coxpls2: Fitting a Cox-Model on PLSR components

In plsRcox: Partial Least Squares Regression for Cox Models and Related Techniques

Fitting a Cox-Model on PLSR components

Description

This function computes the the Cox-Model with PLSR components as the explanatory variables. It uses the package pls.

Usage

coxpls2(Xplan, ...)

## Default S3 method:
coxpls2(
  Xplan,
  time,
  time2,
  event,
  type,
  origin,
  typeres = "deviance",
  collapse,
  weighted,
  scaleX = TRUE,
  scaleY = TRUE,
  ncomp = min(7, ncol(Xplan)),
  methodpls = "kernelpls",
  validation = "CV",
  plot = FALSE,
  allres = FALSE,
  ...
)

## S3 method for class 'formula'
coxpls2(
  Xplan,
  time,
  time2,
  event,
  type,
  origin,
  typeres = "deviance",
  collapse,
  weighted,
  scaleX = TRUE,
  scaleY = TRUE,
  ncomp = min(7, ncol(Xplan)),
  methodpls = "kernelpls",
  validation = "CV",
  plot = FALSE,
  allres = FALSE,
  dataXplan = NULL,
  subset,
  weights,
  model_frame = FALSE,
  model_matrix = FALSE,
  contrasts.arg = NULL,
  ...
)

Arguments

Xplan	a formula or a matrix with the eXplanatory variables (training) dataset
...	Arguments to be passed on to survival::coxph.
time	for right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.
time2	The status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death). For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored. Although unusual, the event indicator can be omitted, in which case all subjects are assumed to have an event.
event	ending time of the interval for interval censored or counting process data only. Intervals are assumed to be open on the left and closed on the right, (start, end]. For counting process data, event indicates whether an event occurred at the end of the interval.
type	character string specifying the type of censoring. Possible values are "right", "left", "counting", "interval", or "interval2". The default is "right" or "counting" depending on whether the time2 argument is absent or present, respectively.
origin	for counting process data, the hazard function origin. This option was intended to be used in conjunction with a model containing time dependent strata in order to align the subjects properly when they cross over from one strata to another, but it has rarely proven useful.
typeres	character string indicating the type of residual desired. Possible values are "martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas", and "scaledsch". Only enough of the string to determine a unique match is required.
collapse	vector indicating which rows to collapse (sum) over. In time-dependent models more than one row data can pertain to a single individual. If there were 4 individuals represented by 3, 1, 2 and 4 rows of data respectively, then collapse=c(1,1,1,2,3,3,4,4,4,4) could be used to obtain per subject rather than per observation residuals.
weighted	if TRUE and the model was fit with case weights, then the weighted residuals are returned.
scaleX	Should the Xplan columns be standardized ?
scaleY	Should the time values be standardized ?
ncomp	The number of components to include in the model. The number of components to fit is specified with the argument ncomp. It this is not supplied, the maximal number of components is used (taking account of any cross-validation).
methodpls	The multivariate regression method to be used. See mvrCv for details.
validation	character. What kind of (internal) validation to use. If validation = "CV", cross-validation is performed. The number and type of cross-validation segments are specified with the arguments segments and segment.type. See mvrCv for details. If validation = "LOO", leave-one-out cross-validation is performed. It is an error to specify the segments when validation = "LOO" is specified.
plot	Should the survival function be plotted ?)
allres	FALSE to return only the Cox model and TRUE for additionnal results. See details. Defaults to FALSE.
dataXplan	an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in dataXplan, the variables are taken from environment(Xplan), typically the environment from which coxpls2 is called.
subset	an optional vector specifying a subset of observations to be used in the fitting process.
weights	an optional vector of 'prior weights' to be used in the fitting process. Should be NULL or a numeric vector.
model_frame	If TRUE, the model frame is returned.
model_matrix	If TRUE, the model matrix is returned.
contrasts.arg	a list, whose entries are values (numeric matrices, functions or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose names are the names of columns of data containing factors.

Details

If allres=FALSE returns only the final Cox-model. If allres=TRUE returns a list with the PLS components, the final Cox-model and the PLSR model. allres=TRUE is useful for evluating model prediction accuracy on a test sample.

Value

If allres=FALSE :

cox_pls

Final Cox-model.

If allres=TRUE :

tt_pls	PLSR components.
cox_pls	Final Cox-model.
pls_mod	The PLSR model.

Author(s)

Frédéric Bertrand
[e-mail]
http://www-irma.u-strasbg.fr/~fbertran/

References

plsRcox, Cox-Models in a high dimensional setting in R, Frederic Bertrand, Philippe Bastien, Nicolas Meyer and Myriam Maumy-Bertrand (2014). Proceedings of User2014!, Los Angeles, page 152.

Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Philippe Bastien, Frederic Bertrand, Nicolas Meyer and Myriam Maumy-Bertrand (2015), Bioinformatics, 31(3):397-404, doi:10.1093/bioinformatics/btu660.

See Also

coxph, plsr

Examples

data(micro.censure)
data(Xmicro.censure_compl_imp)

X_train_micro <- apply((as.matrix(Xmicro.censure_compl_imp)),FUN="as.numeric",MARGIN=2)[1:80,]
X_train_micro_df <- data.frame(X_train_micro)
Y_train_micro <- micro.censure$survyear[1:80]
C_train_micro <- micro.censure$DC[1:80]

(cox_pls_fit=coxpls2(X_train_micro,Y_train_micro,C_train_micro,ncomp=6,validation="CV"))
(cox_pls_fit=coxpls2(~X_train_micro,Y_train_micro,C_train_micro,ncomp=6,validation="CV"))
(cox_pls_fit=coxpls2(~.,Y_train_micro,C_train_micro,ncomp=6,validation="CV",
dataXplan=X_train_micro_df))

rm(X_train_micro,Y_train_micro,C_train_micro,cox_pls_fit)

plsRcox documentation built on Dec. 1, 2022, 1:31 a.m.