rxode2: Facilities for Simulating from ODE-Based Models

stat_amt

R Documentation

Dosing/Amt geom/stat

Description

This is a dosing geom that shows the vertical lines where a dose occurs

Usage

stat_amt(
  mapping = NULL,
  data = NULL,
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

geom_amt(
  mapping = NULL,
  data = NULL,
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

Arguments

`mapping`	Set of aesthetic mappings created by `aes()`. If specified and `inherit.aes = TRUE` (the default), it is combined with the default mapping at the top level of the plot. You must supply `mapping` if there is no plot mapping.
`data`	The data to be displayed in this layer. There are three options: If `NULL`, the default, the data is inherited from the plot data as specified in the call to `ggplot()`. A `data.frame`, or other object, will override the plot data. All objects will be fortified to produce a data frame. See `fortify()` for which variables will be created. A `function` will be called with a single argument, the plot data. The return value must be a `data.frame`, and will be used as the layer data. A `function` can be created from a `formula` (e.g. `~ head(.x, 10)`).
`position`	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The `position` argument accepts the following: The result of calling a position function, such as `position_jitter()`. This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the `position_` prefix. For example, to use `position_jitter()`, give the position as `"jitter"`. For more information and other ways to specify the position, see the layer position documentation.
`show.legend`	logical. Should this layer be included in the legends? `NA`, the default, includes if any aesthetics are mapped. `FALSE` never includes, and `TRUE` always includes. It can also be a named logical vector to finely select the aesthetics to display.
`inherit.aes`	If `FALSE`, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. `borders()`.
`...`	Other arguments passed on to `layer()`'s `params` argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the `position` argument, or aesthetics that are required can not be passed through `...`. Unknown arguments that are not part of the 4 categories below are ignored. Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, `colour = "red"` or `linewidth = 3`. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the `params`. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data. When constructing a layer using a `⁠stat_()⁠` function, the `...` argument can be used to pass on parameters to the `geom` part of the layer. An example of this is `stat_density(geom = "area", outline.type = "both")`. The geom's documentation lists which parameters it can accept. Inversely, when constructing a layer using a `⁠geom_()⁠` function, the `...` argument can be used to pass on parameters to the `stat` part of the layer. An example of this is `geom_area(stat = "density", adjust = 0.5)`. The stat's documentation lists which parameters it can accept. The `key_glyph` argument of `layer()` may also be passed on through `...`. This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

Details

Requires the following aesthetics:

x representing the x values, usually time
amt representing the dosing values; They are missing or zero when no dose is given

Value

This returns a stat_amt in context of a ggplot2 plot

Examples



library(rxode2)
library(units)


## Model from RxODE tutorial
mod1 <- function() {
  ini({
    KA <- 2.94E-01
    CL <- 1.86E+01
    V2 <- 4.02E+01
    Q  <- 1.05E+01
    V3 <- 2.97E+02
    Kin <- 1
    Kout <- 1
    EC50 <- 200
  })
  model({
    C2 <- centr/V2
    C3 <- peri/V3
    d/dt(depot) <- -KA*depot
    d/dt(centr) <-  KA*depot - CL*C2 - Q*C2 + Q*C3
    d/dt(peri)  <-                    Q*C2 - Q*C3
    d/dt(eff)   <- Kin - Kout*(1-C2/(EC50+C2))*eff
  })
}

## These are making the more complex regimens of the rxode2 tutorial

## bid for 5 days
bid <- et(timeUnits="hr") %>%
  et(amt=10000,ii=12,until=set_units(5, "days"))

## qd for 5 days
qd <- et(timeUnits="hr") %>%
      et(amt=20000,ii=24,until=set_units(5, "days"))

## bid for 5 days followed by qd for 5 days

et <- seq(bid,qd) %>% et(seq(0,11*24,length.out=100))

bidQd <- rxSolve(mod1, et, addDosing=TRUE)

# by default dotted and under-stated
plot(bidQd, C2) + geom_amt(aes(amt=amt))

# of course you can make it a bit more visible

plot(bidQd, C2) + geom_amt(aes(amt=amt), col="red", lty=1, linewidth=1.2)

nlmixr2/rxode2 documentation built on Jan. 11, 2025, 8:48 a.m.