NEWS.md

In Waller-SUSAN/gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

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

Waller-SUSAN/gateR documentation built on Feb. 5, 2024, 12:54 p.m.