#' Create figure 'figure_error_alignment_length_mean'
#' @param parameters parameters, as returned by read_collected_parameters
#' @param nltt_stats nLTT statistics, as returned by read_collected_nltt_stats
#' @param esses ESSes, as returned by read_collected_esses
#' @param filename name of the file the figure will be saved to
#' @author Richel Bilderbeek
#' @export
create_figure_error_alignment_length_mean <- function(
parameters,
nltt_stats,
esses,
filename
) {
sti <- NULL; rm(sti) # nolint, should fix warning: no visible binding for global variable
ai <- NULL; rm(ai) # nolint, should fix warning: no visible binding for global variable
pi <- NULL; rm(pi) # nolint, should fix warning: no visible binding for global variable
nltt_stat <- NULL; rm(nltt_stat) # nolint, should fix warning: no visible binding for global variable
scr <- NULL; rm(scr) # nolint, should fix warning: no visible binding for global variable
sequence_length <- NULL; rm(sequence_length) # nolint, should fix warning: no visible binding for global variable
`%>%` <- dplyr::`%>%`
nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
dplyr::summarise(mean = mean(nltt_stat))
testit::assert(all(names(nltt_stat_means)
== c("filename", "sti", "ai", "pi", "mean")))
# Connect the mean nLTT stats and parameters
testit::assert("filename" %in% names(parameters))
testit::assert("filename" %in% names(nltt_stat_means))
df_means <- merge(x = parameters, y = nltt_stat_means, by = "filename", all = TRUE)
# Merge with the ESSes
df_means <- merge(x = df_means, y = esses,
by = c("filename", "sti", "ai", "pi"), all = TRUE)
ggplot2::ggplot(
data = stats::na.omit(df_means),
ggplot2::aes(x = as.factor(scr), y = mean, fill = as.factor(sequence_length))
) + ggplot2::geom_boxplot() +
ggplot2::facet_grid(erg ~ sirg) +
ggplot2::xlab(latex2exp::TeX("Speciation completion rate $\\lambda$")) +
ggplot2::ylab(latex2exp::TeX("Mean nLTT statistics, $\\bar{\\Delta_{nLTT}}$")) +
ggplot2::labs(
fill = latex2exp::TeX("Sequence\nlength $l_a$"),
title = "The effect of alignment length on mean nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
caption = filename
) +
ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
ggplot2::ggsave(file = filename, width = 7, height = 7)
}
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