# 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
