mnirs 0.6.0

Prepare for CRAN submission

• NEWS.md is truncated to the most recent relevant release updates. The full NEWS.md remains in the dev branch.

• Some development functions have been omitted from the package build in expectation of CRAN review. They are still present in dev branch and can be installed with pak::pak("jemarnold/mnirs").

Updated core functions

• filter_mnirs(): Method-specific arguments (e.g. order for method = "butterworth", or width for method = "moving_average") removed from the generic function call. Continue to be passed to the appropriate method via .... Documentation and info/warning/abort messages updated.

• filter_ma() better separates effects of partial and na.rm args:

  • partial = FALSE by default returns NA at edges where insufficient number of samples are available compared to the specified width or span.
  • partial = TRUE calculates mean values at edges, as long as one valid non-NA sample is available.
  • na.rm = FALSE by default behaves as expected with mean(na.rm = FALSE), propagating any NAs in the local window to the calculated mean with a warning.
    • NOTE This differs from the behaviour of na.rm = FALSE in filter_butter(), which errors if there are any internal NAs present. This has not been changed.
  • na.rm = TRUE ignores NAs and calculates local means as long as one valid sample is present.

• plot.mnirs()

  • Add new arg: points = TRUE will plot points in addition to lines, as a useful quick shortcut.
  • Update na.omit now omits non-valid c(NA, NaN, Inf, -Inf) values from plotting, not just NA.

• palette_mnirs() can now accept either a single numeric value specifying the number of colours to return, or any number of (valid) character colour names.

mnirs 0.5.2

Shiny app

• Update online shiny app hosted at https://jemarnold-mnirs-app.share.connect.posit.cloud/ with basic reading and pre-processing functionality.

mnirs 0.5.1

Updated core functions

• read_mnirs() now has better automated channel detection logic for “Artinis” / “Oxysoft” file formats. nirs_channels and time_channel can be left blank to automatically “sample”, “time” (from sample_rate), and nirs channel “2”.

• replace_outliers() now accepts numeric outlier_cutoff values for more precise outlier detection thresholds (previously was integers only). Documentation also updated.

mnirs 0.5.0

Updated core functions

• read_mnirs() expands event_channel to work with integer “lap” numbers, or character event label as previous.
  • Should now work on more .csv file formats; previously read errors may have occured where the file contained header rows above the data table, resulting in improper detection of columns.
  • event_channel can now be specified as an integer lap column, in addition to a character column as previous.
  • Other {mnirs} functions may expect event_channel to be either character or integer-ish.
• extract_intervals():
  • Function arguments start and end are used to specify one or both of a start and end point to the target interval.
  • Specify start/end values with helper functions by_time(), by_label(), by_lap(), and by_sample().
  • Numeric values are automatically coerced to “time” values; Explicit integer values (e.g. 2L) are coerced to “lap”; Character strings are coerced to event “label”.

Package resources

• A rough draft {mnirs} hex icon and package cheatsheet have been added.

mnirs 0.4.2 and prior

• Full previous changelog is available on the github dev branch: https://github.com/jemarnold/mnirs/blob/dev/NEWS.md