nlmePlot: Function to visualize common 'nlme::nlme' growth models.

In pcvr: Plant Phenotyping and Bayesian Statistics

Function to visualize common nlme::nlme growth models.

Description

Models fit using growthSS inputs by fitGrowth (and similar models made through other means) can be visualized easily using this function. This will generally be called by growthPlot.

Usage

nlmePlot(
  fit,
  form,
  df = NULL,
  groups = NULL,
  timeRange = NULL,
  facetGroups = TRUE,
  groupFill = FALSE,
  virMaps = c("plasma")
)

Arguments

fit	A model fit returned by fitGrowth with type="nlme".
form	A formula similar to that in growthSS inputs (or the pcvrForm part of the output) specifying the outcome, predictor, and grouping structure of the data as outcome ~ predictor|individual/group
df	A dataframe to use in plotting observed growth curves on top of the model. This must be supplied for nlme models.
groups	An optional set of groups to keep in the plot. Defaults to NULL in which case all groups in the model are plotted.
timeRange	An optional range of times to use. This can be used to view predictions for future data if the available data has not reached some point (such as asymptotic size).
facetGroups	logical, should groups be separated in facets? Defaults to TRUE.
groupFill	logical, should groups have different colors? Defaults to FALSE. If TRUE then viridis colormaps are used in the order of virMaps.
virMaps	order of viridis maps to use. Will be recycled to necessary length. Defaults to "plasma", but will generally be informed by growthPlot's default.

Value

Returns a ggplot showing an nlme model's credible intervals and optionally the individual growth lines.

Examples

simdf <- growthSim("logistic",
  n = 10, t = 25,
  params = list("A" = c(200, 160), "B" = c(13, 11), "C" = c(3, 3.5))
)

ss <- growthSS(
  model = "logistic", form = y ~ time | id / group, sigma = "none",
  df = simdf, start = NULL, type = "nlme"
)

fit <- fitGrowth(ss)

nlmePlot(fit, form = ss$pcvrForm, groups = NULL, df = ss$df, timeRange = NULL)
nlmePlot(fit, form = ss$pcvrForm, groups = "a", df = ss$df, timeRange = 1:10, groupFill = TRUE)

pcvr documentation built on April 16, 2025, 5:12 p.m.