rxode2 (version 2.0.7)

stat_amt: 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() or 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

Position adjustment, either as a string, or the result of a call to a position adjustment function.

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(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Value

This returns a stat_amt in context of a ggplot2 plot

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

Examples

# NOT RUN {
library(rxode2)
library(units)


## Model from RxODE tutorial
mod1 <-rxode2({
       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
       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, size=1.2)
# }