nlmePlot {pcvr} | R Documentation |
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 |
form |
A formula similar to that in |
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)