datalist {dMod} | R Documentation |
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 |
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 |
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)