R double for loop: outer or apply? Code Answer

I have the following code:

a <- c(1,2,2,3,4,5,6)
b <- c(4,5,6,7,8,8,9)
data <- data.frame(cbind(a,b))
trial <- copy(data)
for (j in 1: ncol(trial)) {
  for (i in 2: nrow(trial)) {
  if (trial[i,j] == trial[i-1,j] & !is.na(trial[i,j]) & !is.na(trial[i-1,j]))  {
     trial[i,j] <- trial[i-1,j] + (0.001*sd(trial[,j], na.rm = T))
    }
 }
}

The code perfectly works, but on a larger dataset is a bit slow. I thought to improve speed by using either the apply or the outer family. The issues are:

1. I know how to apply a single loop with apply, but not as for 2, especially in this case, where I need to replace single values according to case-specific conditions, with another single value (the lag) plus a multiplier of the standard deviation (which is something I need to compute over the whole column;
2. Except for this solved question, I have no experience at all of using outer and vectorised functions instead of loops.

Answer

With data.table

library(data.table)
f <- function(x)ifelse(x==shift(x), x + 0.001* sd(x, na.rm = TRUE), x)
setDT(data)[, lapply(.SD, f), ]

With dplyr

library(dplyr)
f <- function(x)ifelse(x==lag(x), x + 0.001* sd(x, na.rm = TRUE), x)
data %>%
  mutate_each(funs(f))