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Plot Maturity Ogive

Source: R/plot_vital_functions.R
plot_maturity_ogive.Rd

Creates maturity ogive plots with credible intervals. Supports both length-at-maturity and age-at-maturity models.

Usage

plot_maturity_ogive(
  fit,
  type = c("length", "age"),
  data = NULL,
  x_col = NULL,
  maturity_col = "maturity",
  sex_col = "sex",
  sex_labels = c(`1` = "Female", `2` = "Male"),
  x_range = NULL,
  n_points = 500,
  show_data = TRUE,
  show_rug = TRUE,
  show_x50_line = TRUE,
  data_alpha = 0.5,
  ribbon_alpha = 0.25,
  line_width = 1.2,
  colors = NULL,
  colorblind = FALSE,
  facet_sex = TRUE,
  x_lab = NULL,
  y_lab = "Probability of Maturity",
  title = NULL,
  base_size = 12,
  theme_args = list(),
  additional_layers = list()
)

Arguments

fit

A CmdStanMCMC object from fit_bayesian_maturity.

type

Character. Type of maturity model: "length" or "age".

data

Optional data.table/data.frame with observed data.

x_col

Character. Column name for predictor (length or age).

maturity_col

Character. Column name for maturity status.

sex_col

Character. Column name for sex.

sex_labels

Named character vector. Labels for sex in plot legend and facets. Default c("1" = "Female", "2" = "Male").

x_range

Numeric vector of length 2. Range for predictions.

n_points

Integer. Number of points for ogive. Default 500.

show_data

Logical. Show observed data? Default TRUE.

show_rug

Logical. Show rug plot at bottom? Default TRUE.

show_x50_line

Logical. Show vertical line at x50? Default TRUE.

data_alpha

Numeric. Transparency for data. Default 0.5.

ribbon_alpha

Numeric. Transparency for ribbon. Default 0.25.

line_width

Numeric. Width of ogive line. Default 1.2.

colors

Character vector of colors.

colorblind

Logical. Use colorblind-safe palette? Default FALSE.

facet_sex

Logical. Facet by sex for two-sex models? Default TRUE.

x_lab, y_lab

Character. Axis labels. Auto-generated if NULL.

title

Character. Plot title.

base_size

Numeric. Base font size. Default 12.

theme_args, additional_layers

Lists for customization.

Value

A ggplot object.

See also

vignette("visualization") for comprehensive plotting examples.

vignette("fit_bayesian_maturity") for maturity model fitting.

fit_bayesian_maturity, vital_colors, theme_vital

Examples

if (FALSE) { # \dontrun{
# Length-at-maturity
plot_maturity_ogive(L50_fit, type = "length", data = shark_data)

# French labels
plot_maturity_ogive(
  L50_fit,
  type = "length",
  data = shark_data,
  sex_labels = c("1" = "Femelle", "2" = "Mâle")
)

# Age-at-maturity with custom styling
plot_maturity_ogive(
  t50_fit,
  type = "age",
  data = shark_data,
  colors = c("#E63946", "#1D3557"),
  show_rug = TRUE
)
} # }