diff --git a/DESCRIPTION b/DESCRIPTION
index ce664a2..0486223 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -4,7 +4,7 @@ Title: eyeris
Version: 0.0.0.9000
Authors@R:
person(
- given = c("Shawn", "T."),
+ given = "Shawn",
family = "Schwartz",
role = c("aut", "cre"),
email = "stschwartz@stanford.edu",
diff --git a/Makefile b/Makefile
index 3e963e9..4a09a32 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
# default target
-all: uninstall getdeps build install roxygenize readme clean
+all: uninstall getdeps build install roxygenize readme ghpages clean
# debugging target
debug: uninstall build install clean
@@ -49,6 +49,18 @@ readme:
Rscript -e "devtools::build_readme()"
@echo "[ OK ] - README update completed!\n"
+# pkgdown website preview
+website:
+ @echo "[ INFO ] - building eyeris pkgdown docs website preview..."
+ Rscript -e "pkgdown::build_site()"
+ @echo "[ OK ] - pkgdown website preview build completed!\n"
+
+# pkgdown github pages website (jekyll)
+ghpages:
+ @echo "[ INFO ] - building eyeris pkgdown docs website for github pages..."
+ Rscript -e "pkgdown::build_site_github_pages(clean = TRUE, install = FALSE, new_process = FALSE)"
+ @echo "[ OK ] - pkgdown website build for github pages completed!\n"
+
# clean build directory
clean:
@echo "[ INFO ] - cleaning eyeris package build directory..."
diff --git a/NEWS.md b/NEWS.md
new file mode 100644
index 0000000..ae49a9e
--- /dev/null
+++ b/NEWS.md
@@ -0,0 +1,11 @@
+# eyeris 0.0.0.9000
+
+---
+`November 23rd, 2024`
+
+## Major Changes
+- change one
+- change two
+
+## Bug Fixes
+- fix one
diff --git a/R/bidsify.R b/R/bidsify.R
index e59afab..3e1dc99 100644
--- a/R/bidsify.R
+++ b/R/bidsify.R
@@ -36,7 +36,7 @@
#' # Bleed around blink periods just long enough to remove majority of
#' # deflections due to eyelid movements
#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
diff --git a/R/deblink.R b/R/deblink.R
index a8cdd5a..75f3c61 100644
--- a/R/deblink.R
+++ b/R/deblink.R
@@ -13,18 +13,18 @@
#' indicating different numbers of milliseconds pad forward/backward around each
#' missing sample, in the format `c(backward, forward)`.
#'
-#' @return An `eyeris` object with a new column: `pupil_deblink`.
+#' @return An `eyeris` object with a new column: `pupil_raw_{...}_deblink`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
-#' eyeris::deblink(extend = 40) # 40 ms in both directions
-#' }
+#' eyeris::deblink(extend = 40) |> # 40 ms in both directions
+#' plot(seed = 0)
#'
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
-#' eyeris::deblink(extend = c(40, 50)) # 40 ms backward, 50 ms forward
+#' eyeris::deblink(extend = c(40, 50)) |> # 40 ms backward, 50 ms forward
+#' plot(seed = 0)
#'
#' @export
deblink <- function(eyeris, extend = 40) {
diff --git a/R/detransient.R b/R/detransient.R
index ed8b2c5..ffeb6f0 100644
--- a/R/detransient.R
+++ b/R/detransient.R
@@ -11,15 +11,14 @@
#' threshold.
#'
#' @return An `eyeris` object with a new column in `timeseries`:
-#' `pupil_detransient`.
+#' `pupil_raw_{...}_detransient`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
-#' eyeris::detransient()
-#' }
+#' eyeris::detransient() |>
+#' plot(seed = 0)
#'
#' @export
detransient <- function(eyeris, n = 16) {
@@ -42,10 +41,14 @@ detransient_pupil <- function(x, prev_op, n) {
speed <- function(x, y) {
delta <- diff(x) / diff(y)
-
pupil <- abs(cbind(c(NA, delta), c(delta, NA)))
- pupil <- apply(pupil, 1, max, na.rm = TRUE)
- pupil <- ifelse(pupil == -Inf, NA, pupil)
+ pupil <- apply(pupil, 1, function(row) {
+ if (all(is.na(row))) {
+ return(NA) # return NA for all-NA rows
+ } else {
+ return(max(row, na.rm = TRUE)) # only compute max for valid rows
+ }
+ })
return(pupil)
}
diff --git a/R/detrend.R b/R/detrend.R
index cbda42e..02ea51b 100644
--- a/R/detrend.R
+++ b/R/detrend.R
@@ -6,18 +6,17 @@
#' @param eyeris An object of class `eyeris` dervived from [eyeris::load()].
#'
#' @return An `eyeris` object with two new columns in `timeseries`:
-#' `detrend_fitted_betas`, and `pupil_detrend`.
+#' `detrend_fitted_betas`, and `pupil_raw_{...}_detrend`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
#' eyeris::interpolate() |>
#' eyeris::lpfilt(plot_freqz = TRUE) |>
-#' eyeris::detrend()
-#' }
+#' eyeris::detrend() |>
+#' plot(seed = 0)
#'
#' @export
detrend <- function(eyeris) {
diff --git a/R/epoch.R b/R/epoch.R
index 9b31284..336b276 100644
--- a/R/epoch.R
+++ b/R/epoch.R
@@ -80,7 +80,8 @@
#' (`epoch_`).
#'
#' @examples
-#' eye_preproc <- system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' \dontrun{
+#' eye_preproc <- system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
@@ -88,11 +89,89 @@
#' eyeris::lpfilt(plot_freqz = TRUE) |>
#' eyeris::zscore()
#'
+#' # example 1: select 1 second before/after matched event message "PROBE*"
#' eye_preproc |>
#' eyeris::epoch(events = "PROBE*", limits = c(-1, 1))
#'
+#' # example 2: select all samples between each trial
#' eye_preproc |>
-#' eyeris::epoch(events = "TRIALID {trial}") # all samples between each trial
+#' eyeris::epoch(events = "TRIALID {trial}")
+#'
+#' # example 3: grab the 1 second following probe onset
+#' eye_preproc |>
+#' eyeris::epoch(
+#' events = "PROBE_START_{trial}",
+#' limits = c(0, 1)
+#' )
+#'
+#' # example 4: 2 seconds prior to and 1 second after probe onset
+#' eye_preproc |>
+#' eyeris::epoch(
+#' events = "PROBE_START_{trial}",
+#' limits = c(-2, 1),
+#' label = "prePostProbe" # custom epoch label name
+#' )
+#'
+#' # example 5: manual start/end event pairs
+#' # note: here, the `msg` column of each data frame is optional
+#' eye_prepoc |>
+#' eyeris::epoch(
+#' events = list(
+#' data.frame(time = c(11243355), msg = c("TRIALID 0")), # start events
+#' data.frame(time = c(11245956), msg = c("RESPONSE_0")) # end events
+#' )
+#' )
+#'
+#' # example 6: manual start/end event pairs
+#' # note: set `msg` to NA if you only want to pass in start/end timestamps
+#' eye_preproc |>
+#' eyeris::epoch(
+#' events = list(
+#' data.frame(time = c(11243355), msg = NA), # start events
+#' data.frame(time = c(11245956), msg = NA) # end events
+#' )
+#' )
+#'
+#' ## examples with baseline arguments enabled
+#'
+#' # example 7: use mean of 1-s preceding "PROBE_START" (i.e. "DELAY_STOP")
+#' # to perform subtractive baselining of the 1-s PROBE epochs.
+#' eye_preproc |>
+#' eyeris::epoch(
+#' events = "PROBE_START_{trial}",
+#' limits = c(0, 1), # grab 0 seconds prior to and 1 second post PROBE event
+#' label = "prePostProbe", # custom epoch label name
+#' calc_baseline = TRUE,
+#' apply_baseline = TRUE,
+#' baseline_type = "sub", # "sub"tractive baseline calculation is default
+#' baseline_events = "DELAY_STOP_*",
+#' baseline_period = c(-1, 0)
+#' )
+#'
+#' # example 8: use mean of time period between set start/end event messages
+#' # (i.e. between "DELAY_START" and "DELAY_STOP"). In this case, the
+#' # `baseline_period` argument will be ignored since both a "start" and "end"
+#' # message string are provided to the `baseline_events` argument.
+#' eye_preproc |>
+#' eyeris::epoch(
+#' events = "PROBE_START_{trial}",
+#' limits = c(0, 1), # grab 0 seconds prior to and 1 second post PROBE event
+#' label = "prePostProbe", # custom epoch label name
+#' calc_baseline = TRUE,
+#' apply_baseline = TRUE,
+#' baseline_type = "sub", # "sub"tractive baseline calculation is default
+#' baseline_events = c("DELAY_START_*",
+#' "DELAY_STOP_*")
+#' )
+#'
+#' # example 9: additional (potentially helpful) example
+#' start_events <- data.frame(time = c(11243355, 11247588),
+#' msg = c("TRIALID 0", "TRIALID 1"))
+#' end_events <- data.frame(time = c(11245956, 11250506),
+#' msg = c("RESPONSE_0", "RESPONSE_1"))
+#' eye_prepoc |>
+#' eyeris::epoch(events = list(start_events, end_events))
+#' }
#'
#' @export
epoch <- function(eyeris, events, limits = NULL, label = NULL,
diff --git a/R/glassbox.R b/R/glassbox.R
index c6cee8a..599a278 100644
--- a/R/glassbox.R
+++ b/R/glassbox.R
@@ -55,23 +55,32 @@
#' @param ... Additional arguments to override the default, prescribed settings.
#'
#' @examples
-#' \dontrun{
-#' demo_data <- system.file("extdata", "assocret.asc", package = "eyeris")
+#' demo_data <- system.file("extdata", "memory.asc", package = "eyeris")
#'
#' # (1) examples using the default prescribed parameters and pipeline recipe
+#'
#' ## (a) run an automated pipeline with no real-time inspection of parameters
#' output <- eyeris::glassbox(demo_data)
+#' plot(
+#' output,
+#' steps = c(1, 5),
+#' preview_window = c(0, nrow(output$timeseries)),
+#' seed = 0
+#' )
#'
#' ## (b) run a interactive workflow (with confirmation prompts after each step)
-#' output <- eyeris::glassbox(demo_data, confirm = TRUE)
+#' # output <- eyeris::glassbox(demo_data, confirm = TRUE, seed = 0)
+#'
#'
#' # (2) examples overriding the default parameters
-#' output <- eyeris::glassbox(demo_data,
-#' confirm = TRUE,
+#' output <- eyeris::glassbox(
+#' demo_data,
+#' confirm = FALSE, # TRUE if you want to visualize each step in real-time
#' deblink = list(extend = 40),
#' lpfilt = list(plot_freqz = FALSE)
#' )
-#' }
+#'
+#' plot(output, seed = 0)
#'
#' @export
glassbox <- function(file, confirm = FALSE, detrend_data = FALSE,
diff --git a/R/interpolate.R b/R/interpolate.R
index d94b0cd..0dd5def 100644
--- a/R/interpolate.R
+++ b/R/interpolate.R
@@ -8,20 +8,18 @@
#' values on either end, respectively, using the "rule = 2" argument in the
#' `approx()` function.
#'
-#'
#' @param eyeris An object of class `eyeris` dervived from [eyeris::load()].
#'
#' @return An `eyeris` object with a new column in `timeseries`:
-#' `pupil_interpolate`.
+#' `pupil_raw_{...}_interpolate`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
-#' eyeris::interpolate()
-#' }
+#' eyeris::interpolate() |>
+#' plot(seed = 0)
#'
#' @export
interpolate <- function(eyeris) {
@@ -38,8 +36,10 @@ interpolate_pupil <- function(x, prev_op) {
prev_pupil <- x[[prev_op]]
}
- interp_pupil <- zoo::na.approx(prev_pupil,
- na.rm = FALSE, maxgap = Inf,
+ interp_pupil <- zoo::na.approx(
+ prev_pupil,
+ na.rm = FALSE,
+ maxgap = Inf,
rule = 2
)
diff --git a/R/load.R b/R/load.R
index fa4a966..f9dfd8d 100644
--- a/R/load.R
+++ b/R/load.R
@@ -21,10 +21,8 @@
#' @seealso [eyelinker::read.asc()] which this function wraps.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc()
-#' }
#'
#' @export
load_asc <- function(file) {
diff --git a/R/lpfilt.R b/R/lpfilt.R
index c570608..6b84e94 100644
--- a/R/lpfilt.R
+++ b/R/lpfilt.R
@@ -11,17 +11,17 @@
#' @param rs Required minimal attenuation within stopband in dB.
#' @param plot_freqz Boolean flag for displaying filter frequency response.
#'
-#' @return An `eyeris` object with a new column in `timeseries`: `pupil_lpfilt`.
+#' @return An `eyeris` object with a new column in `timeseries`:
+#' `pupil_raw_{...}_lpfilt`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
#' eyeris::interpolate() |>
-#' eyeris::lpfilt(plot_freqz = TRUE)
-#' }
+#' eyeris::lpfilt(plot_freqz = TRUE) |>
+#' plot(seed = 0)
#'
#' @export
lpfilt <- function(eyeris, wp = 4, ws = 8,
diff --git a/R/plot.R b/R/plot.R
index a7747a6..216c83d 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -37,11 +37,11 @@
#'
#' @examples
#' \dontrun{
-#' # using the default 10000 to 20000 ms time subset
-#' plot(eyeris_data)
+#' # example 1: using the default 10000 to 20000 ms time subset
+#' plot(your_eyeris_data_output_here)
#'
-#' # using a custom time subset (i.e., 1 to 500 ms)
-#' plot(eyeris_data, preview_window = c(1, 500))
+#' # example 2: using a custom time subset (i.e., 1 to 500 ms)
+#' plot(your_eyeris_data_output_here, preview_window = c(1, 500))
#' }
#'
#' @rdname plot.eyeris
diff --git a/R/sticker.data.R b/R/sticker.data.R
index 1d89b13..454dfbc 100644
--- a/R/sticker.data.R
+++ b/R/sticker.data.R
@@ -2,5 +2,5 @@
#'
#' @format A png image file that is rendered into the README and html reports.
#'
-#' @keywords eyeris, sticker, logo, hex
+#' @keywords internal
"sticker"
diff --git a/R/zscore.R b/R/zscore.R
index 7c25894..866e001 100644
--- a/R/zscore.R
+++ b/R/zscore.R
@@ -1,13 +1,13 @@
-#' Z-Score pupil timeseries data
+#' z-score pupil timeseries data
#'
#' The intended use of this method is to scale the arbitrary units of the pupil
#' size timeseries to have a mean of `0` and a standard deviation of `1`. This
#' is accomplished by mean centering the data points and then dividing them by
#' their standard deviation (i.e., z-scoring the data, similar to
-#' [base::scale()]). Z-scoring the pupil data is helpful for trial-level and
-#' between-subjects analyses where arbitrary units of pupil size recorded by the
-#' tracker do not scale across participants, and therefore make analyses that
-#' depend on data from more than one participant difficult to interpret.
+#' [base::scale()]). Opting to z-score your pupil data helps with trial-level
+#' and between-subjects analyses where arbitrary units of pupil size recorded by
+#' the tracker do not scale across participants, and therefore make analyses
+#' that depend on data from more than one participant difficult to interpret.
#'
#' @details
#' In general, it is common to z-score pupil data within any given
@@ -34,22 +34,20 @@
#' on the entire pupil timeseries (before epoching the data), and then split and
#' take the mean of the z-scored timeseries as a function of condition variable.
#'
-#'
#' @param eyeris An object of class `eyeris` dervived from [eyeris::load()].
#'
-#' @return A numeric vector giving number of characters (code points) in each
-#' element of the character vector. Missing string have missing length.
+#' @return An `eyeris` object with a new column in `timeseries`:
+#' `pupil_raw_{...}_z`.
#'
#' @examples
-#' \dontrun{
-#' system.file("extdata", "assocret.asc", package = "eyeris") |>
+#' system.file("extdata", "memory.asc", package = "eyeris") |>
#' eyeris::load_asc() |>
#' eyeris::deblink(extend = 50) |>
#' eyeris::detransient() |>
#' eyeris::interpolate() |>
#' eyeris::lpfilt(plot_freqz = TRUE) |>
-#' eyeris::zscore()
-#' }
+#' eyeris::zscore() |>
+#' plot(seed = 0)
#'
#' @export
zscore <- function(eyeris) {
diff --git a/README.Rmd b/README.Rmd
index 42a06ab..a6327ee 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -9,17 +9,16 @@ knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
- out.width = "100%",
- fig.cap = "README FIGURE"
+ out.width = "100%"
)
```
-# `eyeris`: create and run flexible and reproducible pupillometry preprocessing pipelines in R
+# `eyeris`: flexible reproducible pupil preprocessing pipelines in R
-
-
+
+
@@ -55,29 +54,32 @@ to flexibly construct and compare different pipelines.
We hope you enjoy! -shawn
```{r glassbox-example, fig.dpi=300}
-set.seed(1)
+set.seed(32)
library(eyeris)
-demo_data <- system.file("extdata", "assocret.asc", package = "eyeris")
+demo_data <- system.file("extdata", "memory.asc", package = "eyeris")
-eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz = T))
+eyeris_preproc <- glassbox(
+ demo_data,
+ detrend_data = F,
+ lpfilt = list(plot_freqz = T)
+)
```
### step-wise correction of pupillary signal
-
```{r glassbox-plot, echo=TRUE, fig.width=12, fig.height=5, fig.dpi=300}
plot(eyeris_preproc)
```
-### final pre-post correction of pupillary signal (raw -> preprocessed)
-
+### final pre-post correction of pupillary signal (raw ➡ preprocessed)
```{r timeseries-plot, echo=TRUE, fig.width=8, fig.height=5, fig.dpi=300}
plot(eyeris_preproc,
steps = c(1, 5),
preview_window = c(0, nrow(eyeris_preproc$timeseries)))
```
-# Comments, suggestions, questions, issues
+---
+# Comments, suggestions, questions, issues?
Please use the issues tab (https://github.com/shawntz/eyeris/issues) to make note of any bugs, comments, suggestions, feedback, etc... all are welcomed and appreciated, thanks!
diff --git a/README.md b/README.md
index 27df0cb..7443e8b 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,13 @@
-# `eyeris`: create and run flexible and reproducible pupillometry preprocessing pipelines in R
+# `eyeris`: flexible reproducible pupil preprocessing pipelines in R
-
-
+
+
@@ -45,32 +45,27 @@ compare different pipelines.
We hope you enjoy! -shawn
``` r
-set.seed(1)
+set.seed(32)
library(eyeris)
-demo_data <- system.file("extdata", "assocret.asc", package = "eyeris")
+demo_data <- system.file("extdata", "memory.asc", package = "eyeris")
-eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz = T))
+eyeris_preproc <- glassbox(
+ demo_data,
+ detrend_data = F,
+ lpfilt = list(plot_freqz = T)
+)
#> ✔ [ OK ] - Running eyeris::load_asc()
#> ✔ [ OK ] - Running eyeris::deblink()
#> ✔ [ OK ] - Running eyeris::detransient()
#> ✔ [ OK ] - Running eyeris::interpolate()
-#> ! [ INFO ] - No NAs detected in pupil data for interpolation... Skipping!
#> ✔ [ OK ] - Running eyeris::lpfilt()
#> ✔ [ OK ] - Skipping eyeris::detrend()
#> ✔ [ OK ] - Running eyeris::zscore()
```
-
-
-
-
-
-README FIGURE
-
-
-
+
### step-wise correction of pupillary signal
@@ -78,67 +73,9 @@ README FIGURE
plot(eyeris_preproc)
```
-
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-README FIGURE
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-README FIGURE
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-README FIGURE
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+
-README FIGURE
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-README FIGURE
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-README FIGURE
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-
-### final pre-post correction of pupillary signal (raw -\> preprocessed)
+### final pre-post correction of pupillary signal (raw ➡ preprocessed)
``` r
plot(eyeris_preproc,
@@ -146,27 +83,11 @@ plot(eyeris_preproc,
preview_window = c(0, nrow(eyeris_preproc$timeseries)))
```
-
-
+
+
@@ -55,29 +54,32 @@ to flexibly construct and compare different pipelines.
We hope you enjoy! -shawn
```{r glassbox-example, fig.dpi=300}
-set.seed(1)
+set.seed(32)
library(eyeris)
-demo_data <- system.file("extdata", "assocret.asc", package = "eyeris")
+demo_data <- system.file("extdata", "memory.asc", package = "eyeris")
-eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz = T))
+eyeris_preproc <- glassbox(
+ demo_data,
+ detrend_data = F,
+ lpfilt = list(plot_freqz = T)
+)
```
### step-wise correction of pupillary signal
-
```{r glassbox-plot, echo=TRUE, fig.width=12, fig.height=5, fig.dpi=300}
plot(eyeris_preproc)
```
-### final pre-post correction of pupillary signal (raw -> preprocessed)
-
+### final pre-post correction of pupillary signal (raw ➡ preprocessed)
```{r timeseries-plot, echo=TRUE, fig.width=8, fig.height=5, fig.dpi=300}
plot(eyeris_preproc,
steps = c(1, 5),
preview_window = c(0, nrow(eyeris_preproc$timeseries)))
```
-# Comments, suggestions, questions, issues
+---
+# Comments, suggestions, questions, issues?
Please use the issues tab (https://github.com/shawntz/eyeris/issues) to make note of any bugs, comments, suggestions, feedback, etc... all are welcomed and appreciated, thanks!
diff --git a/README.md b/README.md
index 27df0cb..7443e8b 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,13 @@
-# `eyeris`: create and run flexible and reproducible pupillometry preprocessing pipelines in R 
-
-
-
-
-
-README FIGURE
-
-
-