plot.nested.glmnetr: Plot results from a nested.glmnetr() output

View source: R/plot.nested.glmnetr_250501.R

plot.nested.glmnetrR Documentation

Plot results from a nested.glmnetr() output

Description

Plot the nested cross validation performance numbers, cross validated relaxed lasso deviances or coefficients from a nested.glmnetr() call.

Usage

## S3 method for class 'nested.glmnetr'
plot(
  x,
  type = "devrat",
  alpha = NULL,
  gamma = NULL,
  lambda.lo = NULL,
  title = NULL,
  plup = 0,
  coefs = 0,
  comment = TRUE,
  pow = 2,
  ylim = 1,
  plot = 1,
  fold = 1,
  xgbsimple = 0,
  track = 0,
  ...
)

Arguments

x

A nested.glmnetr output object

type

type of plot to be produced from the (nested) cross validation model fits and evaluations. One of c("devrat", "devian", "agree", "intcal", "lincal") to plot estimates of one these performance measures. One of c("lasso", "elastic", "ridge") to plot model coefficients or deviances as function of lambda and to some degree gamma and alpha. Default is "devrat", the fractional reduction in deviance relative to the null model deviance. Use, "devrat" to plot deviance ratios, "devain" to plot devainces, "agree" to plot agreement e.g. R-square or concordance), "lincal" to plot the linear calibration slope coefficients, "intcal" to plot the linear calibration intercept coefficients or "devian" to plot the deviances from the nested cross validation. For each performance measure estimates from the individual (outer) cross validation fold are depicted by thin lines of different colors and styles, while the composite value from all folds is depicted by a thicker black line, and the performance measures naively calculated on the all data using the model derived from all data is depicted in a thicker red line.

alpha

A specific value of alpha for plotting. Used only when type is set to "elastic". Specifies which alpha is to be used for deviance plots. Default is "alpha.min", else must be an element of the alpha vector used in running the elastic net model. This can be reviewed using summary(fit) where fit is a nested.glmnetr() output object. Note, alpha is 1 for the lasso model and alpha is 0 for the ridge model.

gamma

A specific level of gamma for plotting. By default gamma.min will be used. Applies only for types in c("lasso", "elastic").

lambda.lo

A lower limit of lambda when plotting. Applies only for type = "lasso".

title

A title

plup

Plot upper 95 percent two-sided confidence intervals for the deviance plots. Applies only for type = "lasso".

coefs

1 (TRUE) to plot coefficients, else 0 (FALSE) to plot deviances as function of tuning paramters. Only applies for type in c("devrat", "devian", "agree", "intcal", "lincal"). See option 'type'.

comment

Default of TRUE to write to console information on lam and gam selected for output. FALSE will suppress this write to console. Applies only for type = "lasso".

pow

Power to which agreement is to be raised when the "gaussian" model is fit, i.e. 2 for R-square, 1 for correlation. Does not apply to type = "lasso".

ylim

y axis limits for model performance plots, i.e. does not apply to type = "lasso". The ridge model may calibrate very poorly obscuring plots for type of "lincal" or "intcal", so one may specify the ylim value. If ylim is set to 1, then the program will derive a reasonable range for ylim. If ylim is set to 0, then the entire range for all models will be displayed. Does not apply to type = "lasso".

plot

By default 1 to produce a plot, 0 to return the data used in the plot in the form of a list.

fold

By default 1 to display model performance estimates form individual folds (or replicaitons for boostrap evaluations) when type of "agree", "intcal", "lincal", "devrat" for "devian". If 0 then the individual fold calculations are not displayed. When there are many replications as sometimes the case when using bootstrap, one may specify the number of randomly selected lines for plotting.

xgbsimple

1 (default) to include results for the untuned XGB model, 0 to not include.

track

2 to track progress by printing to console, 0 (default) to not track.

...

Additional arguments passed to the plot function.

Value

This program returns a plot to the graphics window, and may provide some numerical information to the R Console.

Author(s)

Walter Kremers (kremers.walter@mayo.edu)

See Also

plot_perf_glmnetr , calplot , plot.cv.glmnetr , nested.glmnetr

Examples


sim.data=glmnetr.simdata(nrows=1000, ncols=100, beta=NULL)
xs=sim.data$xs 
y_=sim.data$yt
yg=sim.data$y_
event=sim.data$event
# for this example we use a small number for folds_n to shorten run time 
fit3 = nested.glmnetr(xs, NULL, yg, event, family="gaussian", folds_n=3, resample=0) 
plot(fit3)
plot(fit3, coefs=1)



glmnetr documentation built on June 8, 2025, 10:12 a.m.