Problems with appending t.test results in a for loop - r

Question

Let me take simulated datasets to explain:
I have dataset dt and dt1
# dataset 1 `dt`
set.seed(12)
dt <- rnorm(5000,mean=10,sd=1)
dt <- data.frame(dt)
dt$group <- c("case","control")
colnames(dt) <- c("severity","group")
head(dt)
severity group
1 8.519432 case
2 11.577169 control
3 9.043256 case
4 9.079995 control
5 8.002358 case
6 9.727704 control
# dataset 2 `dt2`
set.seed(12)
dt2 <- rnorm(200,mean=12,sd=1)
dt2 <- data.frame(dt2)
dt2$group <- c("case2","control2")
colnames(dt2) <- c("severity","group")
head(dt2)
severity group
1 10.51943 case2
2 13.57717 control2
3 11.04326 case2
4 11.07999 control2
5 10.00236 case2
6 11.72770 control2
I am building one 1000 iterations for loop to do the following steps:
randomly take 500 rows from the dt and save as dt_sub
rbind dt_sub with dt2 and save as bd
select only rows with group as either case2 or control from the bd dataset (only cares the difference between these two groups)
t.tests on the variable severity between the case2 and control group
output t.tests results to t
use a for loop to repeat 1000 times
iteratively appends all t.test results to a dataframe results
Following is the code that I built in r
library(broom)
library(dplyr)
iter <- 1000
t <- data.frame()
for (i in 1:iter) {
dt_sub <- dt[sample(nrow(dt),500),]
bd <- rbind(dt_sub,dt2)
compare <- filter(bd, group %in% c("case2", "control"))
compare %>% group_by(group) %>% do(tidy(t.test(severity ~ group,data = compare))) -> t
t$iter <- i
}
results <- do.call(rbind,t)
My question is, this code works well when iter=1, but how should I set the compare %>% group_by(group) %>% do(tidy(t.test(severity ~ group,data = compare))) -> t line to ensure each run's t.test results will not be overwritten when iter ≥ 1? I tried t[i] but failed, anyone could advise please?
Thanks.

Answer 1

Create a function which runs the process once.
library(broom)
library(dplyr)
t_test_function <- function() {
dt_sub <- dt[sample(nrow(dt),500),]
bd <- rbind(dt_sub,dt2)
compare <- filter(bd, group %in% c("case2", "control"))
compare %>%
group_by(group) %>%
do(tidy(t.test(severity ~ group,data = compare))) %>%
ungroup
}
t_test_function()
# group estimate estimate1 estimate2 statistic p.value parameter conf.low
# <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 case2 1.94 11.9 9.99 17.4 9.40e-42 199. #1.72
#2 cont… 1.94 11.9 9.99 17.4 9.40e-42 199. 1.72
# … with 3 more variables: conf.high <dbl>, method <chr>,
# alternative <chr>
Now you can call this iter times using replicate and combine the dataset.
iter <- 5
results <- bind_rows(replicate(iter, t_test_function(), simplify = FALSE), .id = 'iter')
# A tibble: 10 x 12
# iter group estimate estimate1 estimate2 statistic p.value parameter
# <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
# 1 1 case2 1.88 11.9 10.1 17.3 1.05e-40 189.
# 2 1 cont… 1.88 11.9 10.1 17.3 1.05e-40 189.
# 3 2 case2 1.96 11.9 9.97 17.8 9.88e-43 194.
# 4 2 cont… 1.96 11.9 9.97 17.8 9.88e-43 194.
# 5 3 case2 1.94 11.9 9.99 17.9 3.76e-42 184.
# 6 3 cont… 1.94 11.9 9.99 17.9 3.76e-42 184.
# 7 4 case2 2.03 11.9 9.90 18.6 1.82e-44 189.
# 8 4 cont… 2.03 11.9 9.90 18.6 1.82e-44 189.
# 9 5 case2 1.96 11.9 9.97 18.1 7.05e-43 187.
#10 5 cont… 1.96 11.9 9.97 18.1 7.05e-43 187.
# … with 4 more variables: conf.low <dbl>, conf.high <dbl>, method <chr>,
# alternative <chr>