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Changelog

Source: NEWS.md

MoveR v0.3.1

Some minor updates:

  • speed function calculation has been simplified to remove dependency on the trajr package, resulting in a more direct computation method (minor differences from previous versions may occur).
  • drawTracklets function now support color opacity adjustments through alpha argument.
  • IdStateSeq function now handles Boolean (TRUE or FALSE), numeric, and character values. Also, the na.handle argument now allows to specify a replacement for NA values, preventing conflicts with chosen regular expressions.

MoveR v0.3.0

Thanks to Software X journal’s reviewers for insightful comments

  • Make ‘identity’ the default value for the [by] argument in the convert2Tracklets() function.
  • Make ‘frame’ the default value for the [timeCol] argument in the ANND(), resampTracklets(), sinuosity(), speed(), temporalBoot(), temporalTrend(), turnAngle() functions.
  • speed() function now accept [frameR] (frame rate) and [timeU] (time unit) arguments allowing to return speed values according to the desired unit (e.g., pixels per frame, pixels per second).
  • Make “1” the default value for the [sampling] argument in the ANND() function.
  • Change the default value of the [flipY] argument in the readIdTracker() functions from TRUE to FALSE as for other “read” functions
  • Add “AnimalTA” to an error message returned by the DLsampleData() function when the [tracker] argument is misspelled.
  • Add the possibility of retrieving the path to several tracking outputs at the same time using DLsampleData().
  • Solve an error when both [selTrack] and [timeWin] arguments were specified in drawTracklet() with several time windows, drawing only the specified tracklets on the first time window.
  • Processing time of drawTracklet() has also been speed up.
  • The “read” functions aiming to import tracking data from various tracking software now return an object of class (S3) “tracklets”, corresponding to a list of tracklets, meaning that converting the output of “read” functions to a list of tracklets (using convert2Tracklets()) before further processing is no longer needed.
  • Add setInfo() and getInfo() functions to the utilities to specify and retrieve useful information such as frame rate (frameR), scale (scale) and image resolution (imgRes) to the tracklets object, allowing to avoid unnecessary repetition of code over several functions.
  • Add the possibility to subset “varList” and “tracklets” objects using [], also allow to use as.data.frame() on varList object to convert it to a data frame.
  • convert2List() now returns an object of class “varList” which is still a list of variables and conserve the additional information appended to the converted tracklets object, meaning that additional information are conserved over conversion from tracklets to varList and back to tracklets.
  • trackstats() is now deprecated (but still can be used) and is replaced by summary() according to the use of S3 methods for tracklets class objects when importing tracking data.
  • Add the possibility to compute the distance between particles trajectory and a polygon edges using dist2Edge() by setting customFunc = “PolygonArena”.
  • cutTracklets() and sortVertices() functions are now considered as an internal function and cannot be used anymore (prefer using filterTracklets).
  • Reduce code redundancy by creating an internal function to return error messages .errorCheck.

MoveR v0.2.0

  • Add readAnimalTA function to import tracking data from AnimalTA software.
  • Add MSD function to compute mean square displacement of particles according to the equations derived from Kareiva & Shigesada (1983) or Turchin (2015).
  • Modify the Dcoef function to properly use the equations derived from Kareiva & Shigesada (1983) or Turchin (2015) to compute net square displacement index.
  • Improve the speed of the slidWindow function by using stats::filter instead of a ‘for loop’ within the function’s body. NB: while it increases the speed of the slidWindow function, it also make it less flexible, it is not possible to perform a custom computation over the sliding window anymore. Instead, the [statistic] argument allows to choose some already implemented computation methods.
  • some minor modifications in readTrackR function

MoveR v0.1.0

  • This is the development release of the MoveR package.
  • This version is still under active development and might be unstable.