R/convert_to_long_format.R

In FRBCesab/forcis: An R Client to Access the FORCIS Database

#' Reshape and simplify FORCIS data
#'
#' @description
#' Reshapes FORCIS data by pivoting species columns into two columns: `taxa` 
#' (taxon names) and `counts` (taxon abundances). It converts wider `data.frame`
#' to a long format.
#' 
#' @param data a `data.frame`, i.e. a FORCIS dataset, except for CPR North data.
#'
#' @return A `data.frame` reshaped in a long format.
#' 
#' @export
#'
#' @examples
#' # Attach the package ----
#' library("forcis")
#' 
#' # Import example dataset ----
#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
#'                          package = "forcis")
#' 
#' net_data <- read.table(file_name, dec = ".", sep = ";")
#' 
#' # Add 'data_type' column ----
#' net_data$"data_type" <- "Net"
#' 
#' # Dimensions of the data.frame ----
#' dim(net_data)
#' 
#' # Reshape data ----
#' net_data <- convert_to_long_format(net_data)
#' 
#' # Dimensions of the data.frame ----
#' dim(net_data)
#' 
#' # Column names ----
#' colnames(net_data)

convert_to_long_format <- function(data) {
  
  ## Check data object ----
  
  check_if_df(data)
  
  if (get_data_type(data) == "CPR North") {
    stop("This function is not designed to work with 'CPR North' data", 
         call. = FALSE) 
  }
  
  taxa_cols     <- get_species_names(data) 
  metadata_cols <- get_required_columns()
  
  data <- data[ , c(taxa_cols, metadata_cols)]

  tidyr::pivot_longer(data,
                      tidyr::all_of(taxa_cols), 
                      names_to  = "taxa", 
                      values_to = "counts")
}