flexsurvregPlot: Function to visualize 'flexsurv::flexsurvreg' models fit by...

In pcvr: Plant Phenotyping and Bayesian Statistics

Function to visualize flexsurv::flexsurvreg models fit by fitGrowth.

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

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

Arguments

fit	A model fit returned by fitGrowth with type="nls".
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. If the individual and group are specified then the observed growth lines are plotted.
groups	An optional set of groups to keep in the plot. Defaults to NULL in which case all groups in the model are plotted.
df	A dataframe to use in plotting observed growth curves on top of the model. This must be supplied for nls models.
timeRange	Ignored, included for compatibility with other plotting functions.
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 survival model's survival function.

Examples

df <- growthSim("logistic",
  n = 20, t = 25,
  params = list("A" = c(200, 160), "B" = c(13, 11), "C" = c(3, 3.5))
)
ss <- growthSS(
  model = "survival weibull", form = y > 100 ~ time | id / group,
  df = df, type = "flexsurv"
)
fit <- fitGrowth(ss)
flexsurvregPlot(fit, form = ss$pcvrForm, df = ss$df, groups = "a")
flexsurvregPlot(fit,
  form = ss$pcvrForm, df = ss$df,
  facetGroups = FALSE, groupFill = TRUE
)

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