params <-
list(EVAL = FALSE)

## ---- SETTINGS-knitr, include=FALSE-----------------------------------------------------
stopifnot(require(knitr))
options(width = 90)
opts_chunk$set(
  comment = NA,
  message = FALSE,
  warning = FALSE,
  eval = if (isTRUE(exists("params"))) params$EVAL else FALSE,
  dev = "png",
  dpi = 150,
  fig.asp = 0.8,
  fig.width = 5,
  out.width = "60%",
  fig.align = "center"
)

## ---------------------------------------------------------------------------------------
#  library(thurstonianIRT)
#  library(dplyr)
#  library(tidyr)

## ---------------------------------------------------------------------------------------
#  npersons <- 500
#  ntraits <- 5
#  nitems_per_block <- 3
#  nblocks_per_trait <- 9
#  nblocks <- ntraits * nblocks_per_trait / nitems_per_block
#  nitems <- ntraits * nblocks_per_trait
#  ncomparisons <- (nitems_per_block * (nitems_per_block - 1)) / 2 * nblocks

## ---------------------------------------------------------------------------------------
#  set.seed(123)
#  lambda <- runif(nitems, 0.65, 0.96)
#  signs <- c(rep(1, ceiling(nitems / 2)), rep(-1, floor(nitems / 2)))
#  lambda <- lambda * signs[sample(seq_len(nitems))]
#  gamma <- runif(nitems, -1, 1)
#  Phi <- diag(5)

## ---------------------------------------------------------------------------------------
#  sdata <- sim_TIRT_data(
#    npersons = npersons,
#    ntraits = ntraits,
#    nitems_per_block = nitems_per_block,
#    nblocks_per_trait = nblocks_per_trait,
#    gamma = gamma,
#    lambda = lambda,
#    Phi = Phi
#  )

## ---- results="hide"--------------------------------------------------------------------
#  fit_stan <- fit_TIRT_stan(sdata, chains = 1, iter = 1000, warmup = 500)
#  fit_lavaan <- fit_TIRT_lavaan(sdata)
#  fit_mplus <- fit_TIRT_mplus(sdata)

## ---------------------------------------------------------------------------------------
#  eta <- as_tibble(as.data.frame(attributes(sdata)$eta))
#  names(eta) <- paste0("trait", 1:ncol(eta))
#  true_scores <- eta %>%
#    mutate(id = 1:n()) %>%
#    gather(key = "trait", value = "truth", -id)
#  true_summaries <- true_scores %>%
#    group_by(trait) %>%
#    summarise(true_mean = mean(truth), true_sd = sd(truth))
#  
#  pred <- predict(fit_stan) %>%
#    bind_rows(predict(fit_lavaan), predict(fit_mplus), .id = "source") %>%
#    mutate(
#      source = as.character(factor(
#        source, levels = 1:3, labels = c("stan", "lavaan", "mplus")
#      )),
#      trait = tolower(trait)
#    ) %>%
#    inner_join(true_scores, by = c("id", "trait"))
#  
#  pred <- pred %>%
#    inner_join(
#      pred %>%
#        group_by(trait, source) %>%
#        summarise(cor_est_truth = cor(estimate, truth)),
#      by = c("trait", "source")
#    ) %>%
#    mutate(
#      sign = sign(cor_est_truth),
#      estimate = ifelse(sign %in% -1, -estimate, estimate)
#    ) %>%
#    inner_join(true_summaries, by = "trait") %>%
#    group_by(trait, source) %>%
#    mutate(
#      est_mean = mean(estimate),
#      est_sd = sd(estimate)
#    ) %>%
#    ungroup() %>%
#    mutate(
#      ztruth = (truth - true_mean) / true_sd,
#      zestimate = (estimate - est_mean) / est_sd
#    )

## ---------------------------------------------------------------------------------------
#  res <- pred %>%
#    group_by(trait, source) %>%
#    summarise(rel = cor(estimate, truth)^2)
#  
#  res

## ---- include = FALSE-------------------------------------------------------------------
#  testthat::expect_true(all(res$rel > 0.75))

## ---------------------------------------------------------------------------------------
#  cor_matrix <- pred %>%
#    mutate(
#      # ensure correct ordering of traits
#      SC = paste0(source, "_", trait),
#      SC = factor(SC, levels = unique(SC))
#    ) %>%
#    select(id, SC, estimate) %>%
#    spread(key = "SC", value = "estimate") %>%
#    bind_cols(eta, .) %>%
#    select(-id) %>%
#    cor()

## ---------------------------------------------------------------------------------------
#  trait1 <- paste0(c("stan", "lavaan", "mplus"), "_trait1")
#  round(cor_matrix[trait1, trait1], 2)

## ---- include = FALSE-------------------------------------------------------------------
#  for (i in 1:ntraits) {
#    trait_cols <- paste0(c("stan", "lavaan", "mplus"), "_trait", i)
#    testthat::expect_true(all(cor_matrix[trait_cols, trait_cols] > 0.96))
#  }