# R/utility.R In emeryyi/fastcox: Lasso and Elastic-Net Penalized Cox's Regression in High Dimensions Models using the Cocktail Algorithm

#### Defines functions getminerror.barsgetoutputerrlambda.interplamfixnonzeroCoefzeromat

```######################################################################
## These functions are minor modifications or directly copied from the
## glmnet package:
##        Jerome Friedman, Trevor Hastie, Robert Tibshirani (2010).
##        Regularization Paths for Generalized Linear Models via
##        Coordinate Descent.
##        Journal of Statistical Software, 33(1), 1-22.
##        URL http://www.jstatsoft.org/v33/i01/.
## The reason they are copied here is because they are internal functions
## and hence are not exported into the global environment.

zeromat <- function(nvars, nalam, vnames, stepnames) {
ca <- rep(0, nalam)
ia <- seq(nalam + 1)
ja <- rep(1, nalam)
dd <- c(nvars, nalam)
new("dgCMatrix", Dim = dd, Dimnames = list(vnames, stepnames), x = as.vector(ca),
p = as.integer(ia - 1), i = as.integer(ja - 1))
}

nonzeroCoef <- function(beta, bystep = FALSE) {
### bystep = FALSE means which variables were ever nonzero
### bystep = TRUE means which variables are nonzero for each step
nr <- nrow(beta)
if (nr == 1) {
#degenerate
#   case
if (bystep)
apply(beta, 2, function(x) if (abs(x) > 0)
1 else NULL) else {
if (any(abs(beta) > 0))
1 else NULL
}
} else {
beta <- abs(beta) > 0  # this is sparse
which <- seq(nr)
ones <- rep(1, ncol(beta))
nz <- as.vector((beta %*% ones) > 0)
which <- which[nz]
if (bystep) {
beta <- as.matrix(beta[which, ])
nzel <- function(x, which) if (any(x))
which[x] else NULL
apply(beta, 2, nzel, which)
} else which
}
}

lamfix <- function(lam) {
llam <- log(lam)
lam[1] <- exp(2 * llam[2] - llam[3])
lam
}

lambda.interp <- function(lambda, s) {
### lambda is the index sequence that is produced by the model
### s is the new vector at which evaluations are required.
### the value is a vector of left and right indices, and a vector of fractions.
### the new values are interpolated bewteen the two using the fraction
### Note: lambda decreases. you take:
### sfrac*left+(1-sfrac*right)

if (length(lambda) == 1) {
#
#   degenerate
#   case
#   of
#   only
#   one
#   lambda
nums <- length(s)
left <- rep(1, nums)
right <- left
sfrac <- rep(1, nums)
} else {
s[s > max(lambda)] <- max(lambda)
s[s < min(lambda)] <- min(lambda)
k <- length(lambda)
sfrac <- (lambda[1] - s)/(lambda[1] - lambda[k])
lambda <- (lambda[1] - lambda)/(lambda[1] - lambda[k])
coord <- approx(lambda, seq(lambda), sfrac)\$y
left <- floor(coord)
right <- ceiling(coord)
sfrac <- (sfrac - lambda[right])/(lambda[left] - lambda[right])
sfrac[left == right] <- 1
}
list(left = left, right = right, frac = sfrac)
}

err <- function(n, maxit, pmax) {
if (n == 0)
msg <- ""
if (n > 0) {
#fatal
#   error
if (n < 7777)
msg <- "Memory allocation error"
if (n == 7777)
msg <- "All used predictors have zero variance"
if (n == 10000)
msg <- "All penalty factors are <= 0"
n <- 1
msg <- paste("in cocktail fortran code -", msg)
}
if (n < 0) {
#non
#   fatal
#   error
if (n > -10000)
msg <- paste("Convergence for ", -n, "th lambda value not reached after maxit=",
maxit, " iterations; solutions for larger lambdas returned",
sep = "")
if (n < -10000)
msg <- paste("Number of nonzero coefficients along the path exceeds pmax=",
pmax, " at ", -n - 10000, "th lambda value; solutions for larger lambdas returned",
sep = "")
n <- -1
msg <- paste("from cocktail fortran code -", msg)
}
list(n = n, msg = msg)
}

getoutput <- function(fit, maxit, pmax, nvars, vnames) {
nalam <- fit\$nalam
if (nalam < 1)
stop("an empty model has been returned; something is wrong")
nbeta <- fit\$nbeta[seq(nalam)]
nbetamax <- max(nbeta)
lam <- fit\$alam[seq(nalam)]

stepnames <- paste("s", seq(nalam) - 1, sep = "")
dd <- c(nvars, nalam)
if (nbetamax > 0) {
beta <- matrix(fit\$beta[seq(pmax * nalam)], pmax, nalam)[seq(nbetamax),
, drop = FALSE]
df <- apply(abs(beta) > 0, 2, sum)
ja <- fit\$ibeta[seq(nbetamax)]
oja <- order(ja)
ja <- rep(ja[oja], nalam)
ibeta <- cumsum(c(1, rep(nbetamax, nalam)))
beta <- new("dgCMatrix", Dim = dd, Dimnames = list(vnames, stepnames),
x = as.vector(beta[oja, ]), p = as.integer(ibeta - 1), i = as.integer(ja -
1))
} else {
beta <- zeromat(nvars, nalam, vnames, stepnames)
df <- rep(0, nalam)
}
list(beta = beta, df = df, dim = dd, lambda = lam)
}

error.bars <- function(x, upper, lower, width = 0.02, ...)
{
xlim <- range(x)
barw <- diff(xlim) * width
segments(x, upper, x, lower, ...)
segments(x - barw, upper, x + barw, upper, ...)
segments(x - barw, lower, x + barw, lower, ...)
range(upper, lower)
}

getmin <- function(lambda, cvm, cvsd) {
cvmin <- min(cvm)
idmin <- cvm <= cvmin
lambda.min <- max(lambda[idmin])
idmin <- match(lambda.min, lambda)
semin <- (cvm + cvsd)[idmin]
idmin <- cvm <= semin
lambda.1se <- max(lambda[idmin])
list(lambda.min = lambda.min, lambda.1se = lambda.1se)
}
```
emeryyi/fastcox documentation built on Sept. 16, 2017, 10:05 a.m.