lettersim-ot-rsa/09_controls_rsa_all_chs.R

library(readr)
library(dplyr)
library(purrr)
library(tidyr)
library(brms)
library(ggplot2)
library(ggdist)
# library(fda)
library(patchwork)

library(parallel)

n_cores <- parallel::detectCores(all.tests=FALSE, logical=TRUE)
# n_cores <- 14
# options(loo.cores = n_cores)

set.seed(1)

stim_sim <- left_join(
  read_csv(file.path("stim_sim", "preregistered", "jacc.csv")),
  read_csv(file.path("stim_sim", "preregistered", "ot.csv")),
  by = c("char1", "char2")
) |>
  left_join(
    read_csv(file.path("stim_sim", "complexity", "complexity.csv")),
    by = c("char1", "char2")
  ) |>
  left_join(
    read_csv(file.path("stim_sim", "frequency", "frequency.csv")),
    by = c("char1", "char2")
  ) |>
  left_join(
    read_csv(file.path("stim_sim", "phonology", "dominant_phonemes.csv")),
    by = c("char1", "char2")
  ) |>
  left_join(
    read_csv(file.path("stim_sim", "phonology", "letter_names.csv")),
    by = c("char1", "char2")
  ) |>
  mutate(
    rank_jacc = rank(jacc),
    rank_ot = rank(ot),
    rank_comp_dist = rank(comp_dist),
    rank_freq_dist = rank(freq_dist),
    rank_phon_dist = rank(phon_dist),
    rank_name_phon_dist = rank(name_phon_dist)
  ) |>
  rowwise() |>
  mutate(pair_id = paste(sort(c(char1, char2)), collapse="_")) |>
  ungroup()

rdm <- file.path("rdm_data", "time_resolved_all_chs") |>
  list.files(pattern=".*\\.csv", full.names=TRUE) |>
  map_df(read_csv, col_types=c("subj_id"="c")) |>
  left_join(stim_sim, by=c("char1", "char2")) |>
  group_by(subj_id, time) |>
  mutate(rank_eeg_dissim = rank(eeg_dissim)) |>
  ungroup() |>
  arrange(time)

times <- sort(unique(rdm$time))

rdm_poi <- file.path("rdm_data", "period_of_interest_all_chs") |>
  list.files(pattern=".*\\.csv", full.names=TRUE) |>
  map_df(read_csv, col_types=c("subj_id"="c")) |>
  left_join(stim_sim, by=c("char1", "char2")) |>
  group_by(subj_id) |>
  mutate(rank_eeg_dissim = rank(eeg_dissim)) |>
  ungroup()


# fit full model -------------------------------------------

# this is a multivariate model that estimates correlations between all items

# partial corr model

# short function for calculating the population SD
pop_sd <- function(x) sqrt((length(x)-1)/length(x)) * sd(x)

# check correlation priors
lkj_prior <- 1.5

m_rho_prior_full <- c(
  # biased towards 0 for non-diagonal correlations, because lower correlations are more likely in RSA of EEG data
  set_prior(sprintf("lkj(%s)", lkj_prior), class="rescor"),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_eeg_dissim))), class="sigma", resp="rankeegdissim", ub=max(rdm_poi$rank_eeg_dissim)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_jacc))), class="sigma", resp="rankjacc", ub=max(rdm_poi$rank_jacc)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_ot))), class="sigma", resp="rankot", ub=max(rdm_poi$rank_ot)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_comp_dist))), class="sigma", resp="rankcompdist", ub=max(rdm_poi$rank_comp_dist)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_freq_dist))), class="sigma", resp="rankfreqdist", ub=max(rdm_poi$rank_freq_dist)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_phon_dist))), class="sigma", resp="rankphondist", ub=max(rdm_poi$rank_phon_dist)),
  set_prior(sprintf("constant(%s)", pop_sd(1:max(rdm_poi$rank_name_phon_dist))), class="sigma", resp="ranknamephondist", ub=max(rdm_poi$rank_name_phon_dist))
)

m_rho_full_poi <- brm(
  bf(
    mvbind(rank_eeg_dissim, rank_jacc, rank_ot, rank_comp_dist, rank_freq_dist, rank_phon_dist, rank_name_phon_dist) ~ 0
  ) +
    set_rescor(rescor=TRUE),
  family = brmsfamily("gaussian"),
  iter = 24000,
  warmup = 6000,
  chains = 8,
  cores = n_cores,
  seed = 1,
  # centre each dimension since we don't model intercept
  data = mutate(rdm_poi, across(starts_with("rank"), function(x) x - mean(x))),
  prior = m_rho_prior_full,
  save_pars = save_pars(all=TRUE),
  sample_prior = FALSE,
  control = list(adapt_delta = 0.99)
)

# get a vector of response variable names (will match order of correlation matrix)
var_names <- colnames(get_y(m_rho_full_poi))

# get correlation matrices for each draw
cor_samps <- as_draws_df(m_rho_full_poi, "^Lrescor", regex=TRUE) |>
  # convert columns into covariance, correlation, and partial correlation matrix for each draw
  pivot_longer(cols=starts_with("Lrescor"), names_to="idx", values_to="r") |>
  mutate(idx = sub("Lrescor", "", idx, fixed=TRUE)) |>
  mutate(idx = gsub("(\\[)|(\\])", "", idx)) |>
  separate(idx, c("idx1", "idx2"), sep=",") |>
  mutate(idx1=as.integer(idx1), idx2=as.integer(idx2)) |>
  group_by(.chain, .iteration, .draw) |>
  nest() |>
  # get correlation and partial correlation matrix for each draw
  mutate(
    cor_mat = map(
      data, function(x) {
        cov_mat <- matrix(0, nrow=max(x$idx1), ncol=max(x$idx2))
        cov_mat[cbind(x$idx1, x$idx2)] <- x$r
        cov_mat[upper.tri(cov_mat, diag=FALSE)] <- t(cov_mat)[upper.tri(cov_mat, diag=FALSE)]
        colnames(cov_mat) <- var_names
        rownames(cov_mat) <- var_names
        cov2cor(cov_mat)
      }
    ),
    pcor_mat = map(
      cor_mat, function(x) {
        pcor_mat <- corpcor::cor2pcor(x)
        colnames(pcor_mat) <- var_names
        rownames(pcor_mat) <- var_names
        pcor_mat
      }
    ),
    cor_rankeegdissim_rankjacc = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankjacc"]),
    cor_rankeegdissim_rankot = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankot"]),
    cor_rankeegdissim_rankcompdist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankcompdist"]),
    cor_rankeegdissim_rankfreqdist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankfreqdist"]),
    cor_rankeegdissim_rankphondist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankphondist"]),
    cor_rankeegdissim_ranknamephondist = map_dbl(cor_mat, function(x) x["rankeegdissim", "ranknamephondist"]),
    pcor_rankeegdissim_rankjacc = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankjacc"]),
    pcor_rankeegdissim_rankot = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankot"]),
    pcor_rankeegdissim_rankcompdist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankcompdist"]),
    pcor_rankeegdissim_rankfreqdist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankfreqdist"]),
    pcor_rankeegdissim_rankphondist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankphondist"]),
    pcor_rankeegdissim_ranknamephondist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "ranknamephondist"])
  )

# calculate Evidence Ratios for each hypothesis
bf_1 <- sum(cor_samps$cor_rankeegdissim_rankot > 0) / sum(cor_samps$cor_rankeegdissim_rankot < 0)

bf_2a <- sum(cor_samps$cor_rankeegdissim_rankot > cor_samps$cor_rankeegdissim_rankjacc) /
  sum(cor_samps$cor_rankeegdissim_rankot <= cor_samps$cor_rankeegdissim_rankjacc)

bf_2b <- sum(cor_samps$pcor_rankeegdissim_rankot > cor_samps$pcor_rankeegdissim_rankjacc) /
  sum(cor_samps$pcor_rankeegdissim_rankot <= cor_samps$pcor_rankeegdissim_rankjacc)

# save the partial Rho estimates
cor_samps_long <- cor_samps |>
  pivot_longer(c(starts_with("pcor_rankeegdissim"), starts_with("cor_rankeegdissim")), names_to="cor_lab", values_to="Rho") |>
  mutate(
    model = case_when(
      grepl("rankjacc", cor_lab, fixed=TRUE) ~ "Jaccard Distance",
      grepl("rankot", cor_lab, fixed=TRUE) ~ "Wasserstein Distance",
      grepl("rankcompdist", cor_lab, fixed=TRUE) ~ "Complexity Distance",
      grepl("rankfreqdist", cor_lab, fixed=TRUE) ~ "Frequency Distance",
      grepl("rankphondist", cor_lab, fixed=TRUE) ~ "Phonological Distance",
      grepl("ranknamephondist", cor_lab, fixed=TRUE) ~ "Letter Name Phonological Distance",
      .default = NA
    ),
    is_partial = grepl("^pcor", cor_lab)
  ) |>
  dplyr::select(-data, -cor_mat, -pcor_mat)

cor_samps_long |>
  group_by(model, is_partial) |>
  median_hdi(Rho, .width=.89)

saveRDS(cor_samps_long, file.path("estimates", "controls_all_chs_cor_samps_long.rds"))

# fit time-resolved models -----------------------------------------------

# fit models for each time point
# Note: fitting models to all subjects' data, where ranked within subject, gives roughly equivalent peak posteriors to averaging over per-subject Rho estimates

# fit models in parallel for speed
library(future)
plan(multicore, workers=n_cores)

message("Fitting time-resolved models in parallel")

m_rho <- brm_multiple(
  bf(
    mvbind(rank_eeg_dissim, rank_jacc, rank_ot, rank_comp_dist, rank_freq_dist, rank_phon_dist, rank_name_phon_dist) ~ 0
  ) +
    set_rescor(rescor=TRUE),
  family = brmsfamily("gaussian"),
  iter = 10000,
  warmup = 5000,
  chains = 4,
  cores = 1,
  seed = 1,
  # centre each dimension since we don't model intercept, then split by time points into list
  data = rdm |>
    group_by(time) |>
    mutate(across(starts_with("rank"), function(x) x - mean(x))) |>
    ungroup() |>
    group_split(time),
  combine = FALSE,
  prior = m_rho_prior_full,
  control = list(adapt_delta = 0.99),
  save_pars = save_pars(all=TRUE)
)

# get posteriors for each time point
tc <- map_df(1:length(m_rho), function(i) {
  t_i <- times[[i]]
  m_i <- m_rho[[i]]
  var_names_i <- colnames(get_y(m_i))
  
  as_draws_df(m_i, "^Lrescor", regex=TRUE) |>
    # convert columns into covariance, correlation, and partial correlation matrix for each draw
    pivot_longer(cols=starts_with("Lrescor"), names_to="idx", values_to="r") |>
    mutate(idx = sub("Lrescor", "", idx, fixed=TRUE)) |>
    mutate(idx = gsub("(\\[)|(\\])", "", idx)) |>
    separate(idx, c("idx1", "idx2"), sep=",") |>
    mutate(idx1=as.integer(idx1), idx2=as.integer(idx2)) |>
    group_by(.chain, .iteration, .draw) |>
    nest() |>
    # get correlation and partial correlation matrix for each draw
    mutate(
      cor_mat = map(
        data, function(x) {
          cov_mat <- matrix(0, nrow=max(x$idx1), ncol=max(x$idx2))
          cov_mat[cbind(x$idx1, x$idx2)] <- x$r
          cov_mat[upper.tri(cov_mat, diag=FALSE)] <- t(cov_mat)[upper.tri(cov_mat, diag=FALSE)]
          colnames(cov_mat) <- var_names_i
          rownames(cov_mat) <- var_names_i
          cov2cor(cov_mat)
        }
      ),
      pcor_mat = map(
        cor_mat, function(x) {
          pcor_mat <- corpcor::cor2pcor(x)
          colnames(pcor_mat) <- var_names_i
          rownames(pcor_mat) <- var_names_i
          pcor_mat
        }
      ),
      cor_rankeegdissim_rankjacc = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankjacc"]),
      cor_rankeegdissim_rankot = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankot"]),
      cor_rankeegdissim_rankcompdist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankcompdist"]),
      cor_rankeegdissim_rankfreqdist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankfreqdist"]),
      cor_rankeegdissim_rankphondist = map_dbl(cor_mat, function(x) x["rankeegdissim", "rankphondist"]),
      cor_rankeegdissim_ranknamephondist = map_dbl(cor_mat, function(x) x["rankeegdissim", "ranknamephondist"]),
      pcor_rankeegdissim_rankjacc = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankjacc"]),
      pcor_rankeegdissim_rankot = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankot"]),
      pcor_rankeegdissim_rankcompdist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankcompdist"]),
      pcor_rankeegdissim_rankfreqdist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankfreqdist"]),
      pcor_rankeegdissim_rankphondist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "rankphondist"]),
      pcor_rankeegdissim_ranknamephondist = map_dbl(pcor_mat, function(x) x["rankeegdissim", "ranknamephondist"]),
      time = t_i
    ) |>
    dplyr::select(-data, -cor_mat, -pcor_mat)
})

saveRDS(tc, file.path("estimates", "controls_all_chs_timecourse.rds"))