## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 4.5)

## ----sim----------------------------------------------------------------------
library(silentema)
sim <- simulate_ema(N = 60, n_prompts = 40, motifs = "M2", compliance = 0.70, delta = -1,
                    sensor_cor = 0.6, p_probe = 0.05, days = 5, seed = 1)
sim
head(sim$data)

## ----graph--------------------------------------------------------------------
g <- dm_graph(motifs = "M2", sensor = TRUE, probe = TRUE)
g
plot(g)
recoverability(g)

## ----graph2-------------------------------------------------------------------
recoverability(dm_graph(c("M1", "M4")))
recoverability(dm_graph("M6"))

## ----tests--------------------------------------------------------------------
st <- silence_test(sim$data, sim$vars, day = "day")
st
sg <- sensor_gap_test(sim$data, sim$vars, sensor = "S", day = "day")
sg
fatigue_check(sim$data, day = "day")

## ----fit----------------------------------------------------------------------
fit0 <- fit_pairs(sim$data, sim$vars, day = "day")
fit0
confint(fit0)[1:4, ]
prof <- tilt_profile(sim$data, sim$vars, delta_grid = seq(-2, 0.5, by = 0.5), day = "day", probe = "Z")
prof
plot(prof, plausible = c(-1.5, -0.5))

## ----calibrate----------------------------------------------------------------
cs <- calibrate_delta(prof, sim$data, method = "sensor", day = "day")
cs
plot(cs)
calibrate_delta(prof, sim$data, method = "probe", day = "day")

## ----postskip-----------------------------------------------------------------
calibrate_delta(prof, sim$data, method = "postskip", day = "day", n_sim = 5, seed = 2)

## ----report-------------------------------------------------------------------
break_even(prof, delta_max = 1.5)[1:4, ]
cat(missingness_declaration(g, silence = st, sensor_gap = sg, profile = prof, calibration = cs,
                            plausible = c(-1.5, -0.5)), sep = "\n")

## ----fiml---------------------------------------------------------------------
fit_fiml(sim$data, sim$vars)