growth_vs_time_plot: Generate growth vs time plots

In GrowthCurveME: Mixed-Effects Modeling for Growth Data

Generate growth vs time plots

Description

This function provides a wrapper to ggplot2 in order to generate different plots from a growth curve model summary list object generated by the growth_curve_model_fit function. Please refer to the documentation for the 'plot_type' parameter for the different plot options.

Usage

growth_vs_time_plot(
  growth_model_summary_list,
  plot_type = 2,
  growth_metric_name = "growth_metric",
  time_name = "time",
  cluster_name = "cluster",
  plot_title = "Growth vs Time",
  x_axis_breaks = ggplot2::waiver(),
  x_limits = c(NA, NA),
  n_x_axis_breaks = NULL,
  y_axis_breaks = ggplot2::waiver(),
  y_limits = c(NA, NA),
  n_y_axis_breaks = NULL,
  x_axis_text_size = 8,
  y_axis_text_size = 12,
  x_axis_title_size = 14,
  y_axis_title_size = 14,
  plot_title_size = 20,
  geom_point_size = 2,
  geom_line_width = 0.5,
  pred_plot_annotate_value = "double_time",
  annotate_value_text_size = 5
)

Arguments

growth_model_summary_list	A list object created by the growth_curve_model_fit function.
plot_type	A numeric value used to specify the plot type to graph. Values include 1, 2, 3, 4 with descriptions of each below (defaults to 2): 1 - A scatterplot of the growth_metric vs time data where each point is colored by cluster if applicable. 2 - A scatterplot of the growth_metric vs time data where each point is colored by cluster if applicable and the model predicted values are overlayed as line. When a mixed-effect model summary list is input, the predicted values are the ind_fit_value which accounts for both fixed and random-effects. When a least-squares model summary list is input the predicted values are the fitted values accounting for fixed-effects only (pop_fit_value). 3 - A scatterplot version of plot_type = 2 where each cluster is separated into their own plot forming a matrix of growth_metric vs time plots by cluster. 4 - A plot of the estimates and prediction intervals of the model. When a mixed-effects model summary list is input, the prediction intervals are calculated from the median and the 2.5th and 97.5th percentiles of the saemix model simulations to assist in showing the variability of both the population trends and variation among the cluster-level predictions (see compute.sres). When a least-squares model summary list is input, the prediction intervals are calculated through Taylor-series approximations of the nls model (see predFit). By default will also add an annotation of the doubling time with 95% confidence intervals calculated directly from the original model estimates.
growth_metric_name	A character string for specifying the name of the growth metric (y-axis title) to be displayed on the plot. Defaults to "growth_metric".
time_name	A character string for specifying the name of the time variable (x-axis title) to be displayed on the plot. Defaults to "time".
cluster_name	A character string for specifying the name of the cluster variable (legend title) to be displayed on the plot. Defaults to "cluster".
plot_title	A character string for specifying the title to be displayed over the plot. Defaults to "Growth vs Time".
x_axis_breaks	A numeric vector specifying manual numeric breaks. Defaults to ggplot2::waiver(). See scale_x_continuous.
x_limits	A numeric vector of length two providing limits for the x-axis. Use NA to refer to the existing minimum or maximum. Defaults to c(NA, NA). See scale_x_continuous.
n_x_axis_breaks	An integer specifying the number of major breaks for the x-axis. Defaults to NULL. See scale_x_continuous.
y_axis_breaks	A numeric vector specifying manual numeric breaks. Defaults to ggplot2::waiver(). See scale_y_continuous.
y_limits	A numeric vector of length two providing limits for the y-axis. Use NA to refer to the existing minimum or maximum. Defaults to c(NA, NA). See scale_y_continuous.
n_y_axis_breaks	An integer specifying the number of major breaks for the x-axis. Defaults to NULL. See scale_y_continuous.
x_axis_text_size	A numeric value specifying the size of the x-axis text. Defaults to 8. See element_text.
y_axis_text_size	A numeric value specifying the size of the y-axis text. Defaults to 12. See element_text.
x_axis_title_size	A numeric value specifying the size of the x-axis title. Defaults to 14. See element_text.
y_axis_title_size	A numeric value specifying the size of the y-axis title. Defaults to 14. See element_text.
plot_title_size	A numeric value specifying the size of the plot title. Defaults to 20. See element_text.
geom_point_size	A numeric value specifying the size of the points on the graph. Defaults to 2. See geom_point.
geom_line_width	A numeric value specifying the width of the line (applicable only for plot_type = 2, 3, or 4). Defaults to 0.5.
pred_plot_annotate_value	A character string specifying whether to add the doubling time or rate estimates from the model to plot 4. Options include "double_time" for the doubling time with 95% CI, "rate" for the rate estimate with 95% CI, or "none" for no annotation. Defaults to "double_time"
annotate_value_text_size	A numeric value specifying the size of the annotation text. Defaults to 5. See geom_text.

Value

Returns a ggplot2 plot

See Also

growth_curve_model_fit

Examples

# Load example data (exponential data)
data(exp_mixed_data)
# Fit an mixed-effects growth model to the data
exp_mixed_model_summary <- growth_curve_model_fit(
  data_frame = exp_mixed_data,
  function_type = "exponential",
  verbose = FALSE
)
# Create growth vs time plot of data with fitted values (plot_type = 2)
exp_growth_plot <- growth_vs_time_plot(
  growth_model_summary_list = exp_mixed_model_summary,
  plot_type = 2
)
print(exp_growth_plot)

GrowthCurveME documentation built on April 12, 2025, 2:23 a.m.