Bootstrap: Prepare Data

Define Libraries

library("stringr")
library("dplyr")
library("reshape2")

Define Path

dir.wrk <- str_replace(getwd(), "/scripts", "")
dir.data <- file.path(dir.wrk, "data/data_processed")
dir.output <- file.path(dir.wrk, "data/data_permutation_withReplacement")

Define Files

file.dat <- file.path(dir.data, "household_level_data_frequency_table.tsv")

Load Data

dat <- read.delim(file.dat, header = TRUE, stringsAsFactors = FALSE)

dim(dat)
head(dat)

Permute

nperm <- 1000
set.seed(12345)

for (i in 1:nperm) {
    df <- dat
    
    # SAMPLE ROW INDICES ---
    sampled_index <- sample(x = c(1:nrow(df)), size = nrow(df), replace = TRUE)
    
    # GET PERMUTED DATA ---
    dm <- df[sampled_index, ]
    
    
    # WRITE OUTPUT ---
    file.output <- file.path(dir.output, paste("abundance_permmute_", i, ".tsv", 
        sep = ""))
    write.table(dm, file.output, sep = "\t", row.names = FALSE, col.names = TRUE, 
        quote = FALSE)
}