[R-sig-eco] FW: Calculating percentile rank of sample dataset compared to reference dataset in R

[Bede-Fazekas Ákos]

Dear Matthew,

here is one, maybe not the fastest/shortest, solution:
percentiles <- apply(X = df_ref, MARGIN = 2, FUN = quantile, probs = 
seq(from = 0, to = 1, length.out = 101)[-1])
df_sample$percentile_rank <- vapply(X = colnames(df_sample)[-1], 
FUN.VALUE = numeric(nrow(df_sample)), FUN = function(variable_name) 
findInterval(x = df_sample[, variable_name, drop = TRUE], vec = 
percentiles[, variable_name, drop = TRUE]))

HTH,
Ákos Bede-Fazekas
Hungarian Academy of Sciences

2019.08.22. 0:54 keltezéssel, Shank, Matthew írta:
> Hello R-sig-ecology mailing list,
>
>
>
> I’m working on a mutlivariate water quality index where the concentration of parameter i at site j is normalized by calculating the percentile rank of the value using a much larger reference dataset.
>
>
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> As an example, I have generated a sample dataset of water quality parameters (df_sample) and a larger reference dataset (df_ref). I’d like to calculate the percentile rank of each parameter, at each site, using a reference dataset of a much larger size.
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>
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> Example data is below. If anyone has a solution that avoids for loops that would be preferred.
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> #generate sample data
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> df_sample <- data.frame(site = letters[1:10], iron = runif(10, min=0, max=1), nitrate = runif(10, min=0, max=10))
>
> df_sample
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>
>
>
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> #generate reference dataset
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> df_ref <- data.frame(iron = seq(0, 1, length.out = 1000), nitrate = seq(0, 10, length.out = 1000))
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> df_ref
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> # now would like to calculate percentile rank of iron and nitrate at all sites (a:j) based on identical columns in df_ref and include as a new column in df_sample
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>
>
> Many thanks,
> |><̮Mâ̬tt͵)o>
>
>
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