R/exclude_outliers.R

In PhotoGEA: Photosynthetic Gas Exchange Analysis

exclude_outliers <- function(x, col_for_analysis, INDICES, method = 'exclude') {
    UseMethod("exclude_outliers", x)
}

exclude_outliers.data.frame <- function(
    x,
    col_for_analysis,
    INDICES,
    method = 'exclude'
)
{
    if (!tolower(method) %in% c('remove', 'exclude')) {
        stop('`method` must be `remove` or `exclude`')
    }

    do.call(rbind, by(x, INDICES, function(chunk){
        Q <- stats::quantile(
            chunk[[col_for_analysis]],
            probs = c(0.25, 0.75),
            na.rm = TRUE
        )

        iqr <- stats::IQR(chunk[[col_for_analysis]], na.rm = TRUE)

        outlier_threshold_factor <- 1.5
        upper_limit <- Q[2] + outlier_threshold_factor * iqr
        lower_limit <- Q[1] - outlier_threshold_factor * iqr

        rows_to_keep <- is.na(chunk[[col_for_analysis]]) |
            (chunk[[col_for_analysis]] < upper_limit & chunk[[col_for_analysis]] > lower_limit)

        if (tolower(method) == 'remove') {
            chunk[rows_to_keep, ]
        } else {
            chunk[!rows_to_keep, col_for_analysis] <- NA
            chunk
        }
    }))
}

exclude_outliers.exdf <- function(
    x,
    col_for_analysis,
    INDICES,
    method = 'exclude'
)
{
    x$main_data <-
        exclude_outliers(x$main_data, col_for_analysis, INDICES, method)

    return(x)
}