Effective population size history plots — geom_ne

Plot effective population size through time from PSMC, MSMC2, SMC++, and Stairway Plot 2 outputs.

Usage

geom_ne_history(
  mapping = ggplot2::aes(x = .data$time, y = .data$ne, colour = .data$sample_id),
  data = NULL,
  ...,
  sample_id = NULL,
  method = NULL,
  style = c("auto", "step", "line", "point"),
  ci = TRUE,
  colour_by = c("sample_id", "method"),
  size = NULL,
  alpha = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  log_x = TRUE,
  log_y = TRUE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

plot_ne_history(
  data,
  sample_id = NULL,
  method = NULL,
  style = c("auto", "step", "line", "point"),
  ci = TRUE,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  log_x = TRUE,
  log_y = TRUE,
  ...
)

geom_demographic_history(
  mapping = ggplot2::aes(x = .data$time, y = .data$ne, colour = .data$sample_id),
  data = NULL,
  ...,
  sample_id = NULL,
  method = NULL,
  style = c("auto", "step", "line", "point"),
  ci = TRUE,
  colour_by = c("sample_id", "method"),
  size = NULL,
  alpha = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  log_x = TRUE,
  log_y = TRUE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

plot_demographic_history(
  data,
  sample_id = NULL,
  method = NULL,
  style = c("auto", "step", "line", "point"),
  ci = TRUE,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  log_x = TRUE,
  log_y = TRUE,
  ...
)

Arguments

mapping: Aesthetic mapping. Defaults to time, Ne, and sample colour.
data: A ggpop_ne_history object from import_ne_history().
...: Additional geom parameters.
sample_id, method: Optional sample/population or method filters.
style: Draw "auto", "step", "line", or "point" layers. "auto" follows common tool conventions: SMC++ histories use lines, while PSMC, MSMC2, and Stairway Plot 2 histories use step curves.
ci: Draw confidence interval ribbons when ne_lower and ne_upper are available.
colour_by: Colour by sample or method.
size, alpha: Layer appearance.
base_size, base_family: Base theme font controls.
palette: ggpop discrete palette.
log_x, log_y: Use log10 time and Ne axes.
na.rm, show.legend, inherit.aes: Standard ggplot2 layer arguments.
title, subtitle, caption: Optional plot labels. No default title is added.

Value

geom_ne_history() and geom_demographic_history() return a list of ggplot layers. plot_ne_history() and plot_demographic_history() return a ggplot object.

Details

SMC++ bootstrap or replicate trajectories are drawn first as thin low-alpha lines when common columns such as type, plot_type, replicate, or bootstrap identify them. Main trajectories remain visually dominant.

Examples

smcpp <- import_ne_history(
  system.file("extdata", "ne_history", "SMC++", "model.csv", package = "ggpop"),
  type = "smcpp"
)
#> Error: `dir` must point to an existing directory or file.
smcpp |> plot_ne_history()
#> Error: object 'smcpp' not found
smcpp |> ggpop() + geom_ne_history()
#> Error: object 'smcpp' not found