diff --git a/DESCRIPTION b/DESCRIPTION index 7e91950..05ea2d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: gateR Type: Package Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation -Version: 0.1.9 -Date: 2021-06-20 +Version: 0.1.10 +Date: 2022-02-04 Authors@R: c(person(given = "Ian D.", family = "Buller", @@ -41,13 +41,9 @@ License: Apache License (>= 2.0) Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1 +RoxygenNote: 7.1.2 Depends: - R (>= 3.5.0), - spatstat.geom, - spatstat.core, - spatstat.linnet, - spatstat (>= 2.0-0) + R (>= 3.5.0) Imports: fields, graphics, @@ -57,13 +53,19 @@ Imports: rlang, sparr, SpatialPack, + spatstat.geom, stats, tibble, + tools, utils Suggests: + dplyr, + flowWorkspaceData, + ncdfFlow, R.rsp, spelling, - testthat + testthat, + usethis VignetteBuilder: R.rsp Language: en-US URL: https://github.com/Waller-SUSAN/gateR diff --git a/NAMESPACE b/NAMESPACE index d4494fa..6cbca60 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -6,10 +6,6 @@ export(lrr_plot) export(pval_correct) export(pval_plot) export(rrs) -import(spatstat) -import(spatstat.core) -import(spatstat.geom) -import(spatstat.linnet) importFrom(SpatialPack,modified.ttest) importFrom(fields,image.plot) importFrom(grDevices,chull) diff --git a/NEWS.md b/NEWS.md index 8ec8c80..d6282c4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,16 @@ # gateR (development version) +# 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()`. +* 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 diff --git a/R/package.R b/R/package.R index 4d96cf5..5202a2d 100644 --- a/R/package.R +++ b/R/package.R @@ -41,10 +41,7 @@ NULL #' @importFrom rlang abort inform #' @importFrom sparr OS risk #' @importFrom SpatialPack modified.ttest +#' @importFrom spatstat.geom as.im cut.im marks owin ppp #' @importFrom stats na.omit pnorm relevel #' @importFrom tibble add_column -#' @import spatstat.geom -#' @import spatstat.core -#' @import spatstat.linnet -#' @import spatstat NULL diff --git a/cran-comments.md b/cran-comments.md index 9a3f696..94e535e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,21 +1,24 @@ -## This is the nineth resubmission +## This is the tenth resubmission * Updates since previous submission: - * 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' - + * 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 + * Fixed annotation typos in the vignette. Removed packages no longer used in the vignette + * `dplyr`, `ncdfFlow`, `flowWorkspaceData`, and `usethis` now Suggests (for generating random data set `randCyto`) + * Documentation for `pval_correct()` references doi and that throw NOTES in win-builder, Fedora Linux, and Ubuntu Linux but these are valid URLs ## Test environments -* local OS X install, R 4.0.4 +* local OS X install, R 4.1.2 * win-builder, (devel, release, oldrelease) * Rhub * Fedora Linux, R-devel, clang, gfortran - * Ubuntu Linux 16.04 LTS, R-release, GCC - * Windows Server 2008 R2 SP1, R-devel, 32/64 bit + * Ubuntu Linux 20.04.1 LTS, R-release, GCC + * Windows Server 2022, R-devel, 64 bit + * Windows Server 2008 R2 SP1, R-release, 32⁄64 bit * Oracle Solaris 10, x86, 32 bit, R-release + * macOS 10.13.6 High Sierra, R-release, CRAN's setup ## R CMD check results 0 errors | 0 warnings | 0 notes diff --git a/tests/testthat/test-lotrrs.R b/tests/testthat/test-lotrrs.R index 4392a5f..6a007a8 100644 --- a/tests/testthat/test-lotrrs.R +++ b/tests/testthat/test-lotrrs.R @@ -9,7 +9,6 @@ fubar <- fubar1 <- randCyto fubar$g1 <- as.numeric(fubar$g1) fubar1$g2 <- as.numeric(fubar1$g2) - # Tests test_that("lotrrs throws error with invalid arguments", { diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd index 4212ddc..f259e2c 100644 --- a/vignettes/vignette.Rmd +++ b/vignettes/vignette.Rmd @@ -36,12 +36,12 @@ This vignette provides an implementation of the gateR package using a randomly g We start with the necessary packages and seed for the vignette. ```{r packages} - loadedPackages <- c("gateR", "graphics", "maptools", "raster", "sp", "sparr", "spatstat", "stats", "tibble", "utils") + loadedPackages <- c("gateR", "graphics", "stats", "tibble", "utils") invisible(lapply(loadedPackages, library, character.only = TRUE)) set.seed(1234) # for reproducibility ``` -### Generate random toy data using the `spatstat` package +### Generate random toy data Unique function to randomly generate data multivariate normal (MVN) around a central point. Parameters include the centroid coordinates (`centre`), number of observations to generate (`ncell`), and the standard deviation of the normal distribution (`scalar`). diff --git a/vignettes/vignette.html b/vignettes/vignette.html index cc3844a..5a9c0b2 100644 --- a/vignettes/vignette.html +++ b/vignettes/vignette.html @@ -12,7 +12,7 @@ - + gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation @@ -28,7 +28,14 @@ - +