datalist: Generate a datalist object
In dMod: Dynamic Modeling and Parameter Estimation in ODE Models

Description Usage Arguments Details Value Examples

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.

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(...)

`...`	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

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.

Object of class datalist.

Object of class datalist

## 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)