R/new_activity_plots.R

In vulpes-vulpes/batr: Tools for Using Bat Acoustic Monitoring Data in R

#'Plot Activity for a Species at Each Site Within a Project
#'
#'\code{species_daily_site_plot} creates a plot of nightly activity for a chosen
#'species at all sites within a project.
#'
#'@family Basic Plots
#'
#'@param data_path Character. Path to an existing RData file.
#'@param species Character: the four letter species code for the species you
#'  wish to plot. E.g. "Epfu".
#'@param monitoring_start Character, the date the monitoring began (e.g.
#'  "2019-01-01"), leave as NULL to use the earliest data point as the
#'  monitoring start.
#'@param monitoring_end Character, the date the monitoring ceased (e.g.
#'  "2019-01-01"), leave as NULL to use the latest data point as the monitoring
#'  end
#'@param gaps Boolean. Set true to add grey blocks to the plot to indicate
#'  periods in which the recorder was not active (requires log files to be
#'  loaded first using \code{import_logs}. Default is \code{FALSE}.)
#'@param save.directory Character: if provided a .png image of the plot will be
#'  saved in the folder specified. Defaults to \code{NULL}: no output saved.
#'@param y_scale Character. Determines whether scales on the y-axis are matched
#'  or free. Defaults to "free_y" for unmatched axis, set to "fixed" for matched
#'  axis.
#'@param width Number. The width in cm of the plot if saved to file. Default is
#'  25 cm.
#'@param height Number. The height of the plot if saved to file. Default is 20
#'  cm.
#'@param text_size Numeric: adjusts the size of text in the figure.
#'@param date_label Date value: adjusts the formatting of the month labels on
#'  the y-axis. See https://www.statmethods.net/input/dates.html for formatting.
#'@param title Logical vector. If \code{FALSE} (default) title is omitted.
#'
#'@return A plot as an object in the current environment, and a saved image if
#'  selected.
#'
#'@examples
#'\dontrun{
#' species_daily_site_plot(species_night_site_projectname, "Project Name", "Mylu", "2019-01-01", "2019-12-31")
#'}
#'@export
#'
#'
species_daily_site_plot <- function(data_path, species, monitoring_start = NULL,
                                    monitoring_end = NULL, gaps = FALSE, 
                                    save_directory = NULL, y_scale = "free_y", 
                                    width = 15.9, height = 8.43, text_size = 10,
                                    date_label = "%b", title = FALSE) {
  # Subset to selected species
  #species_subset <- dataset[which(dataset$Species==species),]
  #if (!is.null(survey_year)) {
  #  species_subset <- species_subset[which(lubridate::year(species_subset$Night)==survey_year),]
  #}
  # Import data
  .check_data_path(data_path) # Check the data path provided
  # load(data_path) # Load the data path
  dataset <- .location_subsetter(data_path) # Offer to subset locations
  dataset <- dataset[which(dataset$Species==species),] #subset the species
  # Create count table
  counts <- aggregate(dataset$Species, list(
    Night = dataset$Night, Species = dataset$Species, Location = dataset$Location, Latitude = dataset$Latitude, Longitude = dataset$Longitude), FUN=length) # Create intial table
  names(counts)[names(counts) == "x"] <- "Count"
  # Create gap table if needed
  load(data_path)
  if (isTRUE(gaps)) {
    if (!exists("active_dates")) {
      stop("Log file data are missing, please run import_logs and try again.")
    } else {
      gap_list <- .plot_gap_calculator(active_dates)
    }
  }
  # Create monitoring start / end if needed
  if (isTRUE(gaps)) {
    if (is.null(monitoring_start)) {
      monitoring_start <- min(gap_list$xmin)
    }
    if (is.null(monitoring_end)) {
      monitoring_end <- max(gap_list$xmax)
    }
  } else {
    if (is.null(monitoring_start)) {
      monitoring_start <- .monitoring_start_finder(dataset)
    }
    if (is.null(monitoring_end)) {
      monitoring_end <- .monitoring_end_finder(dataset)
    }
  }
  # Create Plot
  species_daily_site_plot <- ggplot2::ggplot() +
    ggplot2::geom_bar(data = counts, mapping = ggplot2::aes(x = Night, y = Count), stat = "identity", fill = "black") +
    ggplot2::scale_y_continuous(name = "Observations per Night") +
    ggplot2::scale_x_date(limits = c(as.Date(monitoring_start),as.Date(monitoring_end)), breaks = scales::pretty_breaks(), date_breaks = "1 month", date_labels =  date_label) +
    ggplot2::facet_wrap(
      ~Location,  ncol = 1, scales = y_scale, strip.position = "top") +#, labeller=location_labeller) +
    ggplot2::geom_hline(yintercept=0) +
    ggplot2::theme_classic() +
    ggplot2::theme(
      plot.title = ggplot2::element_text(hjust = 0.5),
      strip.background = ggplot2::element_blank(),
      strip.text = ggplot2::element_text(hjust = 0),
      text = ggplot2::element_text(size=text_size)
    ) +
    if(isTRUE(gaps)) {
      gap_list <- batr:::.plot_gap_calculator(active_dates)
      ggplot2::geom_rect(data=gap_list, 
                         ggplot2::aes(xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax, alpha=0.9),
                         show.legend = FALSE)
    }
  if(isTRUE(title)) {
    species_daily_site_plot <- species_daily_site_plot + ggplot2::ggtitle(paste("Total Activity of ", species, " by Site", sep = ""))
  }
  # Save plot to a specified folder if requested
  if (!is.null(save_directory)) {
    ggplot2::ggsave(paste(save_directory, "/", species, "_daily_site_plot.png", sep = ""), width = width, height = height, units = "cm")
  }
  # Save plot to a specified folder if requested
  #if (!is.null(save_directory)) {
  #  ggplot2::ggsave(paste(save_directory, "/", species, "_daily_site_plot_", project_name, ".png", sep = ""), width = width, height = height, units = "cm")
  #}
  # Save plot to environment
  #assign(paste(species, "_daily_site_plot_", project_name, sep = ""), species_site_aggregated_plot, envir=globalenv())
  # Plot plot
  return(species_daily_site_plot)
}