Changelog

Source: NEWS.md

mnirs 0.4.1

• Create article “Analysing muscle oxidative capacity with {mnirs}”.
• Add portamon-oxcap.xlsx example file (thanks to Dr. Thomas Tripp and Dr. Martin MacInnis).
• Update train.red_intervals.csv, delete redundant NIRS channels to reduce file size.
• Minors updates to monoexponential family of functions.
  • Fix SS_monoexp3() to not internally look for TD parameter.
  • Remove monoexp_init() from exported to internal.

mnirs 0.4.0

• Create monoexponential(), SS_monoexp3(), and SS_monoexp4() self-starting model functions.
  • monoexponential() is the equation for a 4-parameter monoexponential function with parametera “A”, “B”, “tau”, and “TD”.
  • SS_monoexp*() are self-starting functions for nls() or other curve fitting functions, for either the 4-parameter monoexponential function, or a reduced 3-parameter function without a time delay (“TD”).
  • fix_coef() is used to update a model with any number of parameters set to fixed values, e.g. if the starting or ending values are known a priori. By entering fixed values, the remaining parameters are left free to be optimised (experimental function, may not work when called from within nested function conditions, need to further validate).
    
• Add vo2master.csv example file recorded with VO2 Master Manager app (thanks Philip Skotzke).
• Update read_mnirs() to correctly convert “,” decimal values to numeric (thanks Philip Skotzke).
• Simplify data.table::fread() for .csv files with multiple regional formats.
• replace_invalid() and replace_outliers() now inform the number of samples replaced (thanks Philip Skotzke).

mnirs 0.3.0

• Create peak_slope(). slope() and rolling_slope() become internal.
• Remove na.rm arg from slope(), rolling_slope(), peak_slope() in favour of opinionated na.rm = TRUE behaviour.
  • partial = FALSE effectively covers na.rm = FALSE where fewer than width number valid samples exist in local vector.
  • na.rm arg currently remains in filter_mnirs() functions, but this may be removed in the future.
• Fix read_mnirs() internally read_file() to better handle .csv files.
  • Implement data.table::fread() to handle .csv with empty rows and long string metadata in the header above the data table.
  • Awaiting future expanded data.table implementation across mnirs, i.e. for data.table::froll* functions.
• Fix filter_moving_average() to correctly identify windows where partial = FALSE was not met due to NAs.
• Remove internal roll dependency.
• Update documentation in expectation of CRAN submission.
  • Remove internal function examples to minimise \donttest() issues.

mnirs 0.2.0

• Implement tidy evaluation with rlang and tidyselect.
• Update function documentation & examples, README, vignette.
• Fix filter_moving_average() and rolling_mean() to correctly use partial and na.rm arguments.
• Fix shift_mnirs() to correctly use width and span arguments.

mnirs 0.1.9

• Create rolling_slope() to calculate local linear regression slopes along a vector.
• Integrate [roll][roll::roll-package] for faster rolling median, mean, and lm implementation under certain conditions.
  • Currently used: roll_lm() for rolling_slope(), roll_median() for replace_outliers(), roll_mean() for filter_moving_average().
  • May roll back in favour of data.table::froll_* when 1.17.99+ is updated on CRAN.
• Update local rolling functions with align = c("center", "left", "right") arg.
  • Currently used: internal compute_local_windows() for rolling_slope().
• Update internal compute_local_fun() to allow additional arguments, e.g. for na.rm = TRUE.
• Remove redundant internal numeric rounding. Results may now have floating point precision issues, but avoid compounding rounding error.
  • Affects: filter_mnirs.smooth_spline(), filter_mnirs.moving_average(), parse_sample_rate() and clean_invalid() for read_mnirs(), replace_mnirs(), resample_mnirs(), shift_mnirs(), validate_sample_rate().
• Add hidden bypass_check argument to reduce overhead from validation redundancy.
  • Affects: replace_invalid(), replace_outliers(), replace_missing(), filter_moving_average(), new functions slope(), rolling_slope().
• Update validate_numeric() logic to reduce overhead.

mnirs 0.1.8

• Create extract_intervals() to detect events and extract surrounding data frames.
• Replace internal between() with within() to differentiate from dplyr::between().
• Update README with image of mnirs shiny app.
• Update filter_mnirs() with error message when fc outside 0 Hz and Nyquist frequency.

mnirs 0.1.7

• Minor edits to functions and documentation to improve clarity.
• Changes to user-facing functions:
  • filter_mnirs() and filter_butter() arg from n to order.
  • palette_mnirs() arg from n as either numeric or character, to numeric, with names as the character arg.
  • replace_mnirs(), replace_outleirs(), replace_missing(), and resample_mnirs() arg from method = "NA" to method = "none".
• Revert argument inform to verbose.
• Standardise cli_inform(), cli_warn(), and cli_abort() messages.
• Remove redundant resample_mnirs() argument resample_time.

mnirs 0.1.6

• Create internal numeric vector helper functions
  • signif_whole() applies sig-fig rounding to decimal places, or whole values.
  • signif_trailing() applies decimal or sig-fig rounding and convers to character strings with trailing zeroes, for display.
  • signif_pvalue() applies formatting for p-value display as character strings or significance symbols.
  • seq_range() creates a numeric sequence spanning the range of an ipnut vector.
  • wrap() rotates vector elements from head to tail (or tail to head) by position.
• Add statement about use of generative AI codebots to README.Rmd

mnirs 0.1.5

• Remove redundant validation checks in replace_mnirs().
• Fix erroneous url in _pkgdown.yml.
• Update internal validate_event_channel to error on empty numeric or character column.
• Update test coverage:
  • Cover new options(mnirs.inform = FALSE).
  • Cover unlisted metadata added to create_mnirs_data().
  • Cover hidden plot.mnirs() options.

mnirs 0.1.4

• Update argument inform replaces verbose to display/hide messages & warnings.
• Implement global option to set inform = FALSE with options(mnirs.inform = FALSE).
  • Global option mnirs.inform = FALSE will override functions’ implicit default inform = TRUE.
  • Explicit call inform = TRUE will override the global option.
• Update replace_mnirs() and replace_invalid() with additional arguments.
  • Replace ranges above or below invalid_above and invalid_below, respectively.

mnirs 0.1.3

• Remove redundant file mnirs.test-package.Rd.
• Remove obsolete {utils} dependency.
• Remove redundant nirs_device arg in internal read_data_table().
• Implement air formatter.
• Migrate package development into Positron IDE.

mnirs 0.1.2

• Simplify use of width and span to be centred on idx.
  • Update internal helpers: compute_local_windows() & compute_window_of_valid_neighbours()
  • Update appropriate documentation.
  • Update README, vignette, & examples to width = 10.
• Update examples with @examplesIf (identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")).
  • Not entirely sure this will pass CRAN. May need to update.
• Update create_mnirs_data() to correctly accept listed or unlisted metadata.

mnirs 0.1.1

• Fix formatting error in README.Rmd.
• Remove obsolete code in resample_mnirs.R.
• Add missing tests for replace_mnirs(), resample_mnirs(), and plot.mnirs().
• Update documentation formatting and examples.

mnirs 0.1.0 initial release

• Initial release of reading and cleaning functions.
• Basic README demonstrating functionality.
• Website documentation available here, including function reference index and vignettes.

mnirs 0.0.0.9000

• initial commit.
• project setup.