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| # gateR (development version) | ||
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| ## 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 | ||
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| ## 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 | ||
| * 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 | ||
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| ## gateR v0.1.12 | ||
| * Updated maintainer contact information | ||
| * Updated maintainer contact information | ||
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| ## 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 | ||
| * 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 | ||
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| ## 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 | ||
| * 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 | ||
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| ## 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' | ||
| * 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' | ||
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| ## 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 | ||
| * 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 | ||
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| ## 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 | ||
| * 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 | ||
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| ## gateR v0.1.6 | ||
| * Updated URLs in 'gateR-package.Rd' | ||
| * Updated year in DESCRIPTION | ||
| * Updated URLs in 'gateR-package.Rd' | ||
| * Updated year in DESCRIPTION | ||
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| ## 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()` | ||
| * 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()` | ||
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| ## 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 | ||
| * 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 | ||
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| ## 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 | ||
| * 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,14 @@ | ||
| # Not within. Opposite of %in% | ||
| `%!in%` <- function(x, y)!(`%in%`(x, y)) | ||
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| # False Discovery Rate (Benjamini & Hochberg) | ||
| fdr <- function(pvals, alpha) { | ||
| pcrit <- NULL | ||
| m <- length(pvals) | ||
| for (i in 1:m) { | ||
| if (pvals[i] <= (i/m) * alpha) { | ||
| pcrit <- pvals[i] | ||
| } | ||
| } | ||
| return(max(pcrit, pvals[1])) | ||
| } |
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