gateR (development version)

gateR v0.1.15

Fixed bug in calculation of False Discovery Rate in internal pval_correct() function
Argument plot_cols correctly renamed cols in lrr_plot() function

Migrated R-spatial dependency
Replaced raster in Imports with terra because of imminent package retirement
Updated documentation throughout
Added GitHub R-CMD-check
Updated citation style for CITATION file

Updated package URL and BugReports to renamed GitHub account “lance-waller-lab” (previously “Waller-SUSAN”)
Replaced if() conditions comparing class() to string with inherits() in functions
tools is no longer Imports
utils is now Suggests because “zzz.R” calls the packageDescription() function
ncdfFlow, flowWorkspaceData are no longer Suggests (for generating random data set randCyto) because “Package suggested but not available for checking” in the some CRAN environments
Added CITATION file
Fixed typos in documentation throughout

Updated dependencies spatstat.core and spatstat.linnet packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in spatstat.core were moved to a new package spatstat.random
spatstat.geom, spatstat.core, spatstat.linnet, and spatstat (>=2.0-0) are no longer Depends
spatstat.geom is now Imports
dplyr, ncdfFlow, flowWorkspaceData, and usethis now Suggests (for generating random data set randCyto)
Fixed annotation typos in the vignette. Removed packages no longer used in the vignette

Now rlang is in Depends.
Output for gating() now includes a diagnostic message saved as a character string for reference in a slot called note
A diagnostic message can be viewed running rlang::last_error()$out$note after the unsuccessful run of gating()
Removed redundant @importFrom fields image.plot in ‘package.R’

Updated spatstat package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). Now spatstat.geom, spatstat.core, spatstat.linnet, and spatstat (>= 2.0-0) are in Depends
Fixed check for vars in dat within the gating() function

Updated spatstat package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). spatstat.geom package replaces spatstat package in Imports
Added additional multiple testing corrections, including False Discovery Rate, spatially dependent Sidak correction, independent Sidak correction, and two corrections based on Random Field Theory (Adler and Hasofer or Friston)
The latter two corrections required a new argument bandw to be added to gating(), lotrrs(), and rrs() functions to allow users to specify bandwidth for the kernel density estimation
Updated the calculation of the spatial correlogram in internal pval_correct() function from the correlog() function in the pgrimess package to the modified.ttest() function in the SpatialPack package
Imports lifecycle package to document deprecated arguments doplot and verbose in lotrrs(), rrs(), and gating() functions
In gating() function, creates a categorized im based on critical p-value, assigns that value to every point in a ppp object, and subsets points by category
Removed maptools and sp packages from Imports
Updated links in ‘gateR-package.Rd’ for package updates

Added arguments save_gate, name_gate, and path_gate in lotrrs(), rrs(), and gating() to save plots as PNG files as output
Renamed doplot argument as plot_gate for consistency with new plotting arguments
Added a stop (and return no results) if no significant clusters detected during first gate
Deprecate verbose argument in gating(), rrs(), and lotrrs()
Added try() error catches in rrs() and lotrrs() for c1n and c2n arguments
Changed the right argument in cut() in pval_plot() to “TRUE” (the default for cut)
Removed fullstop in error messages
Added a make.names() check for vars and colnames(dat) in gating()

Added documentation to lotrrs(), rrs(), and gating() about the levels of condition(s)
Fixed bug in lotrrs() that was mislabeling numerator and denominator levels of second condition
Added parameters c1n and c2n in lotrrs(), rrs(), and gating() to specify the numerator level

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