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LazyData
.msaenet.sim.gaussian()
.penalty.factor.init
to support customized penalty factor applied to each coefficient in the initial estimation step. This is useful for incorporating prior information about variable weights, for example, emphasizing specific clinical variables. We thank Xin Wang from University of Michigan for this feedback (#4).type = "dotplot"
in plot.msaenet()
. This plot offers a direct visualization of the model coefficients at the optimal step.init = "ridge"
.lower.limits
and upper.limits
to support coefficient constraints in aenet()
and msaenet()
(#1).README.md
.plot.msaenet()
for extra flexibility: it is now possible to set important properties of the label appearance such as position, offset, font size, and axis titles via the new arguments label.pos
, label.offset
, label.cex
, xlab
, and ylab
.init = "ridge"
, by using the ridge estimation implementation from glmnet
. As a benefit, we now have a more aligned baseline for the comparison between elastic-net based models and MCP-net/SCAD-net based models when init = "ridge"
.tune
and tune.nsteps
to controls this for selecting the optimal model for each step, and the optimal model among all steps (i.e. the optimal step).ebic.gamma
and ebic.gamma.nsteps
to control the EBIC tuning parameter, if ebic
is specified by tune
or tune.nsteps
.?plot.msaenet
for details.gamma
(scaling factor for adaptive weights) to scale
to avoid possible confusion.gammas
to be 3.7 for SCAD-net and 3 for MCP-net.family
in all model types to be "gaussian"
, "binomial"
, "poisson"
, and "cox"
.msaenet.sim.binomial()
, msaenet.sim.poisson()
, msaenet.sim.cox()
to generate simulation data for logistic, Poisson, and Cox regression models.msaenet.fn()
for computing the number of false negative selections in msaenet models.msaenet.mse()
for computing mean squared error (MSE).msaenet.sim.gaussian()
by more vectorization when generating correlation matrices.max.iter
and epsilon
for MCP-net and SCAD-net related functions to have finer control over convergence criterion. By default, max.iter = 10000
and epsilon = 1e-4
.amnet()
to support adaptive MCP-net.asnet()
to support adaptive SCAD-net.msamnet()
to support multi-step adaptive MCP-net.msasnet()
to support for multi-step adaptive SCAD-net.msaenet.nzv.all()
for displaying the indices of non-zero variables in all adaptive estimation steps.predict.msaenet
method allowing users to specify prediction type.coef
for extracting model coefficients. See ?coef.msaenet
for details.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.