,value][is.na(object[[task]][,value])]) else if (is.character(na.treat) && na.treat=="na.rm") object[[task]]=object[[task]][!is.na(object[[task]][,value]),] } } } if (check==TRUE && (any(sapply(missingData, function(x) nrow(x))>0) |any(n.missing>0))) { if (is.null(na.treat)) message("For aggregate-then-rank, na.treat will have to be specified. ", "For rank-then-aggregate, missings will implicitly lead to the algorithm ranked last for the missing test case." ) else if (is.numeric(na.treat)) message("All missings have been replaced by the value ", na.treat,".\n") else if (is.character(na.treat) && na.treat=="na.rm") message("All missings have been removed.") else if (is.function(na.treat)) { message("Missings have been replaced using function ") print(na.treat) } } if (check==TRUE){ attr(object,"n.missing")=n.missing attr(object,"missingData")=missingData } attr(object,"na.treat")=na.treat attr(object,"algorithm")=algorithm attr(object,"value")=value attr(object,"case")=case attr(object,"annotator")=annotator attr(object,"by")=by attr(object,"smallBetter")=smallBetter attr(object,"check")=check class(object)=c("challenge", class(object)) object }