datalist: Generate a datalist object

In dkaschek/dMod: Dynamic Modeling and Parameter Estimation in ODE Models

Generate a datalist object

Description

The datalist object stores time-course data in a list of data.frames. The names of the list serve as identifiers, e.g. of an experimental condition, etc.

Usage

datalist(...)

as.datalist(x, ...)

## S3 method for class 'data.frame'
as.datalist(x, split.by = NULL, keep.covariates = NULL, ...)

## S3 method for class 'list'
as.datalist(x, names = NULL, ..., condition.grid = attr(x, "condition.grid"))

## S3 replacement method for class 'datalist'
names(x) <- value

is.datalist(x)

## S3 method for class 'datalist'
c(...)

Arguments

...	data.frame objects to be coerced into a list and additional arguments
x	object of class data.frame or list. Data frames are required to provide "name", "time" and "value" as columns. Columns "sigma" and "lloq" can be provided. If "sigma" and "lloq" are missing, they are imputed with NA and -Inf, respectively.
split.by	vector of columns names which yield a unique identifier (conditions). If NULL, all columns except for the expected standard columns "name", "time", "value", "sigma" and "lloq" will be selected.
keep.covariates	vector of additional column names which should be kept in the condition.grid.
names	optional names vector, otherwise names are taken from mylist
condition.grid	Optionally, to manually specify a condition.grid
value	The new condition names of the datalist and its condition.grid

Details

Datalists can be plotted, see plotData and merged, see sumdatalist. They are the basic structure when combining model prediction and data via the normL2 objective function.

The standard columns of the datalist data frames are "name" (observable name), "time" (time points), "value" (data value), "sigma" (uncertainty, can be NA), and "lloq" (lower limit of quantification, -Inf by default).

Datalists carry the attribute condition.grid which contains additional information about different conditions, such as dosing information for the experiment. It can be conveniently accessed by the covariates-function. Reassigning names to a datalist also renames the rows of the condition.grid.

Value

Object of class datalist.

Object of class datalist

Examples

## Generate datalist from scratch
mydata1 <- data.frame(name = "A",
                      time = 0:5,
                      value = 0:5,
                      sigma = .1,
                      lloq = -0.5)

mydata2 <- data.frame(name = "A",
                      time = 0:5,
                      value = sin(0:5),
                      sigma = .1)

data <- datalist(C1 = mydata1, C2 = mydata2)
print(data)
plot(data)

## Generate datalist from singla data.frame
times <- seq(0, 2*pi, length.out = 20)
mydata <- data.frame(name = "A", 
                     time = times, 
                     value = c(sin(times), 1.5 * sin(times)), 
                     sigma = .1, 
                     stage = rep(c("upper", "lower"), each = 10),
                     phase = rep(c("first", "second"), each = 20),
                     amplitude = rep(c(1,1.5), each = 20))

data <- as.datalist(mydata, split.by = c("stage", "phase"), keep.covariates = "amplitude")
print(data)
plot(data)

condition.grid <- attr(data, "condition.grid")
print(condition.grid)

dkaschek/dMod documentation built on July 27, 2023, 11:45 p.m.