R/get_data_shortgrass_steppe.R

In weecology/MATSS: Macroecological Analyses of Time Series Structure

#' @title get Shortgrass Steppe rodent data
#' 
#' @inheritParams get_mtquad_data
#' @return list of abundance, covariates, and metadata
#'
#' @export
get_sgs_data <- function(path = file.path(get_default_data_path(), 
                                         "shortgrass-steppe-lter"))
{
    data_tables <- import_retriever_data(path = path)
    sgs_data <- data_tables$shortgrass_steppe_lter_shortgrass_data
    
    # select key columns 
    # filter out unknown species and recaptures
    sgs_data <- sgs_data %>% 
        dplyr::select_at(c("session", "year", "veg", "web", "spp")) %>% 
        dplyr::filter(.data$spp != "NA", 
                      .data$spp != "")
    
    # get data into wide format
    # summarize counts for each species in each period
    sgs_abundance <- sgs_data %>%
        dplyr::count(.data$year, .data$session, .data$spp) %>%
        tidyr::spread(key = .data$spp, value = .data$n, fill = 0)
    
    season <- rep(0, nrow(sgs_abundance))
    season[grepl("Sep", sgs_abundance$session)] <- 0.5
    sgs_abundance$samples <- sgs_abundance$year + season
    
    # split into two dataframes and save
    abundance <- dplyr::select_at(sgs_abundance, dplyr::vars(-c("year", "session", "samples")))
    covariates <- dplyr::select_at(sgs_abundance, c("year", "session", "samples"))
    species_table = tibble::tibble(id = c("CHHI", 
                                          "DIOR", 
                                          "MIOC", 
                                          "MUMU", 
                                          "ONLE", 
                                          "PEFL", 
                                          "PEMA", 
                                          "REME", 
                                          "REMO", 
                                          "SPTR", 
                                          "SYAU", 
                                          "THTA"),
                                   genus = c("Chaetodipus", 
                                             "Dipodomys", 
                                             "Microtus", 
                                             "Mus", 
                                             "Onychomys", 
                                             "Perognathus", 
                                             "Peromyscus", 
                                             "Reithrodontomys", 
                                             "Reithrodontomys", 
                                             "Spermophilus", 
                                             "Sylvilagus", 
                                             "Thomomys"), 
                                   species = c("hispidus", 
                                               "ordii", 
                                               "ochrogaster", 
                                               "musculus", 
                                               "leucogaster", 
                                               "flavus", 
                                               "maniculatus", 
                                               "megalotis", 
                                               "montanus", 
                                               "tridecemlineatus", 
                                               "auduboni", 
                                               "talpoides"))
    
    metadata <- list(timename = "samples", effort = NULL, period = 0.5, 
                     species_table = species_table, 
                     is_community = TRUE, 
                     location = c("latitude" = 40 + 49/60, 
                                  "longitude" = -(104 + 46/60)))
    
    out <- list("abundance" = abundance, 
                "covariates" = covariates, 
                "metadata" = metadata) %>%
        append_retriever_citation(path)
    attr(out, "class") <- "matssdata"
    
    return(out)
}