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# Validating data frames containing edge database (edge list with edge
# attributes) and vertex data bases (vertices with vertex attributes)
# Validates edge list
validateEL <- function(x)
{
# must be data.frame
stopifnot(inherits(x, "data.frame"))
# at least two columns
if (ncol(x) < 2) {
stop("the data frame should contain at least two columns")
}
# Handling NAs
if (any(is.na(x[,1:2]))) {
warning("In first two columns of `x' `NA' elements were replaced with string \"NA\"")
x[,1:2][is.na(x[,1:2])] <- "NA"
}
x
}
# validate vertex database
validateVDB <- function(x)
{
stopifnot(inherits(x, "data.frame"))
# empty data frame
if(nrow(x) == 0)
stop("vertex data frame has no rows")
# duplicated vertex ids
dups <- duplicated(x[,1])
if( any(dups) )
stop(paste("duplicated ids in vertex db:", paste(x[dups,1], collapse=", ")))
# Handling NAs
isna <- is.na(x[,1])
if (any(isna))
{
warning("in `vertices[,1]' `NA' elements were replaced with string \"NA\"")
x[isna, 1] <- "NA"
}
x
}
# validate edge DB versus vertex DB
# returns TRUE or vector of warnings
validNetDB <- function(edb, vdb, test=FALSE)
{
edb <- validateEL(edb)
vdb <- validateVDB(vdb)
errors <- NULL
# TODO ids in el missing in vdb
uvids <- unique(c(edb[,1], edb[,2]))
i <- uvids %in% vdb[,1]
if(!all(i))
errors <- c(errors, paste("some vertex ids in edge db are not found in vertex db:",
paste(uvids[!i], collapse=", ")))
# return
if(is.null(errors)) return(TRUE)
if(test)
return(errors)
else
{
msg <- "vertex and edge data frames are incompatible:"
if(length(errors) > 1L)
stop(paste(msg, paste(paste(seq_along(errors), errors, sep=": ")),
collapse="\n"))
else stop(msg, " ", errors)
}
}
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