#' Create figure_lowest_ess: Which estimated parameter has the lowest ESS?
#' @param esses the ESSes, as returned from read_collected_esses
#' @param filename name of the file the figure will be saved to
create_figure_lowest_ess <- function(
esses,
filename
) {
# Tally the count of each parameter having the lowest ESS per posterior
parameter_names <- c("posterior", "likelihood", "prior", "treeLikelihood", "TreeHeight", "BirthDeath", "birthRate2", "relativeDeathRate2")
esses$lowest <- apply(esses[ , parameter_names], 1, min)
# This is stupid, but could not get something descent to work quickly enough
# Feel encouraged to send an improvement
for (i in seq(1, nrow(esses))) {
this_lowest <- esses$lowest[i]
if (is.na(this_lowest)) {
next
}
for (parameter_name in parameter_names) {
this_value <- esses[ , parameter_name][i]
if (is.na(this_value)) {
next
}
if (this_value == this_lowest) {
esses$lowest[i] <- parameter_name
}
}
}
# Create the factors
esses$lowest <- as.factor(esses$lowest)
# Make a histogram
svg("~/figure_lowest_ess.svg")
ggplot2::ggplot(
data = esses,
ggplot2::aes(x = lowest, fill = lowest)
) +
ggplot2::geom_bar() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, hjust = 1)) +
ggplot2::ggtitle("Parameters with lowest ESS") +
ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) +
ggplot2::labs(caption = "figure_lowest_ess")
ggplot2::ggsave(file = filename, width = 7, height = 7)
}
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