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Simplify assess_bathing_quality_eu() #4

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Simplify assess_bathing_quality_eu() #4

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92b05f0
Simplify assess_bathing_quality_eu()
hsonne Feb 23, 2019
478a466
Update assess_bathing_quality_eu.R
wseis Feb 28, 2019
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40 changes: 16 additions & 24 deletions R/assess_bathing_quality_eu.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,43 +16,35 @@ assess_bathing_quality_eu <- function(e.coli, log = TRUE)
e.coli <- stats::na.omit(e.coli)

if (length(e.coli) < 16) {

warning("Less than 16 e.coli elements. EU directive does need 16 at least.")
}

if (15 < mean(e.coli)) {

if (mean(e.coli) > 15) {
log <- FALSE
}

if (! log) {

e.coli <- log10(e.coli)
}

# sd uses nominator n - 1 which leads an unbiased estimate of the population distribution
sigma <- stats::sd(e.coli)
mu <- mean(e.coli)

sigma <- stats::sd(e.coli) # sd uses nominator n-1 which leads to higher sigmas

q90 <- 1.282 * sigma + mu
q95 <- 1.65 * sigma + mu

levels <- c("excellent", "good", "sufficient", "poor")

if (q95 < log10(500)) {

return(ordered("excellent", levels = levels))
}

if (q95 < log10(1000)) {

return(ordered("good", levels = levels))
}

if (q90 < log10(900)) {

return(ordered("sufficient", levels = levels))
q95 <- 1.650 * sigma + mu

qualities <- c("excellent", "good", "sufficient", "poor")

index <- if (q95 < log10(500)) {
1
} else if (q95 < log10(1000)) {
2
} else if (q90 < log10(900) & q95 < log10(1000)) {
3
} else {
4
}

return(ordered("poor", levels = levels))
factor(qualities[index], levels = qualities, ordered = TRUE)
}