R: Create an event table object

eventTable {RxODE}

R Documentation

Create an event table object

Description

Initializes an object of class ‘EventTable’ with methods for adding and querying dosing and observation records

Usage

eventTable(amount.units = NA, time.units = NA)

Arguments

amount.units

string denoting the amount dosing units, e.g., “mg”, “ug”. Default to NA to denote unspecified units. It could also be a solved RxODE object. In that case, eventTable(obj) returns the eventTable that was used to solve the RxODE object.

time.units

string denoting the time units, e.g., “hours”, “days”. Default to "hours".

An eventTable is an object that consists of a data.frame storing ordered time-stamped events of an (unspecified) PK/PD dynamic system, units (strings) for dosing and time records, plus a list of functions to add and extract event records.

Currently, events can be of two types: dosing events that represent inputs to the system and sampling time events that represent observations of the system with ‘amount.units’ and ‘time.units’, respectively. In the future, additional events may include resetting of state variables (compartments), for instance, to indicate time after “wash-out”, etc.

Value

A modified data.frame with the following accessible functions:

`get.EventTable`	returns the current event table.
`add.dosing`	adds dosing records to the event table. Its arguments are `dose`: numeric scalar, dose amount in `amount.units`; `nbr.doses`: integer, number of doses; `dosing.interval`: required numeric scalar, time between doses in `time.units`, defaults to 24 of `time.units="hours"`; `dosing.to`: integer, compartment the dose goes into (first compartment by default); `rate`: for infusions, the rate of infusion (default is `NULL`, for bolus dosing; `start.time`: required dosing start time; `do.sampling`: logical, should observation sampling records be added at the dosing times? Defaults to `FALSE`. `amount.units`: optional string indicating the dosing units. Defaults to `NA` to indicate as per the original `EventTable` definition. `time.units`: optional string indicating the time units. Defaults to `"hours"` to indicate as per the original `EventTable` definition.
`get.dosing`	returns a data.frame of dosing records.
`clear.dosing`	clears or deletes all dosing from event table
`add.sampling`	adds sampling time observation records to the event table. Its arguments are `time` a vector of time values (in `time.units`). `time.units` an optional string specifying the time units. Defaults to the units specified when the `EventTable` was initialized.
`get.sampling`	returns a data.frame of sampled observation records.
`clear.sampling`	removes all sampling from event table.
`get.obs.rec`	returns a logical vector indicating whether each event record represents an observation or not.
`get.nobs`	returns the number of observation (not dosing) records.
`get.units`	returns a two-element character vector with the dosing and time units, respectively.
`copy`	makes a copy of the current event table. To create a copy of an event table object use `qd2 <- qd$copy()`.
`expand`	Expands the event table for multi-subject solving. This is done by qd$expand(400) for a 400 subject data expansion

Author(s)

Matthew Fidler, Melissa Hallow and Wenping Wang

Examples

# create dosing and observation (sampling) events
# QD 50mg dosing, 5 days followed by 25mg 5 days
#
qd <- eventTable(amount.units = "mg", time.units = "days")
#
qd$add.dosing(dose=50, nbr.doses=5, dosing.interval = 1, do.sampling=FALSE)
#
# sample the system's drug amounts hourly the first day, then every 12 hours
# for the next 4 days
qd$add.sampling(seq(from = 0, to = 1, by = 1/24))
qd$add.sampling(seq(from = 1, to = 5, by = 12/24))
#
#print(qd$get.dosing())     # table of dosing records
print(qd$get.nobs())   # number of observation (not dosing) records
#
# BID dosing, 5 days
bid <- eventTable("mg", "days")  # only dosing
bid$add.dosing(dose=10000, nbr.doses=2*5,
               dosing.interval = 12, do.sampling=FALSE)
#
# Use the copy() method to create a copy (clone) of an existing
# event table (simple assignments just create a new reference to
# the same event table object (closure)).
#
bid.ext <- bid$copy()      # three-day extension for a 2nd cohort
bid.ext$add.dosing(dose = 5000, nbr.doses = 2*3,
                   start.time = 120, dosing.interval = 12, do.sampling = FALSE)

# You can also use the Piping operator to create a table

qd2 <- eventTable(amount.units="mg", time.units="days") %>%
    add.dosing(dose=50, nbr.doses=5, dosing.interval=1, do.sampling=FALSE) %>%
    add.sampling(seq(from=0, to=1, by=1 / 24)) %>%
    add.sampling(seq(from=1, to=5, by=12 / 24))
#print(qd2$get.dosing())     # table of dosing records
print(qd2$get.nobs())   # number of observation (not dosing) records

# Note that piping with %>% will update the original table.

qd3 <- qd2 %>% add.sampling(seq(from=5, to=10, by=6 / 24))
print(qd2$get.nobs())
print(qd3$get.nobs())

[Package RxODE version 0.9.2-0 Index]