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gateR (development version)

gateR v0.1.15

• Fixed ‘Moved Permanently’ content by replacing the old URL with the new URL

gateR v0.1.14

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

gateR v0.1.13

• 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

gateR v0.1.12

• Updated maintainer contact information

gateR v0.1.11

• 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

gateR v0.1.10

• 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

gateR v0.1.9

• 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’

gateR v0.1.8

• 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

gateR v0.1.7

• 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

gateR v0.1.6

• Updated URLs in ‘gateR-package.Rd’
• Updated year in DESCRIPTION

gateR v0.1.5

• 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()

gateR v0.1.4

• 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

gateR v0.1.3

• Removed ncdFlow, flowWorkspaceData, and knitr packages from Suggests
• Created a random data set randCyto and all documentation
• Updated examples and testthat to use randCyto data
• Updated vignette with clearer language

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.