celltrackR 1.2.1

Improved handling of online resources in tests and examples for immunemap integration
functions in accordance with CRAN policy.

Potentially breaking changes:

None.

Minor changes:

• (immunemap-integration.R => parse.immap.json ): now uses jsonlite instead of rjson
  because rjson requires R 4.4.1.
• (immunemap-integration.R => parse.immap.json ): improved handling of cases where the
  internet or immunemap website is down.
• (immunemap-integration.R ): dontrun on examples to avoid errors on CRAN servers due to
  internet problems.
• (testImmuneMapIntegration.R) : added a skip_if_offline for same reasons.
• DESCRIPTION: jsonlite instead of rjson in suggests

Documentation changes:

Minor changes:

• Updated outdated @doctype package to new roxygen recommendation

New data and other updates in v1.0.0

celltrackR 1.0.0

Changes compared to the previous release.

Potentially breaking changes

• replaced the in-package datasets "TCells", "BCells", "Neutrophils" with new data;
  this may break some examples using the old datasets because the new datasets have tracks
  with different IDs, and because they are now 2D projections rather than 3D tracks.
  Details on the data will be available in the celltrackR publication; raw data are
  available from inst/extdata (see the vignettes on QC for how to access those).
• changed the behavior of some of the angle functions like angleToPoint, angleToDir,
  and angleToPlane. In the old version, if the supplied track was more than one step long,
  only the angle from the first step to the reference was considered. This was not very
  compatible with how the other track measures work. The new version therefore computes
  angles with the overall displacement vector of the supplied track. This should not
  alter conclusions too much, but it will change the numeric outputs of some of these
  functions when applied to longer tracks.

Documentation changes:

• All the vignettes were updated to work with the new datasets
• The vignette on QC contains a new section on filtering out non-motile tracks
• A new vignette explicitly describes the preprocessing choices made for the package
  datasets
• The vignette on track simulation now contains examples of how to fit models based
  on the mean squared displacement curve.

Minor changes:

• Moved pracma from 'suggests' to 'imports' as it is now used by multiple functions
  that work with angles
• as.tracks.data.frame now automatically handles a dataframe with 2D tracks if the
  pos.columns argument is left unspecified; earlier, this would have resulted in an error.

CRAN submission

No compatibility changes; updates in DESCRIPTION and compatibility with development version of R.

CelltrackR update 1

Minor updates compared to last version; no compatibility changes.

Release for review

v0.0.0.9000

fixed typo in README and cheatsheet.