Skip to contents

Plot Growth Curves

Source: R/plot_vital_functions.R
plot_growth_curve.Rd

Creates growth curve plots with credible intervals. Automatically handles single-sex and two-sex models.

Usage

plot_growth_curve(
  fit,
  data = NULL,
  age_col = "age",
  length_col = "length",
  sex_col = "sex",
  sex_labels = c(`1` = "Female", `2` = "Male"),
  age_range = NULL,
  n_points = 500,
  show_data = TRUE,
  show_50_ci = TRUE,
  data_alpha = 0.4,
  data_size = 1.5,
  ribbon_alpha = 0.2,
  ribbon_alpha_50 = 0.3,
  line_width = 1.2,
  colors = NULL,
  colorblind = FALSE,
  facet_sex = TRUE,
  x_lab = "Age (years)",
  y_lab = "Length (cm)",
  title = NULL,
  k_based = FALSE,
  which_model = 1L,
  base_size = 12,
  theme_args = list(),
  additional_layers = list()
)

Arguments

fit

A CmdStanMCMC object from fit_bayesian_growth.

data

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

age_col

Character. Column name for age in data. Default "age".

length_col

Character. Column name for length in data. Default "length".

sex_col

Character. Column name for sex in data. Default "sex".

sex_labels

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

age_range

Numeric vector of length 2. Age range for predictions. If NULL, auto-determined from data or defaults to c(0, 30).

n_points

Integer. Number of points for prediction grid. Default 500.

show_data

Logical. Overlay observed data points? Default TRUE.

show_50_ci

Logical. Show 50% credible interval ribbon? Default TRUE.

data_alpha

Numeric. Transparency for data points. Default 0.4.

data_size

Numeric. Size for data points. Default 1.5.

ribbon_alpha

Numeric. Transparency for 95% CI ribbon. Default 0.2.

ribbon_alpha_50

Numeric. Transparency for 50% CI ribbon. Default 0.3.

line_width

Numeric. Width of median line. Default 1.2.

colors

Character vector of colors. If NULL, uses vital_colors().

colorblind

Logical. Use colorblind-safe palette? Default FALSE. When TRUE, overrides colors with vital_colors(, "sex_cb") for two-sex models or vital_colors(, "okabe_ito") otherwise.

facet_sex

Logical. For two-sex models, facet by sex? Default TRUE.

x_lab, y_lab

Character. Axis labels.

title

Character. Plot title. Default NULL.

k_based

Logical. Was the model k-based? Default FALSE.

which_model

Integer. 1=VBGM, 2=Gompertz, 3=Logistic. Default 1.

base_size

Numeric. Base font size for theme. Default 12.

theme_args

List of additional arguments for ggplot2::theme().

additional_layers

List of additional ggplot2 layers to add.

Value

A ggplot object.

See also

vignette("visualization") for comprehensive plotting examples.

vignette("fit_bayesian_growth") for growth model fitting.

compare_growth_models, plot_residuals, vital_colors, theme_vital

Examples

if (FALSE) { # \dontrun{
# Basic usage
plot_growth_curve(growth_fit, data = shark_data)

# French labels
plot_growth_curve(
  growth_fit,
  data = shark_data,
  sex_labels = c("1" = "Femelle", "2" = "Mâle")
)

# Spanish labels
plot_growth_curve(
  growth_fit,
  data = shark_data,
  sex_labels = c("1" = "Hembra", "2" = "Macho")
)

# Customize appearance
plot_growth_curve(
  growth_fit,
  data = shark_data,
  colors = c("#E63946", "#1D3557"),
  theme_args = list(legend.position = "bottom"),
  additional_layers = list(
    geom_hline(yintercept = 100, linetype = "dashed")
  )
)
} # }