## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 4.2)
library(silentema)

## ----silence------------------------------------------------------------------
sim2 <- simulate_ema(N = 60, n_prompts = 40, motifs = "M2", compliance = 0.7, delta = -1, seed = 1)
st <- silence_test(sim2$data, sim2$vars)
st

## ----silence-attr-------------------------------------------------------------
attr(st, "joint")
c(triples = attr(st, "n_triples"), skipped_middle = attr(st, "n_skipped"))

## ----silence-null-------------------------------------------------------------
sim1 <- simulate_ema(N = 60, n_prompts = 40, motifs = "M1", compliance = 0.7, seed = 1)
silence_test(sim1$data, sim1$vars)

## ----single-------------------------------------------------------------------
one <- simulate_ema(N = 1, n_prompts = 200, motifs = "M2", compliance = 0.7, delta = -1, days = 8, seed = 5)
silence_test(one$data, one$vars, day = "day", B = 100, seed = 1)

## ----poly---------------------------------------------------------------------
silence_test(sim1$data, sim1$vars, poly = 2)$p

## ----collider-----------------------------------------------------------------
sim13 <- simulate_ema(N = 300, n_prompts = 56, motifs = c("M1", "M3"), compliance = 0.7, kappa_R = 1, seed = 2)
silence_test(sim13$data, sim13$vars)
recoverability(dm_graph(c("M1", "M3")))$estimator[6]

## ----sensor-------------------------------------------------------------------
sim2s <- simulate_ema(N = 60, n_prompts = 40, motifs = "M2", compliance = 0.7, delta = -1,
                      sensor_cor = 0.6, seed = 3)
sg <- sensor_gap_test(sim2s$data, sim2s$vars, sensor = "S")
sg
attr(sg, "loading")

## ----sensor-null--------------------------------------------------------------
sim1s <- simulate_ema(N = 60, n_prompts = 40, motifs = c("M1", "M3"), compliance = 0.7, sensor_cor = 0.6, seed = 3)
sensor_gap_test(sim1s$data, sim1s$vars, sensor = "S")

## ----fatigue------------------------------------------------------------------
sim3 <- simulate_ema(N = 60, n_prompts = 40, motifs = "M3", compliance = 0.7, kappa_R = 1, seed = 4)
fatigue_check(sim3$data)
fatigue_check(sim2$data)

## ----mc-----------------------------------------------------------------------
rej <- function(motifs, reps = 60, ...) {
  mean(vapply(seq_len(reps), function(r) {
    s <- simulate_ema(N = 60, n_prompts = 40, motifs = motifs, compliance = 0.7, seed = 1000 + r, ...)
    attr(silence_test(s$data, s$vars), "joint")["p"] < 0.05
  }, logical(1)))
}
c(M0 = rej("M0"), M1 = rej("M1"), M2 = rej("M2", delta = -1))