Changelog • geoChronR

Dealt with changes to R’s handling of package versions that was throwing errors.
Added some better error messages in storey() to try to help with issue 89

Reference to spatstat.explore::CDF.density replaced with spatstat.univar::CDF.density following update to spatstat v3.0.0

added oxcal.code.export.path option to runOxcal() to allow users to optionally save the oxcal model code before it runs

Attempted to fix the bug that resulted from the rEDM v1.15.0 name change of make_surrogate_data to SurrogateData

Fixed the many if(is.na(parameter))... statements that broke with R version 4.2
Modified the use of the spatstat package (from spatstat.core to spatstat.summary) to accommodate the changes in that package.

Fixed a bug in writeBacon() where remove.rejected didn’t work properly if there was exactly one rejected date. Thanks @JanPetrik1 for reporting - see issue 71.

Added an ask.reservoir option to runBacon() that connects to the same parameter in writeBacon(). Setting ask.reservoir = FALSE will allow for non-interactive code that uses runBacon() and includes reservoir corrections. Thanks @JanPetrik1 for reporting - see issue 70 for details.

Fixed shape mapping bug with unknown archiveType (thanks Sarah Ivory for reporting)

Moved nuspectral to suggested package, as it’s rarely used and requires compilation See issue 62
Removed devtools from required packages - it shouldn’t be necessary.

Add an option to erase the bacon tempdir (if using) before each run, and set to default.
Fixed bug in writeBacon() that was making the model overwriting option not work properly. Thanks Sofia Kjellman for reporting the bug.

Better error messages in binTs()
Better error handling in pcaEns()

Fixed bug in createOxCalModel() that was causing errors with IntCal20
Suppressed non important warning (“Density was normalised within the computed range of x values [0, 1]”“) in pvalMonteCarlo() that occurred during ecdf estimation

add time.var option to runBam()
better error handling in ar1Surrogates()
better logic and consistency checking in mapAgeEnsembleToPaleoData()
Create median variable option now included in mapAgeEnsembleToPaleoData()

Fix (at least temporarily) rare bugs in pcaEns() and fdr()

A bunch of quality of life improvements
Better integration with new lipdR classes
A new function to create multi-model ensembles! createMultiModelEnsemble()

removed unused arima() in createSyntheticTimeseries()

Added explicit references to astrochron function linterp() in computeSpectraEns(). See issue 55

Improved documentation
runBchron(): which.table parameter changed to meas.table.num for consistency.

Removed jitterPositions option following Bchron update. See issue 53

Added handling for shapes in mapTs() for tibbles.

Fixed bug writing Bchron output into LiPD structure. Thanks @alexkjames for recognizing the bug.

Modified the use of the spatstat package (to spatstat.core) to accommodate the changes in that package.
Moved astrochron back to a “required” package, now that it’s back.

Moved astrochron to a “suggested” package, after it was removed from CRAN.

Fixed sampleBaconAges() for handling different versions of R and rbacon.

Improve and document the export.quantiles option in plotTimeseriesEnsRibbons
Fix bug in plotTimeAvailabilityTs() when only one instance of the group.var see issue 49
Added support for flipping timeseries vertically in plotTimeseriesStack to match interpertations, based on TS metadata, specified in invert.var. Details in ?plotTimeseriesStack. See issue 30

Better automatic detection for mapping ranges in baseMap()

Added interoperability with “tidyTs” objects, that is, TS objects expressed as tidy (or nested) tibbles.
Fixed binding warning in plotTimeAvailabilityTs()
Fixed bug in mapTs() when the regions were really small

Fixed a bug in plotTimeAvailabililyTs() where if group.var had a variable with a single instance it would fail.

Added a NEWS.md file to track changes to the package.
Added pkgdown documentation, website available at nickmckay.github.io/GeoChronR
Updated vignettes for consistency with Geochronology manuscript and version 1.0.0
Fixed typo in plotCorEns() legend when using use.fdr = FALSE

This release marks the submission of the manuscript describing geoChronR to “Geochronology”, the manuscript, which is under discussion, is available here.
Major changes to parameter names (terms within functions) were made for version 1.0.0, standardizing them all to lower case, period separated terminology. If you’ve been using geoChronR for awhile, this will almost certainly break some of your code, sorry.