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#' Plots of results
#'
#' @description Creates a set of time series, density, or trace plots.
#'
#' @param x object of class \code{ss_fit}
#' @param plot_type type of plots, options are
#' \code{"timeseries", "density", "trace"}
#' @param n_col number of columns for grid plots
#' @param n_sep increments of x axis ticks in years
#' @param file_path file path for plots
#' @param title boolean indicating if plots should contain titles
#' @param save boolean indicating if plots should be saved, if \code{FALSE}, the
#' plots will be printed instead, default is \code{save = FALSE} (ignored if
#' \code{file_path} is provided)
#' @param device character string with format used in \code{ggsave}
#' @param width plot width in \code{units}, for grid plots adjusted for the
#' number of plot columns \code{n_col}
#' @param height plot height in \code{units}, for grid plots adjusted for the
#' number of plot rows implied by \code{n_col}
#' @param units units for plot size (\code{"in", "cm", "mm", or "px"})
#' @param highlighted_area data frame with two columns called \code{start} and
#' \code{end} containing start and end date, e.g. \code{1990.25} and
#' \code{1992.75} for 1990 Q2 until 1992 Q4
#' (only used if \code{plot_type = "timeseries"})
#' @param plot_start start of x axis in years, e.g., \code{1990.5} (only used if
#' \code{plot_type = "timeseries"})
#' @param plot_end end of x axis in years, e.g., \code{2010.25} (only used if
#' \code{plot_type = "timeseries"})
#' @param alpha cut off value for posterior (only used if
#' \code{plot_type = "density"})
#' @param include_burnin logical indicating if burnin phase should be included
#' (only used if \code{plot_type = "trace"})
#' @param ... ignored
#'
#' @inheritParams define_ssmodel
#' @inheritParams transform_results
#'
#' @return nothing
#'
#' @export
plot.ss_fit <- function(
x,
plot_type = "timeseries",
estimate = "median",
data = data,
n_col = 3,
n_sep = 5,
file_path = NULL,
title = TRUE,
save = FALSE,
device = "jpg",
width = 10,
height = 3,
units = "in",
highlighted_area = NULL,
plot_start = NULL,
plot_end = NULL,
alpha = 0.05,
include_burnin = FALSE,
...
) {
# check file path
if (is.null(file_path) && save) {
warnings("No file path provided, figures will not be saved.")
} else if (!is.null(file_path)) {
dir.create(file_path, showWarnings = FALSE)
save <- TRUE
}
if (plot_type == "timeseries") {
df <- transform_results(
fit = x,
data = data,
estimate = estimate
)
plot_time_series(
df = df,
settings = x$settings,
n_col = n_col,
n_sep = n_sep,
highlighted_area = highlighted_area,
plot_start = plot_start,
plot_end = plot_end,
file_path = file_path,
title = title,
save = save,
device = device,
width = width,
height = height,
units = units
)
} else if (plot_type == "density") {
plot_densities(
fit = x,
file_path = file_path,
n_col = n_col,
alpha = alpha,
save = save,
title = title,
device = device,
width = width,
height = height,
units = units
)
} else if (plot_type == "trace") {
plot_trace(
fit = x,
file_path = file_path,
include_burnin = include_burnin,
n_col = n_col,
alpha = alpha,
save = save,
title = title,
device = device,
width = width,
height = height,
units = units
)
} else {
stop("No valid 'plot_type' provided.")
}
}
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