initStrat {REMixed} | R Documentation |
Initialization strategy
Description
Selecting an initialization point by grouping biomarkers of project and running the SAEM. Initial condition is then selected using maximum log-likelihood.
Usage
initStrat(
project,
alpha,
ObsModel.transfo,
Nb_genes = 2,
trueValue = NULL,
pop.set = NULL,
useSettingsInAPI = FALSE,
conditionalDistributionSampling = FALSE,
print = TRUE,
digits = 2,
unlinkTemporaryProject = TRUE,
seed = NULL
)
Arguments
project |
directory of the Monolix project (in .mlxtran). If NULL, the current loaded project is used (default is NULL). |
alpha |
named list of named vector " |
ObsModel.transfo |
list containing two lists of transformations and two vectors linking each transformations to their observation model name in the Monolix project. The list should include identity transformations and be named Both
|
Nb_genes |
Size of group of genes. |
trueValue |
-for simulation purposes- named vector of true value for parameters. |
pop.set |
population parameters setting for initialization (see details). |
useSettingsInAPI |
logical, if the settings for SAEM should not be changed from what is currently set in the project. |
conditionalDistributionSampling |
logical, if conditional distribution estimation should be done on the final project. |
print |
logical, if the results and algotihm steps should be displayed in the console (default to TRUE). |
digits |
number of digits to print (default to 2). |
unlinkTemporaryProject |
If temporary project (of genes group) is deleted (defaut: TRUE) |
seed |
value of the seed used to initialize the group (see set.seed). |
Details
For population parameter estimation settings, see (<https://monolixsuite.slp-software.com/r-functions/2024R1/setpopulationparameterestimationsettings>).
Value
a list of outputs for every group of genes tested with composition of the group, final parameter estimates, final scores estimates (OFV, AIC, BIC, BICc), temporary project directory. The final selected set is initialize in the project.
Examples
## Not run:
project <- getMLXdir()
ObsModel.transfo = list(S=list(AB=log10),
linkS="yAB",
R=rep(list(S=function(x){x}),5),
linkR = paste0("yG",1:5))
alpha=list(alpha0=NULL,
alpha1=setNames(paste0("alpha_1",1:5),paste0("yG",1:5)))
initStrat(project,alpha,ObsModel.transfo,seed=1710)
## End(Not run)