R/plot_timeDiff.R

Defines functions plot_timeDiff

Documented in plot_timeDiff

#' @title Plot units of time elapsed between sampling points over the time series.
#' @description This function plots the amount of time that has elapsed since the last sampled unit time.
#' @param data The original data frame
#'
#' @export
#' @param example Logical. If TRUE will use the paleodiatom data from Spanbauer et al. (2014), else will use input data.
#' @param print print plots to device when print = T. Default print = T.
#' @return Function returns a data frame in long format with columns specifying site name, time (or spatial unit), variable (e.g. species identity), and value (e.g. species count).
#' @references Spanbauer, Trisha L., et al. "Prolonged instability prior to a regime shift." PLoS One 9.10 (2014): e108936.

plot_timeDiff <- function(data,
             example = FALSE,
             print = TRUE,
             xLabel = "time"){
        temp <- data %>%
            # group_by(time) %>%
            filter(value > 0) %>%
            dplyr::select(-site, -value, -variable) %>%
            distinct(sortVar, .keep_all = T) %>%
            arrange(sortVar) %>%
            #ungroup() %>%
            mutate(sampDiff = as.integer(round(abs(
                lead(sortVar) - sortVar
            )))) %>%
            as_tibble()

        p1 <- ggplot(data = temp, aes(y =  sampDiff, x = sortVar)) +
            geom_line() +
            theme_classic() +
            xlab(xLabel)


        if (example == T) {
            p1 <- p1 +
                xlab("\nyears before 1942") +
                ylab("time since last observation\n") +
                theme(text = element_text(size = 18),
                      axis.text.x = element_text(angle =
                                                     90, hjust = 1)) +
                scale_x_continuous(
                    labels = function(x)
                        paste0(x * -1)
                )
        }

        if (print == T) {
            print(p1)
        }

    }
TrashBirdEcology/regimeDetectionMeasures documentation built on Oct. 13, 2019, 5:15 p.m.