plsRcox (version 1.7.0)

plsRcox: Partial least squares Regression generalized linear models

Description

This function implements an extension of Partial least squares Regression to Cox Models.

Usage

plsRcox(Xplan, ...)
## S3 method for class 'default':
plsRcoxmodel(Xplan,time,time2,event,type,
origin,typeres="deviance", collapse, weighted, scaleX=TRUE, 
scaleY=TRUE, nt=min(2,ncol(Xplan)),limQ2set=.0975, 
dataPredictY=Xplan, pvals.expli=FALSE,alpha.pvals.expli=.05,
tol_Xi=10^(-12),weights,control, sparse=FALSE,
sparseStop=TRUE,allres=TRUE, verbose=TRUE,...)
## S3 method for class 'formula':
plsRcoxmodel(Xplan,time,time2,event,type,
origin,typeres="deviance", collapse, weighted,scaleX=TRUE,
scaleY=NULL,dataXplan=NULL, nt=min(2,ncol(Xplan)),
limQ2set=.0975, dataPredictY=Xplan, pvals.expli=FALSE, 
model_frame=FALSE, alpha.pvals.expli=.05,tol_Xi=10^(-12),
weights,subset,control,sparse=FALSE,sparseStop=TRUE,
allres=TRUE, verbose=TRUE,...)

Arguments

Xplan

a formula or a matrix with the eXplanatory variables (training) dataset

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=

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 e

type

character string specifying the type of censoring. Possible values are "right", "left", "counting", "interval", or "interval2". The default is "right" or "counting"

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 rar

typeres

character string indicating the type of residual desired. Possible values are "martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas", and "scaledsch".

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,

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 ?

nt

number of components to be extracted

limQ2set

limit value for the Q2

dataPredictY

predictor(s) (testing) dataset

pvals.expli

should individual p-values be reported to tune model selection ?

alpha.pvals.expli

level of significance for predictors when pvals.expli=TRUE

tol_Xi

minimal value for Norm2(Xi) and $\mathrm{det}(pp' \times pp)$ if there is any missing value in the dataX. It defaults to $10^{-12}$

weights

an optional vector of 'prior weights' to be used in the fitting process. Should be NULL or a numeric vector.

subset

an optional vector specifying a subset of observations to be used in the fitting process.

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 take

model_frame

If TRUE, the model frame is returned.

method

the method to be used in fitting the model. The default method "glm.fit" uses iteratively reweighted least squares (IWLS). User-supplied fitting functions can be supplied either as a function or a character string naming a function, with a fu

control

a list of parameters for controlling the fitting process. For glm.fit this is passed to glm.control.

sparse

should the coefficients of non-significant predictors (<alpha.pvals.expli) be set to 0

sparseStop

should component extraction stop when no significant predictors (<alpha.pvals.expli) are found

verbose

Should some details be displayed ?

...

arguments to pass to plsRmodel.default or to plsRmodel.formula

Value

• Depends on the model that was used to fit the model.

Details

A typical predictor has the form response ~ terms where response is the (numeric) response vector and terms is a series of terms which specifies a linear predictor for response. A terms specification of the form first + second indicates all the terms in first together with all the terms in second with any duplicates removed.

A specification of the form first:second indicates the the set of terms obtained by taking the interactions of all terms in first with all terms in second. The specification first*second indicates the cross of first and second. This is the same as first + second + first:second.

The terms in the formula will be re-ordered so that main effects come first, followed by the interactions, all second-order, all third-order and so on: to avoid this pass a terms object as the formula.

Non-NULL weights can be used to indicate that different observations have different dispersions (with the values in weights being inversely proportional to the dispersions); or equivalently, when the elements of weights are positive integers w_i, that each response y_i is the mean of w_i unit-weight observations.

References

Fr?d?ric{Fr'ed'eric} Bertrand, Myriam Maumy-Bertrand et Nicolas Meyer (2011). R?gression{R'egression} B?ta{B^eta} PLS. Preprint.

See Also

plsR and plsRglm

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]

plsRcox(X_train_micro,time=Y_train_micro,event=C_train_micro,nt=5)
plsRcox(~X_train_micro,time=Y_train_micro,event=C_train_micro,nt=5)

plsRcox(Xplan=X_train_micro,time=Y_train_micro,event=C_train_micro,nt=5,sparse=TRUE,
alpha.pvals.expli=.15)
plsRcox(Xplan=~X_train_micro,time=Y_train_micro,event=C_train_micro,nt=5,sparse=TRUE,
alpha.pvals.expli=.15)