Change log of the R package ‘chronosphere’

chronosphere 0.6.1 - 2023-08-17

Changed

• The examples included in the package were malformatted. The examples were corrected.

chronosphere 0.6.0 - 2023-08-14

Changed

• IMPORTANT: Dataset identifier coordinates were changed: dat -> src, var -> ser. This reflects changes of the database that were necessary so formal variables can be introduced.

chronosphere 0.5.0 - 2023-05-23

Added

• the configure() function to support setting of global variables: curl, timeout and remote (debugging)
• 'tinytest' - dependencies
• 'curl' as suggest, curl support for datasets() and fetch()
• new example data to show the use of datadir

Removed

• plate tectonic reconstruction-related functionality to package 'rgplates'
• Spatial and RasterArrays refactored into package 'via'
• shaper() function, color palettes() to 'restools' (to be published soon)

chronosphere 0.4.1 - 2021-04-16 (build 80)

Added

• added the platemodel example to the package’s files
• fixed wrong example

chronosphere 0.4.0 - 2020-10-18 (build 79 - CRAN submission take 2)

Added

• vignette url fix

chronosphere 0.4.0 - 2020-10-18 (build 78 - Initial CRAN submission)

Added

• minor fixes

chronosphere 0.4.0 (build 77) - 2020-10-13

Added

• package collate in DESCRIPTION
• The SpatialArray class is added to the package, mimicking RasterArrays for vector objects.
• The SpatialList class is added, to be used in the SpatialStack.
• The XArray class-union is made for the efficient generalization of methods shared by RasterArray and SpatialArray. Shared methods are impplemented.
• the spTransform() function is implemented for SpatialStacks and SpatialArrays.
• the apply() function gained the MARGIN=NULL submethod. THis submethod is useful for the iteration of functions for every XArray item.
• The mapedge() function for the quick calculation of map edges in non-equirectangular projections.
• the ‘coasts’ data demo object of the PaleoMAP Paleocoastlines
• types() generic and SpatialArray-method is added.

Changed

• Multiple RasterArray methods are now generalized for the XArray and are no longer specific to RasterArrays.
• vignette was renamed from chronos.Rmd to chronosphere.Rmd, references to ‘clim’ were removed and uses ‘coasts’ now instead

Removed

• the reporting tools added in build 75 are removed as they require further testing
• the ‘clim’ demo object was removed to decrease the size of the package

Known issues/missing features

• SpatialArrays and SpatialStacks do not have a default plotting method yet.
• The apply() function has limit utility on SpatialArrays.
• rare issues with res/ver defaulting, use explicit ver and res to ensure correct download

chronosphere 0.3.1 (build 76) - 2020-09-23

Added

• Forced UTF-8 encoding for the registry tables
• added API call to chronosphere object attributes.

chronosphere 0.3.1 (build 75) - 2020-09-20

Added

• create_metadata() and report() to create data report based on the pbdb download
• generate_bib() and related functions to generate bibliography for report
• capitalize() to capitalise strings - for formatting purposes
• pkg_file() to access files within the package
• template files to inst/rmarkdown/

chronosphere 0.3.1 (build 74) - 2020-08-20

Added

• The SpatialLinesDataFrame-method of the reconstruct() function.

chronosphere 0.3.1 (build 73) - 2020-08-07

Added

• The reference() and info() functions. The new reference() function is now used within fetch().

Fixed

• minor bugs.

chronosphere 0.3.0 (build 72) - 2020-07-30

Added

• The ‘plateperiod’ argument was accidentally deleted during update to build 69, now it is live again.

chronosphere 0.3.0 (build 71) - 2020-07-14

Changed

• Fixed forced download of registry table when datadir was given and data were already present on disk/storage device

chronosphere 0.3.0 (build 70) - 2020-06-11

Added

• datasets() function gained the ‘dat’, ‘master’ and ‘greetings’ arguments. The default setting of the function only downloads the list of datasets (dat) and variables (var). Setting the ‘dat’ argument to a character entry will download the list of all archives from that dataset. Setting the master argument to ‘master=TRUE’ will download a list of all archives, which is expected to be very long in the near future. The argument ‘greetings=TRUE’ will display a reminder that additional versions and resolutions are available.
• the downloaded objects now have chronosphere attributes. These record the accession information used previously, which allows the repetition of function call, if necessary - including changes.
• fetch() can return the function call, using call=TRUE. This can be either an expression or a terminal message, depending on the settings of call.expr=TRUE/FALSE.
• fetch() can be used with an already downloaded the chronosphere-object to either redownload it, or get its download function call.
• fetch() can be used to return multiple variables from the same dataset. These will be concatenated into a list, unless they are RasterArrays, in which case fetch() will try to cbind() them
• the extent() method of the RasterArray class
• the server log log.csv is only checked once per session.

Removed

• The dataindex() deprecated placeholder function was removed. Use datasets() instead.
• previous updates to reconstruct()

chronosphere 0.2.2 (build 69) - 2020-03-11

Changed

• reconstruct - defense against bad ages
• rotationModels() and validCoords() added

chronosphere 0.2.2 (build 68) - 2020-03-11

Changed

• reconstruct - defense against bad long/lat

chronosphere 0.2.2 (build 67) - 2020-03-06

Changed

• bug fixes

chronosphere 0.2.2 (build 66) - 2020-03-05

Added

• new method extract(‘RasterArray’, ‘matrix’)
• by=NULL is added as to extract(‘RasterArray’, ‘data.frame’)

Changed

• bug fix of newbounds() when col was given.
• by=NULL is the new default of extract(‘RasterArray’, ‘data.frame’). The function was redesigned to accomodate n-dimensional RasterArray input.
• bug fix of dimnames(‘RasterArray’)

chronosphere 0.2.2 (build 65) - 2020-02-20

Added

• plateperiod argument of the reconstruct() function

chronosphere 0.2.2 (build 64) - 2020-02-20

Changed

• mapplot overlap offset fixed

chronosphere 0.2.2 (build 63) - 2020-02-18

Added

• rotate-method for the RasterArray class

chronosphere 0.2.2 (build 62) - 2020-02-17

Added

• zzz.R with chronosphere package help file

Changed

• the dataindex() function was renamed to datasets()

chronosphere 0.2.1 (build 61) - 2020-02-14

Changed

• mapplot() coordinate reset fixed
• IPCC palettes added

chronosphere 0.2.1 (build 60) - 2020-02-12

Changed

• corrected documentation problems

chronosphere 0.2.1 (build 59) - 2020-01-27

Added

• support for shapefile fetching

Changed

• fetch() defaults to the coarsest resolution (highest res entry, new default is res=NULL)

chronosphere 0.2.1 (build 58) - 2020-01-12

Added

• the nums(), colnums() and rownums() functions
• the … argument to fetch to reach variable-specific loading options

Changed

• Fixed issue with offline reconstruction method (one entry in an age with enumerate = FALSE)

chronosphere 0.2.0 (build 57) - 2019-12-11 (CRAN initial submission, take 3)

Changed

• replaced all occurrences of T and F with TRUE and FALSE respectively
• on.exit statements for mapplot() and showPal()
• RasterArray constructor now works for stacks that do not have the same length as the dim product (with warning)
• Fixed bug with colnames and rownames assignment
• t() copies colnames and rownames attributes
• Raster variable loading is now done with R code provided by the server
• renamed NEWS file to NEWS.md

chronosphere 0.2.0 (build 56) - 2019-12-03 (CRAN initial submission, take 2)

Added

• return value documentation for all functions
• on.exit() statements where options and par are changed.

Changed

• description field in DESCRIPTION
• LazyData is set to false
• usage entries for ‘dems’ and ‘clim’

chronosphere 0.2.0 (build 55) - 2019-11-29 (CRAN initial submission)

Added

• support for NAs in the RasterArray constructor and defenses
• ‘clim’ data object
• bug fix for the apply() RasterArray method

Changed

• [[ of RasterArrays now wrap output in a RasterArray by default.
• reconstruct() function’s local submodule no longer returns coordinates for points that are situated on plates that did not exist on the at reconstruction date (matrix method returns NA coordinates, Sp methods omit)