R/coxpls3DR.R, R/coxpls3DR.default.R, R/coxpls3DR.formula.R
coxpls3DR.RdThis function computes the PLSR model with the Residuals of a Cox-Model
fitted with an intercept as the only explanatory variable as the response
and Xplan as explanatory variables. Default behaviour uses the Deviance
residuals. It uses the package plsRglm.
coxpls3DR(Xplan, ...)
# S3 method for default
coxpls3DR(
Xplan,
time,
time2,
event,
type,
origin,
typeres = "deviance",
collapse,
weighted,
scaleX = TRUE,
scaleY = TRUE,
nt = min(7, ncol(Xplan)),
typeVC = "none",
plot = FALSE,
allres = FALSE,
sparse = FALSE,
sparseStop = TRUE,
...
)
# S3 method for formula
coxpls3DR(
Xplan,
time,
time2,
event,
type,
origin,
typeres = "deviance",
collapse,
weighted,
scaleX = TRUE,
scaleY = TRUE,
nt = min(7, ncol(Xplan)),
typeVC = "none",
plot = FALSE,
allres = FALSE,
dataXplan = NULL,
subset,
weights,
model_frame = FALSE,
sparse = FALSE,
sparseStop = TRUE,
model_matrix = FALSE,
contrasts.arg,
...
)a formula or a matrix with the eXplanatory variables (training) dataset
Arguments to be passed on to survival::coxph and to
plsRglm::PLS_lm.
for right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.
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.
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.
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.
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.
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.
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.
if TRUE and the model was fit with case weights, then
the weighted residuals are returned.
Should the Xplan columns be standardized ?
Should the time values be standardized ?
Number of PLSR components to fit.
type of leave one out crossed validation. Several procedures are available and may be forced.
no crossed validation
as in SIMCA for datasets without missing values and with all values predicted as those with missing values for datasets with any missing values
all values predicted as those with missing values for datasets with any missing values
predict a response value for an x with any missing value as those with missing values and for an x without any missing value as those without missing values.
Should the survival function be plotted ?)
FALSE to return only the Cox model and TRUE for additionnal results. See details. Defaults to FALSE.
should the coefficients of non-significant predictors
(<alpha.pvals.expli) be set to 0
should component extraction stop when no significant
predictors (<alpha.pvals.expli) are found
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
coxpls3DR is called.
an optional vector specifying a subset of observations to be used in the fitting process.
an optional vector of 'prior weights' to be used in the
fitting process. Should be NULL or a numeric vector.
If TRUE, the model frame is returned.
If TRUE, the model matrix is returned.
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.
If allres=FALSE :
Final Cox-model.
If
allres=TRUE :
PLSR components.
Final Cox-model.
The PLSR model.
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.
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.
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_pls3DR_fit <- coxpls3DR(X_train_micro,Y_train_micro,C_train_micro,nt=7))
#> ____************************************************____
#> ____Component____ 1 ____
#> ____Component____ 2 ____
#> ____Component____ 3 ____
#> ____Component____ 4 ____
#> ____Component____ 5 ____
#> ____Component____ 6 ____
#> ____Component____ 7 ____
#> ____Predicting X without NA neither in X nor in Y____
#> ****________________________________________________****
#>
#> Call:
#> coxph(formula = YCsurv ~ ., data = tt_pls3DR)
#>
#> coef exp(coef) se(coef) z p
#> Comp_1 0.8534 2.3476 0.2209 3.864 0.000111
#> Comp_2 1.0599 2.8862 0.3260 3.251 0.001150
#> Comp_3 0.9169 2.5016 0.4353 2.106 0.035166
#> Comp_4 0.9094 2.4827 0.4183 2.174 0.029697
#> Comp_5 0.1663 1.1809 0.2790 0.596 0.551259
#> Comp_6 0.8359 2.3068 0.4452 1.877 0.060455
#> Comp_7 0.4368 1.5478 0.2469 1.769 0.076872
#>
#> Likelihood ratio test=57.92 on 7 df, p=3.919e-10
#> n= 80, number of events= 17
(cox_pls3DR_fit2 <- coxpls3DR(~X_train_micro,Y_train_micro,C_train_micro,nt=7))
#> Error in model.matrix(mt0, mf0, , contrasts.arg = contrasts.arg): argument "contrasts.arg" is missing, with no default
(cox_pls3DR_fit3 <- coxpls3DR(~.,Y_train_micro,C_train_micro,nt=7,dataXplan=X_train_micro_df))
#> Error in model.matrix(mt0, mf0, , contrasts.arg = contrasts.arg): argument "contrasts.arg" is missing, with no default
(cox_pls3DR_fit4 <- coxpls3DR(~.,Y_train_micro,C_train_micro,nt=7,typeVC="none",
data=X_train_micro_df,sparse=TRUE))
#> Error in model.matrix(mt0, mf0, , contrasts.arg = contrasts.arg): argument "contrasts.arg" is missing, with no default
(cox_pls3DR_fit5 <- coxpls3DR(~.,Y_train_micro,C_train_micro,nt=7,typeVC="none",
data=X_train_micro_df,sparse=TRUE,sparseStop=FALSE))
#> Error in model.matrix(mt0, mf0, , contrasts.arg = contrasts.arg): argument "contrasts.arg" is missing, with no default
rm(X_train_micro,Y_train_micro,C_train_micro,cox_pls3DR_fit,cox_pls3DR_fit2,
cox_pls3DR_fit3,cox_pls3DR_fit4,cox_pls3DR_fit5)
#> Warning: object 'cox_pls3DR_fit2' not found
#> Warning: object 'cox_pls3DR_fit3' not found
#> Warning: object 'cox_pls3DR_fit4' not found
#> Warning: object 'cox_pls3DR_fit5' not found