How can I view the source code for a particular `predict` function? [duplicate]

Question

Based on the documentation, predict is a polymorphic function in R and a different function is actually called depending on what is passed as the first argument.

However, the documentation does not give any information about the names of the functions that predict actually invokes for any particular class.

Normally, one could type the name of a function to get its source, but this does not work with predict.

If I want to view the source code for the predict function when invoked on objects of the type glmnet, what is the easiest way?

Answer 1

You can use look for a function using getAnywhere

getAnywhere("predict.glmnet")
## A single object matching ‘predict.glmnet’ was found
## It was found in the following places
##   registered S3 method for predict from namespace glmnet
##   namespace:glmnet
## with value
## 
## function (object, newx, s = NULL, type = c("link", "response", 
##     "coefficients", "nonzero", "class"), exact = FALSE, offset, 
##     ...) 
## {
##     type = match.arg(type)
##     if (missing(newx)) {
##         if (!match(type, c("coefficients", "nonzero"), FALSE)) 
##             stop("You need to supply a value for 'newx'")
##     }
##     if (exact && (!is.null(s))) {
##         lambda = object$lambda
##         which = match(s, lambda, FALSE)
##         if (!all(which > 0)) {
##             lambda = unique(rev(sort(c(s, lambda))))
##             object = update(object, lambda = lambda)
##         }
##     }
##     a0 = t(as.matrix(object$a0))
##     rownames(a0) = "(Intercept)"
##     nbeta = rbind2(a0, object$beta)
##     if (!is.null(s)) {
##         vnames = dimnames(nbeta)[[1]]
##         dimnames(nbeta) = list(NULL, NULL)
##         lambda = object$lambda
##         lamlist = lambda.interp(lambda, s)
##         nbeta = nbeta[, lamlist$left, drop = FALSE] * lamlist$frac + 
##             nbeta[, lamlist$right, drop = FALSE] * (1 - lamlist$frac)
##         dimnames(nbeta) = list(vnames, paste(seq(along = s)))
##     }
##     if (type == "coefficients") 
##         return(nbeta)
##     if (type == "nonzero") 
##         return(nonzeroCoef(nbeta[-1, , drop = FALSE], bystep = TRUE))
##     if (inherits(newx, "sparseMatrix")) 
##         newx = as(newx, "dgCMatrix")
##     nfit = as.matrix(cbind2(1, newx) %*% nbeta)
##     if (object$offset) {
##         if (missing(offset)) 
##             stop("No offset provided for prediction, yet used in fit of glmnet", 
##                 call. = FALSE)
##         if (is.matrix(offset) && dim(offset)[[2]] == 2) 
##             offset = offset[, 2]
##         nfit = nfit + array(offset, dim = dim(nfit))
##     }
##     nfit
## }
## <environment: namespace:glmnet>

Answer 2

Calling methods(predict) will show you all the methods that have been defined for particular classes, e.g.:

> methods(predict)
 [1] predict.ar*                predict.Arima*             predict.arima0*            predict.glm               
 [5] predict.HoltWinters*       predict.lm                 predict.loess*             predict.mlm               
 [9] predict.nls*               predict.poly               predict.ppr*               predict.prcomp*           
[13] predict.princomp*          predict.smooth.spline*     predict.smooth.spline.fit* predict.StructTS*

The predict function for a glmnet is more than likely just predict.glmnet.