R/reduce_data.R

In HOPE-UIB-BIO/R-Ratepol-package: R-Ratepol: Estimating Rate of Change in Temporal Sequences

#' @title Reduce datasets
#' @param data_source_reduce List with `community`, `age`, and `age_un`
#' @param check_taxa Logical. Should columns be check for redundnat data?
#' @param check_levels Logical. Should rows be check for redundnat data?
#' @description
#' Check the community dataset for redundnat taxa and levels
#' and filter them out.
#' @keywords internal
reduce_data <-
  function(data_source_reduce,
           check_taxa = TRUE,
           check_levels = TRUE) {
    RUtilpol::check_class("data_source_reduce", "list")

    RUtilpol::check_class("check_taxa", "logical")

    RUtilpol::check_class("check_levels", "logical")

    if (
      isTRUE(check_taxa)
    ) {
      valid_taxa <-
        (colSums(data_source_reduce$community, na.rm = TRUE) > 0)

      data_source_reduce$community <-
        data_source_reduce$community %>%
        dplyr::select(
          dplyr::any_of(
            c(names(valid_taxa[valid_taxa]))
          )
        )
    }

    if (
      isTRUE(check_levels) # if filter out samples without individuals
    ) {
      valid_levels <-
        (rowSums(data_source_reduce$community, na.rm = TRUE) > 0)

      valid_levels_reduced <- valid_levels[valid_levels]

      data_source_reduce$age <-
        data_source_reduce$age %>%
        tibble::rownames_to_column("sample_id") %>%
        dplyr::filter(
          .data$sample_id %in% names(valid_levels_reduced)
        ) %>%
        tibble::column_to_rownames("sample_id")

      data_source_reduce$community <-
        data_source_reduce$community %>%
        tibble::rownames_to_column("sample_id") %>%
        dplyr::filter(
          .data$sample_id %in% names(valid_levels_reduced)
        ) %>%
        tibble::column_to_rownames("sample_id")

      if (
        isFALSE(is.null(data_source_reduce$age_un))
      ) {
        data_source_reduce$age_un <-
          data_source_reduce$age_un[, valid_levels]
      }
    }

    return(data_source_reduce)
  }