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.
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
)Returns a ggplot2 plot
A list object created by the
growth_curve_model_fit function.
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.
A character string for specifying the name of the growth metric (y-axis title) to be displayed on the plot. Defaults to "growth_metric".
A character string for specifying the name of the time variable (x-axis title) to be displayed on the plot. Defaults to "time".
A character string for specifying the name of the cluster variable (legend title) to be displayed on the plot. Defaults to "cluster".
A character string for specifying the title to be displayed over the plot. Defaults to "Growth vs Time".
A numeric vector specifying manual numeric breaks.
Defaults to ggplot2::waiver(). See scale_x_continuous.
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.
An integer specifying the number of major breaks
for the x-axis. Defaults to NULL.
See scale_x_continuous.
A numeric vector specifying manual numeric breaks.
Defaults to ggplot2::waiver(). See scale_y_continuous.
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.
An integer specifying the number of major breaks
for the x-axis. Defaults to NULL.
See scale_y_continuous.
A numeric value specifying the size of the
x-axis text. Defaults to 8. See element_text.
A numeric value specifying the size of the
y-axis text. Defaults to 12. See element_text.
A numeric value specifying the size of the
x-axis title. Defaults to 14. See element_text.
A numeric value specifying the size of the
y-axis title. Defaults to 14. See element_text.
A numeric value specifying the size of the plot
title. Defaults to 20. See element_text.
A numeric value specifying the size of the points
on the graph. Defaults to 2. See geom_point.
A numeric value specifying the width of the line (applicable only for plot_type = 2, 3, or 4). Defaults to 0.5.
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"
A numeric value specifying the size of
the annotation text. Defaults to 5. See geom_text.
growth_curve_model_fit
# \donttest{
# 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)
# }
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