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Create a tidy run-level variables table

Source: R/project_extensions.R
variables_table.Rd

Aggregates event tables, confound tables, and scan inventory into a single run-level tibble with normalized identifiers and nested list-columns. This is a lightweight variables layer for downstream R workflows rather than a full model-spec engine.

Usage

variables_table(
  x,
  subid = ".*",
  task = ".*",
  run = ".*",
  session = ".*",
  include = c("events", "confounds"),
  scope = c("all", "raw", "derivatives"),
  pipeline = NULL
)

Arguments

x

A bids_project object.

subid

Regex pattern to match subject IDs.

task

Regex pattern to match tasks.

run

Regex pattern to match runs.

session

Regex pattern to match sessions.

include

Which variable sources to include. Supported values are "events" and "confounds".

scope

Query scope used for scan inventory. One of "all", "raw", or "derivatives".

pipeline

Optional derivative pipeline name to restrict derivative scan inventory.

Value

A tibble with one row per run and list-columns scans, events, and confounds when available.

Examples

# \donttest{
tryCatch({
  ds001_path <- get_example_bids_dataset("ds001")
  proj <- bids_project(ds001_path)
  vt <- variables_table(proj)
  print(vt)
  unlink(ds001_path, recursive = TRUE)
}, error = function(e) message("Example requires internet: ", e$message))
#> Rows: 158 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 156 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 149 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 185 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 184 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 186 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 150 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 169 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 175 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 166 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 175 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 169 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 135 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 138 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 146 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 177 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 187 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 172 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 170 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 162 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 160 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 163 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 166 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 165 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 172 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 167 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 158 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 175 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 173 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 173 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 150 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 153 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 168 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 149 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 156 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 148 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 151 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 172 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 162 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 168 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 173 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 162 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 149 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 127 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 135 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 121 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 141 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 157 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): trial_type
#> dbl (7): onset, duration, cash_demean, control_pumps_demean, explode_demean,...
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> Project does not have fmriprep derivatives enabled. Cannot search for confound files.
#> No confound data found for the given selection.
#> # A tibble: 48 × 8
#>    .subid .session .task                .run  scans    n_scans events   n_events
#>    <chr>  <chr>    <chr>                <chr> <list>     <int> <list>      <int>
#>  1 01     ""       balloonanalogriskta… 01    <tibble>       1 <tibble>      158
#>  2 01     ""       balloonanalogriskta… 02    <tibble>       1 <tibble>      156
#>  3 01     ""       balloonanalogriskta… 03    <tibble>       1 <tibble>      149
#>  4 02     ""       balloonanalogriskta… 01    <tibble>       1 <tibble>      185
#>  5 02     ""       balloonanalogriskta… 02    <tibble>       1 <tibble>      184
#>  6 02     ""       balloonanalogriskta… 03    <tibble>       1 <tibble>      186
#>  7 03     ""       balloonanalogriskta… 01    <tibble>       1 <tibble>      150
#>  8 03     ""       balloonanalogriskta… 02    <tibble>       1 <tibble>      169
#>  9 03     ""       balloonanalogriskta… 03    <tibble>       1 <tibble>      175
#> 10 04     ""       balloonanalogriskta… 01    <tibble>       1 <tibble>      166
#> # ℹ 38 more rows
# }