In BEQI2: Benthic Ecosystem Quality Index 2

# number of pooling runs (hard coded TODO: in JSON-file?)
nRuns <- 10L

# pool by water body, ecotope, year and period (period is implicit by selection)
# Note: pool identifier POOLID is only unique per strata
d <- ldply(
    .data = 1:nRuns,
    .fun = function(i) {
        d <- ddply(
            .data = d_beqi, 
            .variables = c("OBJECTID", "ECOTOPE", "YEAR"), 
            .fun = function(x) {

                # extract unique samples
                ux <- unique(subset(x = x, select = c(ID, AREA)))

                # pooling
                ux$POOLID <- pool(
                    sampleId = ux$ID, 
                    area = ux$AREA, 
                    targetArea = settings$pooling$targetarea
                )

                # merge pool identifiers to original data set
                x$POOLID <- ux$POOLID[match(x = x$ID, table = ux$ID)]

                # return result
                x
            }
        )
        d$POOLRUN <- i
        d
    }
)

toLog("INFO", "storing pooling results...")
tmp <- dcast(
    data = unique(d[, c("ID", "POOLRUN", "POOLID")]), 
    ID ~ POOLRUN, 
    value.var= "POOLID"
)
write.csv(x = tmp, file = settings$files$pooling, row.names = FALSE, na = "")
tmp <- as.matrix(tmp[, -1])
toLog("INFO", "pooling results have been stored.")

The samples in the BEQI2-input file have been pooled. An average of r round(100 * sum(is.na(tmp))/ length(tmp), 2) percent of the samples could not be pooled in each run. These samples have been removed. Each sample has been pooled for at least r min(apply(X = tmp, MARGIN = 1, FUN = function(x) {sum(!is.na(x))})) out of 10 times. The results have been written to r basename(settings$files$pooling).

# remove samples that cannot be pooled
d <- d[!is.na(d$POOLID), ]

d_beqi <- d
rm(d)

BEQI2 documentation built on May 2, 2019, 8:19 a.m.