inst/doc/introduction.R

In triact: Analyzing the Lying Behavior of Cows from Accelerometer Data

## ----include = FALSE----------------------------------------------------------
library(triact)

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options(digits.secs = 1)

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options(triact_table = "data.frame")

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?Triact

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input_dir <-  system.file("extdata", package = "triact") 

files <- list.files(input_dir)

print(files)

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cat(paste(readLines(file.path(input_dir, files[1]), n = 30), collapse = "\n"))

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my_triact <- Triact$new()

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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 = ".")

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my_triact$load_files(input = input_dir,
                     id_substring = c(1, 5),
                     timeFwdUpRight_cols = c(1, -2, 3, -4),
                     skip = "DATA")

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head(my_triact$data)

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str(my_triact$data)

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?cows_5hz

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str(cows_5hz)

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my_triact <- Triact$new()

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my_triact$load_table(cows_5hz)

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my_triact$add_lying()

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str(my_triact$data)

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my_triact$add_side(left_leg = TRUE)

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str(my_triact$data)

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my_triact$add_activity()

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str(my_triact$data)

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?bout_summary

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bouts_summary <- my_triact$summarize_bouts()

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head(bouts_summary)

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bouts_summary <- my_triact$summarize_bouts(bout_type = "lying")

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head(bouts_summary)

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?interval_summary

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int_summary <- my_triact$summarize_intervals()

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head(int_summary)

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str(int_summary)

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int_summary <- my_triact$summarize_intervals(interval = "30 min",
                                             lag_in_s = 10 * 60)

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head(int_summary)

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str(int_summary)

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int_summary <- my_triact$summarize_intervals(bouts = TRUE,
                                             side = TRUE)

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str(int_summary)

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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")

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st_ups <- my_triact$extract_standup()

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print(st_ups)

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l_downs <- my_triact$extract_liedown(sec_before = 3, sec_after = 3)

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head(l_downs[[1]])