Changes in version 0.1.16 (2025-08-29)                 

gateR v0.1.16

  - Renamed 'package.R' to 'gateR-package.R' after Roxygen (>=7.3.0)
    update
  - Fixed Rd \link{} targets missing package within 'gateR-package.Rd'
  - Updated vignette with updated package version and dependencies

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