R/get_data_mtquad.R

In weecology/MATSS: Macroecological Analyses of Time Series Structure

#' @title get Montana plant quad time-series data
#'
#' @param path where to load the raw data files from
#' @return list of abundance, covariates, and metadata
#' 
#' @export

get_mtquad_data <- function(path = file.path(get_default_data_path(), 
                                             "mapped-plant-quads-mt"))
{
    mtquad_data_tables <- import_retriever_data(path = path)
    
    mtquad_data <- mtquad_data_tables$mapped_plant_quads_mt_allrecords_density %>%
        dplyr::select_at(dplyr::vars(-c("objectid", "seedling", "x", "y"))) %>%
        dplyr::group_by(.data$year, .data$species, .data$quad) %>%
        dplyr::summarize(abundance = sum(.data$stems)) %>%
        dplyr::group_by(.data$year, .data$species) %>%
        dplyr::summarize(abundance = sum(.data$abundance)) %>%
        tidyr::spread(key = .data$species, value = .data$abundance, fill = 0) %>%
        dplyr::ungroup()
    
    abundance <- dplyr::select(mtquad_data, -.data$year)
    covariates <- dplyr::select(mtquad_data, .data$year)
    species_table <- mtquad_data_tables$mapped_plant_quads_mt_species_list %>%
        dplyr::mutate(id = paste(.data$species, .data$density), 
                      genus = sub("^unknown", NA, .data$species), 
                      species = ifelse(is.na(.data$genus), NA, 
                                       sub("^sp.|unknown]$", NA, .data$density)), 
                      density = .data$cover, 
                      cover = .data$annual, 
                      annual = .data$growthform, 
                      growthform = NULL) %>%
        dplyr::select(.data$id, .data$genus, .data$species, dplyr::everything()) %>%
        tibble::add_row(id = "unknown")
    metadata <- list(timename = "year", effort = NULL, 
                     species_table = species_table, 
                     is_community = TRUE, 
                     location = c("latitude" = 46 + 22/60, 
                                  "longitude" = -(105+5/60)))
    
    out <- list("abundance" = abundance, 
                "covariates" = covariates, 
                "metadata" = metadata) %>%
        append_retriever_citation(path)
    attr(out, "class") <- "matssdata"
    
    return(out)
}