In gvegayon/biteme:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = ".8\\linewidth",
  fig.width = 10
)

library(biteme)

# Loading the data
fnames <- list.files("all_bites", pattern = "dyad", full.names = TRUE)
dyads  <- suppressMessages(lapply(fnames, readr::read_csv))

# Turning times into integers
dyads <- lapply(dyads, function(x) {
  x$BiteTime_hms <- as.integer(x$BiteTime_hms)
  as.matrix(x[,1:2])
})

# Running the permutation tests
cl <- parallel::makeForkCluster(8)
ans02 <- perm_test(dyads[[2]], biteme:::timegap, R = 1e4, cl = cl)

ans <- lapply(
  dyads, perm_test, statistic = biteme:::timegap, R = 100000, cl = cl
  )
parallel::stopCluster(cl)

plot(ans[[23]], breaks=100)
plot(ans[[22]], breaks=100)

pvals<-unlist(sapply(ans, "[[", "pval", simplify = FALSE))
pvals <- sort(pvals)
cols <- rep("tomato", length(pvals))
cols[which(pvals <= .05)] <- "steelblue"

op <- par(mai = par()$mai + c(.5,0,0,0))

barplot(pvals, las=2, cex.names=1, col=cols, border=NA)
abline(h=.05, lwd=2, lty=2)
text(x = 2, y = .05, labels = "p-value 0.05", pos = 3)
title(
  "p-values from the permuitation tests",
  xlab = "",
  ylab = "p-value"
)
par(op)

gvegayon/biteme documentation built on June 16, 2021, 5:30 p.m.