This function fits the specified ordinary least squares or
parsimonious regression (plsr, pcr, ridge, and lars methods)
depending on the arguments provided, and returns estimates of
coefficients and (co-)variances in a monomvn friendly
format
regress(X, y, method = c("lsr", "plsr", "pcr", "lasso", "lar",
"forward.stagewise", "stepwise", "ridge", "factor"), p = 0,
ncomp.max = Inf, validation = c("CV", "LOO", "Cp"),
verb = 0, quiet = TRUE)data.frame, matrix, or vector of inputs X
matrix of responses y of row-length equal to the
leading dimension (rows) of X, i.e., nrow(y) ==
nrow(X); if y is a vector, then nrow may be
interpreted as length
describes the type of parsimonious
(or shrinkage) regression, or ordinary least squares.
From the pls package we have "plsr"
(plsr, the default) for partial least squares and
"pcr" (pcr) for standard principal
component regression. From the lars package (see the
"type" argument to lars)
we have "lasso" for L1-constrained regression, "lar"
for least angle regression, "forward.stagewise" and
"stepwise" for fast implementations of classical forward
selection of covariates. From the MASS package we have
"ridge" as implemented by the lm.ridge
function. The "factor" method treats the first p
columns of y as known factors
when performing regressions, 0 <= p <= 1
is the proportion of the
number of columns to rows in the design matrix before an
alternative regression method (except "lsr")
is performed as if least-squares regression “failed”.
Least-squares regression is
known to fail when the number of columns is greater than or
equal to the number of rows.
The default setting, p = 0, forces the specified
method to be used for every regression unless
method = "lsr" is specified but is unstable.
Intermediate settings of p allow the user
to specify that least squares regressions are preferred only
when there are sufficiently more rows in the design matrix
(X) than columns. When method = "factor" the p
argument represents an integer (positive) number of initial columns
of y to treat as known factors
maximal number of (principal) components to consider
in a method---only meaningful for the "plsr" or
"pcr" methods. Large settings can cause the execution to be
slow as they drastically increase the cross-validation (CV) time
method for cross validation when applying
a parsimonious regression method. The default setting
of "CV" (randomized 10-fold cross-validation) is the faster method,
but does not yield a deterministic result and does not apply for
regressions on less than ten responses. "LOO"
(leave-one-out cross-validation)
is deterministic, always applicable, and applied automatically whenever
"CV" cannot be used. When standard least squares is
appropriate, the methods implemented the
lars package (e.g. lasso) support model choice via the
"Cp" statistic, which defaults to the "CV" method
when least squares fails. This argument is ignored for the
"ridge" method; see details below
whether or not to print progress indicators. The default
(verb = 0) keeps quiet. This argument is provided for
monomvn and is not intended to be set by the user
via this interface
causes warnings about regressions to be silenced
when TRUE
regress returns a list containing
the components listed below.
a copy of the function call as used
a copy of the method input argument
depends on the method used: is NA when
method = "lsr"; is the number of principal
components for method = "pcr" and method = "plsr";
is the number of non-zero components in the coefficient vector
($b, not counting the intercept) for any of the
lars methods; and gives the chosen
\(\lambda\) penalty parameter for method = "ridge"
if method is one of c("lasso",
"forward.stagewise", "ridge"), then this field records the
\(\lambda\) penalty parameter used
matrix containing the estimated regression coefficients,
with ncol(b) = ncol(y) and the intercept
in the first row
(biased corrected) maximum likelihood estimate of residual covariance matrix
All methods (except "lsr") require a scheme for
estimating the amount of variability explained by increasing numbers
of non-zero coefficients (or principal components) in the model.
Towards this end, the pls and lars packages support
10-fold cross validation (CV) or leave-one-out (LOO) CV estimates of
root mean squared error. See pls and lars for
more details. The regress function uses CV in all cases
except when nrow(X) <= 10, in which case CV fails and
LOO is used. Whenever nrow(X) <= 3 pcr
fails, so plsr is used instead.
If quiet = FALSE then a warning
is given whenever the first choice for a regression fails.
For pls methods, RMSEs
are calculated for a number of components in 1:ncomp.max where
a NULL value for ncomp.max it is replaced with
ncomp.max <- min(ncomp.max, ncol(y), nrow(X)-1)
which is the max allowed by the pls package.
Simple heuristics are used to select a small number of components
(ncomp for pls), or number of coefficients (for
lars) which explains a large amount of the variability (RMSE).
The lars methods use a “one-standard error rule” outlined
in Section 7.10, page 216 of HTF below. The
pls package does not currently support the calculation of
standard errors for CV estimates of RMSE, so a simple linear penalty
for increasing ncomp is used instead. The ridge constant
(lambda) for lm.ridge is set using the optimize
function on the GCV output.
Bjorn-Helge Mevik and Ron Wehrens (2007). The pls Package: Principal Component and Partial Least Squares Regression in R. Journal of Statistical Software 18(2)
Bradley Efron, Trevor Hastie, Ian Johnstone and Robert Tibshirani (2003). Least Angle Regression (with discussion). Annals of Statistics 32(2); see also http://www-stat.stanford.edu/~hastie/Papers/LARS/LeastAngle_2002.pdf
monomvn, blasso,
lars in the lars library,
lm.ridge in the MASS library,
plsr and pcr in the
pls library
# NOT RUN {
## following the lars diabetes example
data(diabetes)
attach(diabetes)
## Ordinary Least Squares regression
reg.ols <- regress(x, y)
## Lasso regression
reg.lasso <- regress(x, y, method="lasso")
## partial least squares regression
reg.plsr <- regress(x, y, method="plsr")
## ridge regression
reg.ridge <- regress(x, y, method="ridge")
## compare the coefs
data.frame(ols=reg.ols$b, lasso=reg.lasso$b,
plsr=reg.plsr$b, ridge=reg.ridge$b)
## summarize the posterior distribution of lambda2 and s2
detach(diabetes)
# }
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