I need to speed up code using data.table. I am getting stuck on how to reference variables that are being indexed from a vector.
data:
df <- data.frame(
id=c(1,1,1,2,2,2,3,3,3),
year=as.character(c(2014, 2015, 2016, 2015, 2015, 2016, NA, NA, 2016)),
code=c(1,2,2, 1,2,3, 3,4,5),
dv1=1:9,
dv2=2:10
) %>% as.data.table()
dtplyr code:
cols <- c("dv1", "dv2")
test <- function(data, columns, group) {
for(i in seq_along(columns)) {
sub1 <- df %>%
select("id", columns[i], group) %>%
group_by(.data[[group]]) %>%
summarise(mean=mean(.data[[columns[i]]], na.rm=T), sd=sd(.data[[columns[i]]], na.rm=T)) %>%
ungroup() %>%
as_tibble()
print(sub1)
}
}
data.table attempt:
test <- function(data, columns, group) {
for(i in seq_along(columns)) {
sub1 <- df %>%
.[, .(id, columns[i], group)] %>%
.[, .(mean(.data[[columns[i]]], na.rm=T), sd=sd(.data[[columns[i]]], na.rm=T)), by=.data[[group]]] %>%
as_tibble()
print(sub1)
}
}
test(data=df, columns=cols, group="year")
This works on a single variable:
df %>%
.[, .(id, dv1, year)] %>%
.[, .(mean(dv1, na.rm=T), sd=sd(dv1, na.rm=T)), by=year] %>%
as_tibble()
.data
is not used in data.table
select
here and that is why you also don't need .[, .(id, columns[i], group)]
in data.table
version.get
to get column values based on string.Since this is just an example I have not tried to simplify the loop so that you can add more complicated stuff in there later.
library(data.table)
cols <- c("dv1", "dv2")
test <- function(data, columns, group) {
for(i in columns) {
sub1 <-df[, .(mean(get(i), na.rm=T), sd=sd(get(i), na.rm=T)), by=year]
print(sub1)
}
}
test(data=df, columns=cols, group="year")
# year V1 sd
#1: 2014 1.00 NA
#2: 2015 3.67 1.528
#3: 2016 6.00 3.000
#4: <NA> 7.50 0.707
# year V1 sd
#1: 2014 2.00 NA
#2: 2015 4.67 1.528
#3: 2016 7.00 3.000
#4: <NA> 8.50 0.707