I would like to use R for solving a problem of experimental design in which I will randomly assign my experimental units to treatment or control groups. The problem is the following:
Let's say that I have 120 plants with unique IDs (subsetted in 4 different clones), 3 time points, 2 pathogens, 2 control groups. Therefore, for each time point I would like to assign for each clone: -3 of pathogen A, 3 of pathogen B, 2 of control A and 2 of control B.
clones <- c(rep("clone A", 30), rep("clone B", 30), rep("clone C", 30), rep("clone D", 30))
IDs <- 1:120
plants <- data.frame(IDs = IDs,
clones = clones)
# How can I randomly assign the following for each IDs?
control <- c("control A", "control B")
pathogen <- c("pathogen A", "Pathogen B")
time_point <- c("T1", "T2", "T3")
Thanks for the help!
library(tidyverse)
# ensure to use the same kind of randomness
# required for reproducibility
set.seed(1)
group <- c(
rep("Pathogen A", 3),
rep("Pathogen B", 3),
rep("control A", 2),
rep("control B", 2)
)
sampling <-
# Every clone has all groups
expand_grid(
group,
clone = c("Clone A", "Clone B", "Clone C", "Clone D"),
time = c("T1", "T2", "T3")
) %>%
arrange(clone) %>%
mutate(id = row_number()) %>%
# random group assignment stratified for each clone and time
group_by(clone, time) %>%
mutate(group = group %>% sample())
sampling
#> # A tibble: 120 × 4
#> # Groups: clone, time [12]
#> group clone time id
#> <chr> <chr> <chr> <int>
#> 1 control B Clone A T1 1
#> 2 Pathogen A Clone A T2 2
#> 3 Pathogen B Clone A T3 3
#> 4 Pathogen B Clone A T1 4
#> 5 Pathogen A Clone A T2 5
#> 6 control B Clone A T3 6
#> 7 control A Clone A T1 7
#> 8 Pathogen B Clone A T2 8
#> 9 Pathogen A Clone A T3 9
#> 10 Pathogen A Clone A T1 10
#> # … with 110 more rows
sampling %>%
group_by(clone) %>%
summarise(
min_id = min(id),
max_id = max(id)
)
#> # A tibble: 4 × 3
#> clone min_id max_id
#> <chr> <int> <int>
#> 1 Clone A 1 30
#> 2 Clone B 31 60
#> 3 Clone C 61 90
#> 4 Clone D 91 120
sampling %>%
filter(clone == "Clone A")
#> # A tibble: 30 × 4
#> # Groups: clone, time [3]
#> group clone time id
#> <chr> <chr> <chr> <int>
#> 1 control B Clone A T1 1
#> 2 Pathogen A Clone A T2 2
#> 3 Pathogen B Clone A T3 3
#> 4 Pathogen B Clone A T1 4
#> 5 Pathogen A Clone A T2 5
#> 6 control B Clone A T3 6
#> 7 control A Clone A T1 7
#> 8 Pathogen B Clone A T2 8
#> 9 Pathogen A Clone A T3 9
#> 10 Pathogen A Clone A T1 10
#> # … with 20 more rows
Created on 2022-04-15 by the reprex package (v2.0.1)