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#' Generate continental plot of index trajectories.
#'
#' Generates the trajectory plot of continental indices.
#'
#' @param indices_list List of indices of annual abundance and other results produced by
#' \code{generate_cont_indices}
#' @param ci_width quantile to define the width of the plotted credible interval. Defaults to 0.95, lower = 0.025 and upper = 0.975
#' @param select logical flag to indicate if the continental data need to be selected out of an indices_list object that includes stratum, national, or other region-types. Default is FALSE
#' @param min_year Minimum year to plot
#' @param max_year Maximum year to plot
#' @param species Species name to be added onto the plot
#' @param title_size Specify font size of plot title. Defaults to 20
#' @param axis_title_size Specify font size of axis titles. Defaults to 18
#' @param axis_text_size Specify font size of axis text. Defaults to 16
#' @param add_observed_means Should the plot include points indicated the observed mean counts. Defaults to FALSE. Note: scale of observed means and annual indices may not match due to imbalanced sampling among strata
#'
#' @return ggplot of continental indices
#'
#' @importFrom ggplot2 ggplot theme element_blank element_line
#' labs geom_line geom_ribbon aes element_text
#' @importFrom grDevices grey
#'
#'
#' @name bbsBayes-deprecated
#' @seealso \code{\link{plot_cont_indices}}
#' @keywords internal
NULL
#' @rdname bbsBayes-deprecated
#' @section \code{plot_cont_indices}:
#' For \code{plot_cont_indices()}, use \code{plot_indices()}.
#'
#' @export
#'
#'
plot_cont_indices <- function(indices_list = NULL,
select = FALSE,
ci_width = 0.95,
min_year = NULL,
max_year = NULL,
species = "",
title_size = 20,
axis_title_size = 18,
axis_text_size = 16,
add_observed_means = FALSE)
{
.Deprecated(new = "plot_indices",
msg = "plot_cont_indices() is deprecated in favour of plot_indices()")
Year <- NULL; rm(Year)
Index <- NULL; rm(Index)
obs_mean <- NULL; rm(obs_mean)
lci <- NULL; rm(lci)
uci <- NULL; rm(uci)
indices = indices_list$data_summary
if(select){
indices = indices[which(indices$Region_Type == "continental"),]
}
lq = (1-ci_width)/2
uq = ci_width+lq
lqc = paste0("Index_q_",lq)
uqc = paste0("Index_q_",uq)
indices$lci = indices[,lqc]
indices$uci = indices[,uqc]
if (!is.null(min_year))
{
indices <- indices[which(indices$Year >= min_year), ]
}
if(!is.null(max_year))
{
indices <- indices[which(indices$Year <= max_year), ]
}
mny = min(indices$Year)
mxy = max(indices$Year)
yys = pretty(seq(mny, mxy))
yys = c(yys[-length(yys)],mxy)
if(add_observed_means){
p <- ggplot2::ggplot() +
ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
axis.line = ggplot2::element_line(colour = "black"),
plot.title = ggplot2::element_text(size = title_size),
axis.title = ggplot2::element_text(size = axis_title_size),
axis.text = ggplot2::element_text(size = axis_text_size)) +
ggplot2::labs(title = paste(species, " Continental Trajectory and raw mean counts", sep = ""),
x = "Year",
y = "Annual index of abundance (mean count)") +
ggplot2::geom_point(data = indices,ggplot2::aes(x = Year,y = obs_mean),colour = grDevices::grey(0.6))+
ggplot2::geom_line(data = indices, ggplot2::aes(x = Year, y = Index)) +
ggplot2::geom_ribbon(data = indices, ggplot2::aes(x = Year, ymin = lci, ymax = uci), alpha = 0.12)+
ggplot2::scale_x_continuous(breaks = yys)+
ggplot2::scale_y_continuous(limits = c(0,NA))
}else{
p <- ggplot2::ggplot() +
ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
axis.line = ggplot2::element_line(colour = "black"),
plot.title = ggplot2::element_text(size = title_size),
axis.title = ggplot2::element_text(size = axis_title_size),
axis.text = ggplot2::element_text(size = axis_text_size)) +
ggplot2::labs(title = paste(species, " Continental Trajectory", sep = ""),
x = "Year",
y = "Annual index of abundance (mean count)") +
ggplot2::geom_line(data = indices, ggplot2::aes(x = Year, y = Index)) +
ggplot2::geom_ribbon(data = indices, ggplot2::aes(x = Year, ymin = lci, ymax = uci), alpha = 0.12)+
ggplot2::scale_x_continuous(breaks = yys)+
ggplot2::scale_y_continuous(limits = c(0,NA))
}
return(p)
}
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