## ----include = FALSE---------------------------------------------------------- library(triact) ## ----------------------------------------------------------------------------- options(digits.secs = 1) ## ----------------------------------------------------------------------------- options(triact_table = "data.frame") ## ----------------------------------------------------------------------------- ?Triact ## ----------------------------------------------------------------------------- input_dir <- system.file("extdata", package = "triact") files <- list.files(input_dir) print(files) ## ----------------------------------------------------------------------------- cat(paste(readLines(file.path(input_dir, files[1]), n = 30), collapse = "\n")) ## ----------------------------------------------------------------------------- my_triact <- Triact$new() ## ----------------------------------------------------------------------------- my_triact$load_files(input = input_dir, id_substring = c(1, 5), timeFwdUpRight_cols = c(1, -2, 3, -4), time_format = "%Y-%m-%d %H:%M:%OS", tz = "Europe/Zurich", skip = "DATA", sep = ";", header = FALSE, dec = ".") ## ----------------------------------------------------------------------------- my_triact$load_files(input = input_dir, id_substring = c(1, 5), timeFwdUpRight_cols = c(1, -2, 3, -4), skip = "DATA") ## ----------------------------------------------------------------------------- head(my_triact$data) ## ----------------------------------------------------------------------------- str(my_triact$data) ## ----------------------------------------------------------------------------- ?cows_5hz ## ----------------------------------------------------------------------------- str(cows_5hz) ## ----------------------------------------------------------------------------- my_triact <- Triact$new() ## ----------------------------------------------------------------------------- my_triact$load_table(cows_5hz) ## ----------------------------------------------------------------------------- my_triact$add_lying() ## ----------------------------------------------------------------------------- str(my_triact$data) ## ----------------------------------------------------------------------------- my_triact$add_side(left_leg = TRUE) ## ----------------------------------------------------------------------------- str(my_triact$data) ## ----------------------------------------------------------------------------- my_triact$add_activity() ## ----------------------------------------------------------------------------- str(my_triact$data) ## ----------------------------------------------------------------------------- ?bout_summary ## ----------------------------------------------------------------------------- bouts_summary <- my_triact$summarize_bouts() ## ----------------------------------------------------------------------------- head(bouts_summary) ## ----------------------------------------------------------------------------- bouts_summary <- my_triact$summarize_bouts(bout_type = "lying") ## ----------------------------------------------------------------------------- head(bouts_summary) ## ----------------------------------------------------------------------------- ?interval_summary ## ----------------------------------------------------------------------------- int_summary <- my_triact$summarize_intervals() ## ----------------------------------------------------------------------------- head(int_summary) ## ----------------------------------------------------------------------------- str(int_summary) ## ----------------------------------------------------------------------------- int_summary <- my_triact$summarize_intervals(interval = "30 min", lag_in_s = 10 * 60) ## ----------------------------------------------------------------------------- head(int_summary) ## ----------------------------------------------------------------------------- str(int_summary) ## ----------------------------------------------------------------------------- int_summary <- my_triact$summarize_intervals(bouts = TRUE, side = TRUE) ## ----------------------------------------------------------------------------- str(int_summary) ## ----------------------------------------------------------------------------- cow_id = "cow01" data_01 <- my_triact$data[my_triact$data$id == cow_id, ] plot(!lying ~ time, data = data_01, type = "l", ylab = "", yaxt = "n", bty = "n") lines(ifelse(side == "R", 0, NA) ~ time, data = data_01, col = "orange") lines(ifelse(side == "L", 0, NA) ~ time, data = data_01, col = "purple") axis(2, at = c(0, 1), labels = c("lying", "standing"), las = 1, lwd = 0) legend(x = "center", legend = c("right", "left"), col = c("orange", "purple"), lwd = 1, bty = "n", title = "lying side") ## ----------------------------------------------------------------------------- st_ups <- my_triact$extract_standup() ## ----------------------------------------------------------------------------- print(st_ups) ## ----------------------------------------------------------------------------- l_downs <- my_triact$extract_liedown(sec_before = 3, sec_after = 3) ## ----------------------------------------------------------------------------- head(l_downs[[1]])