marginalPlot | R Documentation |
Marginal plot of x against the unadjusted predicted y. This is mainly used to obtain marginal relationships between x and the unadjusted predicted y. Marginal plots have a faster execution compared to partial plots (Friedman, 2001).
marginalPlot(object, xvar.names, tm.unq, subset, plot.it = FALSE, path_saveplot = NULL, Verbose = TRUE, ...)
object |
A boosting object of class |
xvar.names |
Names of the x-variables to be used. By default, all variables are plotted. |
tm.unq |
Unique time points used for the plots of x against y. By default, the deciles of the observed time values are used. |
subset |
Vector indicating which rows of the x-data to be used for the analysis. The default is to use the entire data. |
plot.it |
Should plots be displayed? If |
path_saveplot |
Provide the location where plot should be saved. By default the plot will be saved at temporary folder. |
Verbose |
Display the path where the plot is saved? |
... |
Further arguments passed to or from other methods. |
Marginal plot of x values specified by
xvar.names
against the unadjusted predicted y-values over a set
of time points specified by tm.unq
. Analysis can be restricted to
a subset of the data using subset
.
Hemant Ishwaran, Amol Pande and Udaya B. Kogalur
Friedman J.H. Greedy function approximation: a gradient boosting machine, Ann. of Statist., 5:1189-1232, 2001.
## Not run: ##------------------------------------------------------------ ## Synthetic example (Response is continuous) ## High correlation, quadratic time with quadratic interaction ##------------------------------------------------------------- #simulate the data dta <- simLong(n = 50, N = 5, rho =.80, model = 2,family = "Continuous")$dtaL #basic boosting call boost.grow <- boostmtree(dta$features, dta$time, dta$id, dta$y, family = "Continuous", M = 300) #plot results #x1 has a linear main effect #x2 is quadratic with quadratic time trend marginalPlot(boost.grow, "x1",plot.it = TRUE) marginalPlot(boost.grow, "x2",plot.it = TRUE) #Plot of all covariates. The plot will be stored as the "MarginalPlot.pdf" # in the current working directory. marginalPlot(boost.grow,plot.it = TRUE) ##------------------------------------------------------------ ## Synthetic example (Response is binary) ## High correlation, quadratic time with quadratic interaction ##------------------------------------------------------------- #simulate the data dta <- simLong(n = 50, N = 5, rho =.80, model = 2,family = "Binary")$dtaL #basic boosting call boost.grow <- boostmtree(dta$features, dta$time, dta$id, dta$y, family = "Binary", M = 300) #plot results #x1 has a linear main effect #x2 is quadratic with quadratic time trend marginalPlot(boost.grow, "x1",plot.it = TRUE) marginalPlot(boost.grow, "x2",plot.it = TRUE) #Plot of all covariates. The plot will be stored as the "MarginalPlot.pdf" # in the current working directory. marginalPlot(boost.grow,plot.it = TRUE) ##---------------------------------------------------------------------------- ## spirometry data ##---------------------------------------------------------------------------- data(spirometry, package = "boostmtree") #boosting call: cubic B-splines with 15 knots spr.obj <- boostmtree(spirometry$features, spirometry$time, spirometry$id, spirometry$y, family = "Continuous",M = 300, nu = .025, nknots = 15) #marginal plot of double-lung group at 5 years dltx <- marginalPlot(spr.obj, "AGE", tm.unq = 5, subset = spr.obj$x$DOUBLE==1,plot.it = TRUE) #marginal plot of single-lung group at 5 years sltx <- marginalPlot(spr.obj, "AGE", tm.unq = 5, subset = spr.obj$x$DOUBLE==0,plot.it = TRUE) #combine the two plots dltx <- dltx[[2]][[1]] sltx <- sltx[[2]][[1]] plot(range(c(dltx[[1]][, 1], sltx[[1]][, 1])), range(c(dltx[[1]][, -1], sltx[[1]][, -1])), xlab = "age", ylab = "predicted y", type = "n") lines(dltx[[1]][, 1][order(dltx[[1]][, 1]) ], dltx[[1]][, -1][order(dltx[[1]][, 1]) ], lty = 1, lwd = 2, col = "red") lines(sltx[[1]][, 1][order(sltx[[1]][, 1]) ], sltx[[1]][, -1][order(sltx[[1]][, 1]) ], lty = 1, lwd = 2, col = "blue") legend("topright", legend = c("DLTx", "SLTx"), lty = 1, fill = c(2,4)) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.