penCSC — penCSC • CSCNet

Function to fit penalized cause-specific-cox with elastic-net penalty.

Usage

penCSC(
  time,
  status,
  vars.list,
  data,
  alpha.list,
  lambda.list,
  standardize = TRUE,
  keep = NULL
)

Arguments

time: A character showing the name of the time variable in the data.
status: A character showing the name of the status/event variable in the data.
vars.list: A named list containing the variables to be included in each cause-specific model. Variables can be vectors of variable names or a one sided formula. Names of the list must be the events and exactly the same as values in the status variable. See `Examples` for details.
data: A data frame containing the information of the variables.
alpha.list: A named list containing the single alpha values of each cause-specific model. Names of the list must be the events and exactly the same as values in the status variable. See `Examples` for details.
lambda.list: A named list containing the single lambda values of each cause-specific model. Names of the list must be the events and exactly the same as values in the status variable. See `Examples` for details.
standardize: Logical indicating whether the variables must be standardized or not. Default is TRUE.
keep: A character vector of the names of variables that should not be shrunk. Default is NULL.

Value

A named list containing all the information related to the used data and the fitted models for all causes. Use $ to explore all the involved information.

References

Friedman J, Hastie T, Tibshirani R (2010). "Regularization Paths for Generalized Linear Models via Coordinate Descent." Journal of Statistical Software, 33(1), 1-22. doi:10.18637/jss.v033.i01 , https://www.jstatsoft.org/v33/i01/.

Therneau T (2022). A Package for Survival Analysis in R. R package version 3.3-1, https://CRAN.R-project.org/package=survival.

Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, et al. Welcome to the tidyverse. J Open Source Softw. 2019 Nov 21;4(43):1686.

Bache S, Wickham H (2022). magrittr: A Forward-Pipe Operator for R. https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr.

Author

Shahin Roshani

Examples


library(riskRegression)
#> riskRegression version 2022.03.22

data(Melanoma)

vl <- list('1'=c('age','sex','ulcer','thick'),

          '2'=~age+sex+epicel+thick+ici)

al <- list('1'=0,'2'=.5)

ll <- list('1'=.01,'2'=.04)

penCSC(time='time',status='status',vars.list=vl,

      data=Melanoma,alpha.list=al,lambda.list=ll)
#> $`Event: 1`
#> 4 x 1 sparse Matrix of class "dgCMatrix"
#>                       1
#> age          0.01184358
#> sexMale      0.42366136
#> ulcerpresent 1.11871164
#> thick        0.10816182
#> 
#> $`Event: 2`
#> 7 x 1 sparse Matrix of class "dgCMatrix"
#>                        1
#> age           0.03494673
#> sexMale       .         
#> epicelpresent .         
#> thick         .         
#> ici1          .         
#> ici2          .         
#> ici3          .         
#>