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gateR (development version)

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