In BENMMI: Benthic Multi-Metric Index

ITI: Infaunal Trophic Index

The average percentage of the total abundance per sample without an ITI classification (Gittenberger and van Loon, 2013) is given below:

if (tibble::has_name(d_mmi, "ITI_GROUP")) {
    d <- d_mmi %>%
        filter(!CARNIVORE | is.na(CARNIVORE)) %>%
        group_by(OBJECTID, HABITAT, YEAR) %>%
        mutate(N = sum(VALUE)) %>%
        filter(has_iti(taxon = TAXON, group = ITI_GROUP)) %>%
        summarise(ITI_MISSING = 100 * (1 - sum(VALUE) / unique(N)))
} else {
    d <- d_mmi %>% 
        filter(!CARNIVORE | is.na(CARNIVORE)) %>%
        group_by(OBJECTID, HABITAT, YEAR) %>%
        mutate(N = sum(VALUE)) %>%
        filter(has_iti(taxon = TAXON)) %>%
        summarise(ITI_MISSING = 100 * (1 - sum(VALUE) / unique(N)))
}

d %>% xtable %>%
    print(type = "html")

Note that in r sum(d$ITI_MISSING > 20) cases, more than 20% of the total abundance does not have an ITI classification.

BENMMI documentation built on Oct. 23, 2020, 8:24 p.m.