55 lines
1.5 KiB
R
55 lines
1.5 KiB
R
library(tidyverse)
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split_df <- function(df, test) {
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list(i = filter(df, {{ test }}), o = filter(df, !{{ test }}))
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}
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path <- snakemake@input[[1]]
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df <- readr::read_tsv(
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path,
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col_types = "iccddddddd",
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col_names =
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c("year",
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"species",
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"unit",
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"ave_lower",
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"ave_upper",
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"min_lower",
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"min_upper",
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"max_lower",
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"max_upper",
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"limit"
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)
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) %>%
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# there are some TTHM/HHA5 entries in here twice, use the ones with limits
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filter(!str_detect(species, "(TTHM|HAA5)") | limit > 0)
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has_limit <- df %>%
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group_by(species) %>%
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summarize(limit = max(limit)) %>%
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filter(limit > 0) %>%
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pull(species)
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limited <- split_df(df, species %in% has_limit)
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binned_limit <- limited$i %>%
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group_by(species) %>%
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summarize(av = max(ave_upper), mx = max(max_upper), limit = max(limit), .groups = "drop") %>%
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mutate(bin = case_when(mx == 0 ~ "undetected",
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mx > limit ~ "over",
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mx > limit / 10 ~ "over10",
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mx > limit / 100 ~ "over100",
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TRUE ~ "safeIGuess")) %>%
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filter(bin != "undetected") %>%
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arrange(bin, species) %>%
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readr::write_tsv(snakemake@output[["limit"]])
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detected_nolimit <- limited$o %>%
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group_by(species) %>%
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summarize(av = max(ave_upper), mx = max(max_upper)) %>%
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mutate(detected = mx > 0) %>%
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filter(detected) %>%
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arrange(species) %>%
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readr::write_tsv(snakemake@output[["nolimit"]])
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