Merge pull request #87 from craddm/develop

Develop into master

Author: craddm

.github/workflows/R-CMD-check.yaml

@@ -64,10 +64,15 @@ jobs:
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
+      - name: Install hdf5 on mac
+        if: runner.os == 'macOS'
+        run: brew install hdf5
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+          remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Check
@@ -82,3 +87,8 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov(type = c("tests", "examples"), exclusions = "R/view_ica.R")
+        shell: Rscript {0}

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: eegUtils
 Type: Package
 Title: Utilities for Electroencephalographic (EEG) Analysis 
-Version: 0.6.1
-Date: 2021-02-21
+Version: 0.6.2
+Date: 2021-06-08
 Authors@R: c(
   person("Matt", "Craddock", role = c("aut", "cre", "cph"), email = "[email protected]"),
   person("Matti", "Vuorre", role = "ctb", email = "[email protected]"),
@@ -20,7 +20,6 @@ Imports:
     ggplot2,
     dplyr (>= 1.0.0),
     scales,
-    mgcv,
     purrr,
     shiny,
     tidyr (>= 1.0.0),
@@ -42,7 +41,8 @@ Imports:
 Depends:
   R (>= 3.3.0)
 RoxygenNote: 7.1.1
-Suggests: testthat,
+Suggests: 
+    testthat,
     vdiffr,
     covr,
     knitr,
@@ -54,7 +54,9 @@ Suggests: testthat,
     fICA,
     edfReader,
     ini,
-    R.matlab
+    R.matlab,
+    hdf5r,
+    mgcv
 URL: https://github.com/craddm/eegUtils, https://craddm.github.io/eegUtils
 BugReports: https://github.com/craddm/eegUtils/issues
 VignetteBuilder: knitr

NAMESPACE

@@ -44,6 +44,7 @@ S3method(compute_psd,eeg_evoked)
 S3method(compute_psd,eeg_group)
 S3method(compute_tfr,default)
 S3method(compute_tfr,eeg_epochs)
+S3method(compute_tfr,eeg_evoked)
 S3method(compute_tfr,eeg_group)
 S3method(eeg_average,default)
 S3method(eeg_average,eeg_epochs)
@@ -57,6 +58,7 @@ S3method(eeg_combine,eeg_evoked)
 S3method(eeg_combine,eeg_tfr)
 S3method(eeg_combine,list)
 S3method(eeg_combine,tfr_average)
+S3method(eeg_decompose,default)
 S3method(eeg_decompose,eeg_epochs)
 S3method(eeg_downsample,default)
 S3method(eeg_downsample,eeg_data)
@@ -71,13 +73,16 @@ S3method(eeg_reference,eeg_epochs)
 S3method(electrode_locations,data.frame)
 S3method(electrode_locations,eeg_data)
 S3method(electrode_locations,eeg_epochs)
+S3method(electrode_locations,eeg_tfr)
 S3method(epoch_data,default)
 S3method(epoch_data,eeg_data)
 S3method(epoch_data,eeg_epochs)
 S3method(epoch_stats,eeg_epochs)
 S3method(erp_image,data.frame)
+S3method(erp_image,default)
 S3method(erp_image,eeg_ICA)
 S3method(erp_image,eeg_epochs)
+S3method(erp_image,eeg_tfr)
 S3method(events,eeg_data)
 S3method(events,eeg_epochs)
 S3method(export_bva,default)
@@ -87,6 +92,7 @@ S3method(filter,eeg_data)
 S3method(filter,eeg_epochs)
 S3method(filter,eeg_evoked)
 S3method(filter,eeg_tfr)
+S3method(fit_glm,default)
 S3method(fit_glm,eeg_epochs)
 S3method(fortify,eeg_ICA)
 S3method(fortify,eeg_data)
@@ -294,8 +300,6 @@ importFrom(ggplot2,fortify)
 importFrom(graphics,abline)
 importFrom(graphics,par)
 importFrom(matrixStats,rowMedians)
-importFrom(matrixStats,rowSds)
-importFrom(mgcv,gam)
 importFrom(plotly,event_data)
 importFrom(plotly,plot_ly)
 importFrom(plotly,renderPlotly)

NEWS.md

@@ -1,4 +1,22 @@
-# eegUtils 0.6.0.9999
+# eegUtils 0.6.2
+
+### Function changes
+- added support for `EEGLAB` .set files saved in newer Matlab file formats.
+- changed first argument of `eeg_filter()` to `data` instead of `.data`
+- added some more informative user messages for importing data and adding electrode locations.
+- `erp_image()` now supports `eeg_tfr` objects.
+
+### Internal changes / bug fixes
+
+- When combining three or more continuous `eeg_data` objects, `eeg_combine()` would substantially undercorrect the timing of events in the third file - this is now fixed.
+- `groups` parameter for `topoplot()` now correctly passed for all types of object.
+- `stat_tests.R` file removed, will be reimplemented elsewhere
+- Long standing issues with import of channel locations from EEGLAB files hopefully fixed...
+- `rm_baseline()` for `eeg_evoked` no longer uses `data.table`
+- `as.data.frame.eeg_evoked()` handles grouped data better.
+- `import_set()` now handles all EEGLAB formats better.
+
+# eegUtils 0.6.1
 
 ### Function changes
 

R/ar-faster.R

@@ -256,6 +256,7 @@ faster_cine <- function(data,
 
   epochs <- split(data$signals,
                   data$timings$epoch)
+  n_epochs <- length(epochs)
 
   # Work out which chans are bad in each epoch according to FASTER
   bad_chans <- lapply(epochs,
@@ -303,7 +304,17 @@ faster_cine <- function(data,
                     new_epochs)
   epochs <- epochs[!names(epochs) %in% broken_epochs]
   epochs <- data.table::rbindlist(epochs)
-  data$signals <- as.data.frame(epochs)
+  data$signals <- tibble::as_tibble(epochs)
+  data$reject$cine_list <- bad_chans
+  data$reject$cine_total <- unlist(lapply(bad_chans,
+                                          length))
+
+  if (length(bad_chans) > 0) {
+    message(paste0(length(bad_chans), " of ", n_epochs, " epochs had at least one channel interpolated."))
+    message(paste0("Max number of channels interpolated in one epoch: ", max(data$reject$cine_total)))
+  } else {
+    message("No channels were interpolated in single epochs.")
+  }
   data
 }
 

R/baseline_correction.R

@@ -248,24 +248,23 @@ rm_baseline.eeg_evoked <- function(data,
                                    ...) {
 
   orig_cols <- channel_names(data)
-  # Edit to handle cases where multiple epochs/participants, now that the internal structure differs
-  if (is.null(time_lim)) {
-    data$signals <- data.table::as.data.table(as.data.frame(data))
-    data$signals <- data$signals[, c(orig_cols) := lapply(.SD,
-                                                          function(x) x - mean(x)),
-                                 by = c("participant_id", "epoch"),
-                                 .SDcols = orig_cols]
+  n_times <- length(unique(data$timings$time))
+  n_epochs <- nrow(data$epochs)
+  n_chans <- length(orig_cols)
+  base_times <- get_epoch_baselines(data,
+                                    time_lim)
 
-  } else {
+  data$signals <- as.matrix(data$signals)
+  dim(data$signals) <- c(n_times,
+                         n_epochs,
+                         n_chans)
+  data$signals <- baseline_epo(data$signals, base_times)
 
-    data$signals <- data.table::as.data.table(as.data.frame(data))
-    data$signals <-
-      data$signals[, c(orig_cols) := lapply(.SD,
-                                            function(x) x - mean(x[time > time_lim[1] & time < time_lim[2]])),
-       .SDcols = orig_cols,
-       by = c("participant_id", "epoch")]
-  }
-  data$signals <- tibble::as_tibble(data$signals[, ..orig_cols])
+  data$signals <- array(data$signals,
+                        dim = c(n_epochs * n_times, n_chans))
+  colnames(data$signals) <- orig_cols
+  data$signals <- tibble::as_tibble(data$signals)
+  #names(data$signals) <- elecs
   data
 }
 

R/channel_management.R

@@ -253,7 +253,6 @@ electrode_locations <- function(data, ...) {
 #'   not available be removed? (Defaults to FALSE).
 #' @param montage Name of an existing montage set. Defaults to NULL.
 #' @importFrom dplyr inner_join pull left_join distinct
-#' @import ggplot2
 #' @importFrom tibble is_tibble
 #' @describeIn electrode_locations Adds standard locations to a data frame in
 #'   long format
@@ -280,21 +279,21 @@ electrode_locations.data.frame <- function(data,
       dplyr::pull(electrodeLocs[, electrode])
 
     if (!all(elecs)) {
-      message(paste("Electrodes not found: ",
+      message(paste("Electrode locations not found: ",
                     paste(unique(data[, electrode])[!elecs, ],
                           sep = ",")))
     } else if (!any(elecs)) {
-      stop("No matching electrodes found.")
+      stop("No matching electrode locations found.")
     }
   } else {
     elecs <-
       unique(data[, electrode]) %in% electrodeLocs[, electrode,
                                                    drop = TRUE]
     if (!all(elecs)) {
-      message("Electrodes not found: ",
+      message("Electrodes locations not found: ",
               paste(unique(data[, electrode])[!elecs], collapse = " "))
     } else if (!any(elecs)) {
-      stop("No matching electrodes found.")
+      stop("No matching electrode locations found.")
     }
 
   }
@@ -313,7 +312,6 @@ electrode_locations.data.frame <- function(data,
 }
 
 #' @param overwrite Overwrite existing channel info. Defaults to FALSE.
-#' @import ggplot2
 #' @describeIn electrode_locations Adds standard locations to the chan_info field of an eeg_data object.
 #' @export
 
@@ -329,8 +327,7 @@ electrode_locations.eeg_data <- function(data,
             overwrite = overwrite)
 }
 
-#' @import ggplot2
-#' @describeIn electrode_locations Adds standard locations to the chan_info field of an eeg_data object.
+#' @describeIn electrode_locations Adds standard locations to the chan_info field of an `eeg_data` object.
 #' @export
 
 electrode_locations.eeg_epochs <- function(data,
@@ -345,6 +342,8 @@ electrode_locations.eeg_epochs <- function(data,
             overwrite = overwrite)
 }
 
+#' @describeIn electrode_locations Adds standard locations to the chan_info field of an `eeg_tfr` object.
+#' @export
 electrode_locations.eeg_tfr <- function(data,
                                         drop = FALSE,
                                         montage = NULL,

R/class_handling.R

@@ -149,7 +149,7 @@ eeg_psd <- function(data,
 }
 
 
-#' Function to create an object of class `eeg_GA`
+#' Function to create an object of class `eeg_group`
 #'
 #' @noRd
 
@@ -274,70 +274,6 @@ eeg_evoked <- function(data,
   value
 }
 
-#' Function to create an S3 object of class "eeg_stats".
-#'
-#' @author Matt Craddock \email{matt@@mattcraddock.com}
-#' @param statistic Calculated statistic (e.g. t-statistic)
-#' @param pvals calculated p-values for that statistic
-#' @param chan_info String of character names for electrodes.
-#' @param timings Unique timepoints remaining in the data.
-#' @param method Type of statistical test
-#' @keywords internal
-
-eeg_stats <- function(statistic,
-                      chan_info,
-                      pvals,
-                      timings,
-                      method) {
-
-  value <- list(statistic = statistic,
-                pvals = tibble::as_tibble(pvals),
-                chan_info = chan_info,
-                timings = timings,
-                method = method,
-                version = utils::packageVersion("eegUtils"))
-  class(value) <- "eeg_stats"
-  value
-}
-
-new_eeg_lm <- function(coefficients,
-                       std_err,
-                       t_stats,
-                       r_sq,
-                       chan_info,
-                       epochs,
-                       timings,
-                       formula) {
-
-  stopifnot(is.data.frame(coefficients))
-  stopifnot(is.data.frame(std_err))
-  stopifnot(is.data.frame(t_stats))
-  stopifnot(is.data.frame(r_sq))
-  #stopifnot(is.data.frame(chan_info))
-  stopifnot(rlang::is_formula(formula))
-
-  new_eeg_stats(
-    coefficients = coefficients,
-    std_err = std_err,
-    t_stats = t_stats,
-    r_sq = r_sq,
-    timings = timings,
-    epochs = epochs,
-    chan_info = chan_info,
-    formula = formula,
-    class = "eeg_lm"
-  )
-}
-
-new_eeg_stats <- function(...,
-                          class = character()) {
-
-  new_obj <- list(...)
-  structure(
-    new_obj,
-    class = c(class, "eeg_stats")
-  )
-}
 
 #' Function to create an S3 object of class "eeg_ICA".
 #'
@@ -360,7 +296,8 @@ eeg_ICA <- function(mixing_matrix,
                     chan_info,
                     srate,
                     epochs,
-                    algorithm) {
+                    algorithm,
+                    version = utils::packageVersion("eegUtils")) {
 
   value <- list(mixing_matrix = mixing_matrix,
                 unmixing_matrix = unmixing_matrix,

R/data_averaging.R

@@ -59,7 +59,7 @@ eeg_average.eeg_epochs <- function(data,
     }
   } else {
     col_names <- names(data$epochs)
-    col_names <- col_names[!(col_names %in% c("epoch"))]
+    col_names <- col_names[!(col_names %in% c("epoch", "recording", "event_type"))]
   }
 
   data$signals <-
@@ -94,7 +94,7 @@ eeg_average.eeg_epochs <- function(data,
   data
 }
 
-#' @describeIn eeg_average average an eeg_epochs object over epochs.
+#' @describeIn eeg_average average an `eeg_epochs` object over epochs.
 #' @export
 eeg_average.eeg_evoked <- function(data,
                                    cols = NULL,
@@ -200,7 +200,11 @@ average_tf <- function(data,
     } else {
       stop("Averaging of fourier coefficients not supported.")
   }
-  data$timings <- tibble::tibble(time = as.numeric(dimnames(data$signals)[["time"]]))#dplyr::filter(data$timings, epoch == 1)
+  data$timings <-
+    tibble::tibble(
+      time = rep(as.numeric(dimnames(data$signals)[["time"]]), new_epos),
+      epoch = rep(1:new_epos, each = n_times)
+      )#dplyr::filter(data$timings, epoch == 1)
   data
 }