Description Usage Arguments Details Value Author(s) References See Also Examples
Applies CausalKinetiX framework to rank variables and models according to their stability.
1 | CausalKinetiX(D, times, env, target, models = NA, pars = list())
|
D |
data matrix. Should have dimension n x (L*d), where n is the number of repetitions (over all experiments), L is the number of time points and d is the number of predictor variables. |
times |
vector of length L specifying the time points at which data was observed. |
env |
integer vector of length n encoding to which experiment each repetition belongs. |
target |
integer specifing which variable is the target. |
models |
list of models. Each model is specified by a list of vectors specifiying the variables included in the interactions of each term. If NA, then models are constructed automatically using the parameters in pars. |
pars |
list of the following parameters: Additionally all parameters used in CausalKinetiX.modelranking can also be specified here. |
For further details see the references.
object of class 'CausalKinetiX' consisting of the following elements
models |
list of the individually scored models. |
model.scores |
vector containing the score for each model. |
variable.scores |
vector containing the score of each variable. |
ranking |
vector specifying the ranking of each variable. |
Niklas Pfister, Stefan Bauer and Jonas Peters
Pfister, N., S. Bauer, J. Peters (2018). Identifying Causal Structure in Large-Scale Kinetic Systems ArXiv e-prints (arXiv:1810.11776).
The function CausalKinetiX.modelranking
can
be used if the variable ranking is not required.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Generate data from Maillard reaction
simulation.obj <- generate.data.maillard(target=6,
env=rep(1:3, 5),
L=15,
seed=5,
par.noise=list(noise.sd=1))
D <- simulation.obj$simulated.data
time <- simulation.obj$time
env <- simulation.obj$env
target <- simulation.obj$target
## Fit data using CausalKinetiX
ck.fit <- CausalKinetiX(D, time, env, target,
pars=list(expsize=1,
average.reps=TRUE))
# variable ranking (here the true parent is variable 4)
print(ck.fit$ranking)
|
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