Generate clutch names

The lifelihood() function requires a clutch argument. It’s a vector containing the names of the clutch columns. The order should be: first clutch first date, first clutch second date, first clutch clutch size, second clutch first date, first clutch second date, second clutch clutch size, and so on. If the observation with the most clutches is, for example, 10, then the vector must be of size 10 x 3 = 30 (3 elements per clutch: first date, second date and size).

For practical reasons, it is easier to generate this vector programmatically, particularly if your dataset contains a large number of clutches.

Load libraries & data

library(lifelihood)
library(tidyverse)
#> ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
#> ✔ dplyr     1.1.4     ✔ readr     2.1.5
#> ✔ forcats   1.0.0     ✔ stringr   1.5.1
#> ✔ ggplot2   3.5.2     ✔ tibble    3.3.0
#> ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
#> ✔ purrr     1.0.4     
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag()    masks stats::lag()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

df <- fakesample |>
  mutate(
    type = as.factor(type),
    geno = as.factor(geno)
  )

Let’s say my clutch names looks like this: clutch_start_1, clutch_end_1, clutch_size_1, clutch_start_2, clutch_end_2, clutch_size_2, and so on. This goes up to clutch_start_28, clutch_end_28, clutch_size_28.

We can generate this vector with the following function:

generate_clutch_vector <- function(N) {
  return(paste(
    "clutch",
    rep(c("start", "end", "size"), N),
    rep(1:N, each = 3),
    sep = "_"
  ))
}
clutchs <- generate_clutch_vector(28)
clutchs
#>  [1] "clutch_start_1"  "clutch_end_1"    "clutch_size_1"   "clutch_start_2" 
#>  [5] "clutch_end_2"    "clutch_size_2"   "clutch_start_3"  "clutch_end_3"   
#>  [9] "clutch_size_3"   "clutch_start_4"  "clutch_end_4"    "clutch_size_4"  
#> [13] "clutch_start_5"  "clutch_end_5"    "clutch_size_5"   "clutch_start_6" 
#> [17] "clutch_end_6"    "clutch_size_6"   "clutch_start_7"  "clutch_end_7"   
#> [21] "clutch_size_7"   "clutch_start_8"  "clutch_end_8"    "clutch_size_8"  
#> [25] "clutch_start_9"  "clutch_end_9"    "clutch_size_9"   "clutch_start_10"
#> [29] "clutch_end_10"   "clutch_size_10"  "clutch_start_11" "clutch_end_11"  
#> [33] "clutch_size_11"  "clutch_start_12" "clutch_end_12"   "clutch_size_12" 
#> [37] "clutch_start_13" "clutch_end_13"   "clutch_size_13"  "clutch_start_14"
#> [41] "clutch_end_14"   "clutch_size_14"  "clutch_start_15" "clutch_end_15"  
#> [45] "clutch_size_15"  "clutch_start_16" "clutch_end_16"   "clutch_size_16" 
#> [49] "clutch_start_17" "clutch_end_17"   "clutch_size_17"  "clutch_start_18"
#> [53] "clutch_end_18"   "clutch_size_18"  "clutch_start_19" "clutch_end_19"  
#> [57] "clutch_size_19"  "clutch_start_20" "clutch_end_20"   "clutch_size_20" 
#> [61] "clutch_start_21" "clutch_end_21"   "clutch_size_21"  "clutch_start_22"
#> [65] "clutch_end_22"   "clutch_size_22"  "clutch_start_23" "clutch_end_23"  
#> [69] "clutch_size_23"  "clutch_start_24" "clutch_end_24"   "clutch_size_24" 
#> [73] "clutch_start_25" "clutch_end_25"   "clutch_size_25"  "clutch_start_26"
#> [77] "clutch_end_26"   "clutch_size_26"  "clutch_start_27" "clutch_end_27"  
#> [81] "clutch_size_27"  "clutch_start_28" "clutch_end_28"   "clutch_size_28"

The only disadvantage of this technique is that the clutch names have to have a specific pattern.