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

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

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

v0.1.12

• Updated maintainer contact information

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

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

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'
• Added Zenodo DOI

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

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

v0.1.6

• 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
• Removed '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)
• Removed fullstop in error messages
• Added a make.names() check for vars and colnames(dat) in gating()
• Updated URLs in gateR-package.Rd