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#' Plots output of \code{\link{computeMemory}}
#'
#' @description Plots the ecological memory pattern yielded by \code{\link{computeMemory}}.
#'
#' @usage plotMemory(
#' memory.output = NULL,
#' title = "Ecological memory pattern",
#' legend.position = "right",
#' filename = NULL
#' )
#'
#' @param memory.output a dataframe with one time series per column.
#' @param title character string, name of the numeric column to be used as response in the model.
#' @param legend.position character vector, names of the numeric columns to be used as predictors in the model.
#' @param filename character string, name of output pdf file. If NULL or empty, no pdf is produced. It shouldn't include the extension of the output file.
#'
#' @author Blas M. Benito <blasbenito@gmail.com>
#'
#' @return A ggplot object.
#'
#' @seealso \code{\link{computeMemory}}
#'
#' @examples
#'#loading data
#'data(palaeodataMemory)
#'
#'#plotting memory pattern
#'plotMemory(memory.output = palaeodataMemory)
#'
#'
#'@export
plotMemory <- function(
memory.output = NULL,
title = "Ecological memory pattern",
legend.position = "right",
filename = NULL
){
#to dataframe
memory.output.df <- memory.output$memory
#guessing units of Lags
if((memory.output.df[2, "Lag"] - memory.output.df[1, "Lag"]) < 1){
lag.units <- "ky"
} else {
lag.units <- "years"
}
#plot
plot.memory <- ggplot(data=memory.output.df, aes(x=Lag, y=median, group=Variable, color=Variable, fill=Variable)) +
geom_ribbon(aes(ymin=min, ymax=max), alpha=0.3, colour=NA) +
geom_line(alpha=0.6, size=1.5) +
scale_color_viridis(discrete=TRUE) +
scale_fill_viridis(discrete=TRUE) +
scale_x_continuous(breaks=unique(memory.output.df$Lag), expand=c(0,0)) +
scale_y_continuous(expand=c(0,0)) +
xlab(paste("Lag (", lag.units, ")", sep="")) +
ylab("Relative importance") +
theme(strip.text.x = element_text(size = 12),
legend.position = legend.position,
axis.text.x = element_text(size=12)) +
ggtitle(title) +
cowplot::theme_cowplot()
print(plot.memory)
#plots to pdf
if(!is.null(filename)){ggsave(filename = paste(filename, ".pdf", sep = ""))}
}
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