Prepare for CRAN v0.1.11 release

* 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
* `ncdfFlow`, `flowWorkspaceData` are no longer Suggests (for generating random data set `randCyto`) because "Package suggested but not available for checking" in some CRAN environments
* Added CITATION file
* Fixed typos in documentation throughout

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gateR
 Type: Package
 Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
-Version: 0.1.10
-Date: 2022-02-04
+Version: 0.1.11
+Date: 2022-08-25
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",
@@ -32,7 +32,7 @@ Description: Estimates statistically significant marker combination values withi
         another group (i.e., healthy control), successively, using various combinations (i.e.,
         "gates") of markers to examine features of cells that may be different between
         groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
-        function that is estimated using the 'sparr' package. Details about the 'sparr' package
+        function estimated using the 'sparr' package. Details about the 'sparr' package
         methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
         about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
         More information about relative risk functions using kernel density estimation can be
@@ -41,7 +41,7 @@ License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Depends: 
     R (>= 3.5.0)
 Imports: 
@@ -55,18 +55,15 @@ Imports:
     SpatialPack,
     spatstat.geom,
     stats,
-    tibble,
-    tools,
-    utils
+    tibble
 Suggests:
     dplyr,
-    flowWorkspaceData,
-    ncdfFlow,
     R.rsp,
     spelling,
     testthat,
-    usethis
+    usethis,
+    utils
 VignetteBuilder: R.rsp
 Language: en-US
-URL: https://github.com/Waller-SUSAN/gateR
-BugReports: https://github.com/Waller-SUSAN/gateR/issues
+URL: https://github.com/lance-waller-lab/gateR
+BugReports: https://github.com/lance-waller-lab/gateR/issues

NEWS.md

@@ -1,5 +1,14 @@
 # gateR (development version)
 
+# 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

R/gating.R

@@ -15,20 +15,20 @@
 #' @param name_gate Optional, character. The filename of the visualization(s). The default is "gate_k" where "k" is the gate number.
 #' @param path_gate Optional, character. The path of the visualization(s). The default is the current working directory.
 #' @param rcols Character string of length three (3) specifying the colors for: 1) group A (numerator), 2) neither, and 3) group B (denominator) designations. The defaults are \code{c("#FF0000", "#cccccc", "#0000FF")} or \code{c("red", "grey80", "blue")}.
-#' @param lower_lrr Optional, numeric. Lower cut-off value for the log relative risk value in the color key (typically a negative value). The default is no limit and the color key will include the minimum value of the log relative risk surface. 
-#' @param upper_lrr Optional, numeric. Upper cut-off value for the log relative risk value in the color key (typically a positive value). The default is no limit and the color key will include the maximum value of the log relative risk surface.
-#' @param c1n Optional, character. The name of the level for the numerator of condition A. The default is null and the first level is treated as the numerator. 
-#' @param c2n Optional, character. The name of the level for the numerator of condition B. The default is null and the first level is treated as the numerator.
+#' @param lower_lrr Optional, numeric. Lower cut-off value for the log relative risk value in the color key (typically a negative value). The default is no limit, and the color key will include the minimum value of the log relative risk surface. 
+#' @param upper_lrr Optional, numeric. Upper cut-off value for the log relative risk value in the color key (typically a positive value). The default is no limit, and the color key will include the maximum value of the log relative risk surface.
+#' @param c1n Optional, character. The name of the level for the numerator of condition A. The default is NULL, and the first level is treated as the numerator. 
+#' @param c2n Optional, character. The name of the level for the numerator of condition B. The default is NULL, and the first level is treated as the numerator.
 #' @param win Optional. Object of class \code{owin} for a custom two-dimensional window within which to estimate the surfaces. The default is NULL and calculates a convex hull around the data.
 #' @param ... Arguments passed to \code{\link[sparr]{risk}} to select resolution.
 #' @param doplot `r lifecycle::badge("deprecated")` \code{doplot} is no longer supported and has been renamed \code{plot_gate}.
 #' @param verbose `r lifecycle::badge("deprecated")` \code{verbose} is no longer supported; this function will not display verbose output from internal \code{\link[sparr]{risk}} function.
 #'
 #' @details This function performs a sequential gating strategy for mass cytometry data comparing two levels with one or two conditions. Gates are typically two-dimensional space comprised of two fluorescent markers. The two-level comparison allows for the estimation of a spatial relative risk function and the computation of p-value based on an assumption of asymptotic normality. Cells within statistically significant areas are extracted and used in the next gate. This function relies heavily upon the \code{\link[sparr]{risk}} function. Basic visualization is available if \code{plot_gate = TRUE}. 
 #' 
-#' The \code{vars} argument must be a vector with an even-numbered length where the odd-numbered elements are the markers used on the x-axis of a gate and the even-numbered elements are the markers used on the y-axis of a gate. For example, if \code{vars = c("V1", "V2", "V3", and "V4")} then the first gate is "V1" on the x-axis and "V2" on the y-axis and then the second gate is V3" on the x-axis and "V4" on the y-axis. Makers can be repeated in successive gates. 
+#' The \code{vars} argument must be a vector with an even-numbered length where the odd-numbered elements are the markers used on the x-axis of a gate, and the even-numbered elements are the markers used on the y-axis of a gate. For example, if \code{vars = c("V1", "V2", "V3", and "V4")} then the first gate is "V1" on the x-axis and "V2" on the y-axis and then the second gate is V3" on the x-axis and "V4" on the y-axis. Makers can be repeated in successive gates. 
 #' 
-#' The \code{n_condition} argument specifies if the gating strategy is performed for one condition or two conditions. If \code{n_condition = 1}, then the function performs a one condition gating strategy using the internal \code{rrs} function, which computes the statistically significant areas (clusters) of a relative risk surface at each gate and selects the cells within the clusters specified by the \code{numerator} argument. If \code{n_condition = 2}, then the function performs a two conditions gating strategy using the internal \code{lotrrs} function, which computes the statistically significant areas (clusters) of a ratio of relative risk surfaces at each gate and selects the cells within the clusters specified by the \code{numerator} argument. The condition variable(s) within \code{dat} must be of class 'factor' with two levels. The first level is considered the numerator (i.e., "case") value and the second level is considered the denominator (i.e., "control") value. The levels can also be specified using the \code{c1n} and \code{c2n} parameters. See the documentation for the internal \code{rrs} and \code{lotrrs} functions for more details.
+#' The \code{n_condition} argument specifies if the gating strategy is performed for one condition or two conditions. If \code{n_condition = 1}, then the function performs a one condition gating strategy using the internal \code{rrs} function, which computes the statistically significant areas (clusters) of a relative risk surface at each gate and selects the cells within the clusters specified by the \code{numerator} argument. If \code{n_condition = 2}, then the function performs a two conditions gating strategy using the internal \code{lotrrs} function, which computes the statistically significant areas (clusters) of a ratio of relative risk surfaces at each gate and selects the cells within the clusters specified by the \code{numerator} argument. The condition variable(s) within \code{dat} must be of class 'factor' with two levels. The first level is considered the numerator (i.e., "case") value, and the second level is considered the denominator (i.e., "control") value. The levels can also be specified using the \code{c1n} and \code{c2n} parameters. See the documentation for the internal \code{rrs} and \code{lotrrs} functions for more details.
 #' 
 #' The p-value surface of the ratio of relative risk surfaces is estimated assuming asymptotic normality of the ratio value at each gridded knot. The bandwidth is fixed across all layers.
 #' 
@@ -138,7 +138,7 @@ gating <- function(dat,
   }
 
   ## win
-  if (!is.null(win) & class(win) != "owin") { stop("'win' must be class 'owin'") }
+  if (!is.null(win) & !inherits(win, "owin")) { stop("'win' must be class 'owin'") }
 
   # Format data input
   dat <- dat[!is.na(dat[ , which(colnames(dat) %in% vars[1])]) &

R/lotrrs.R

@@ -12,16 +12,16 @@
 #' @param name_gate Optional, character. The filename of the visualization. The default is "gate".
 #' @param path_gate Optional, character. The path of the visualization. The default is the current working directory.
 #' @param rcols Character string of length three (3) specifying the colors for: 1) group A (numerator), 2) neither, and 3) group B (denominator) designations. The defaults are \code{c("#FF0000", "#cccccc", "#0000FF")} or \code{c("red", "grey80", "blue")}.
-#' @param lower_lrr Optional, numeric. Lower cut-off value for the log relative risk value in the color key (typically a negative value). The default is no limit and the color key will include the minimum value of the log relative risk surface. 
-#' @param upper_lrr Optional, numeric. Upper cut-off value for the log relative risk value in the color key (typically a positive value). The default is no limit and the color key will include the maximum value of the log relative risk surface.
-#' @param c1n Optional, character. The name of the level for the numerator of condition A. The default is null and the first level is treated as the numerator. 
-#' @param c2n Optional, character. The name of the level for the numerator of condition B. The default is null and the first level is treated as the numerator.
+#' @param lower_lrr Optional, numeric. Lower cut-off value for the log relative risk value in the color key (typically a negative value). The default is no limit, and the color key will include the minimum value of the log relative risk surface. 
+#' @param upper_lrr Optional, numeric. Upper cut-off value for the log relative risk value in the color key (typically a positive value). The default is no limit, and the color key will include the maximum value of the log relative risk surface.
+#' @param c1n Optional, character. The name of the level for the numerator of condition A. The default is NULL, and the first level is treated as the numerator. 
+#' @param c2n Optional, character. The name of the level for the numerator of condition B. The default is NULL, and the first level is treated as the numerator.
 #' @param win Optional. Object of class \code{owin} for a custom two-dimensional window within which to estimate the surfaces. The default is NULL and calculates a convex hull around the data.
 #' @param ... Arguments passed to \code{\link[sparr]{risk}} to select resolution.
 #' @param doplot `r lifecycle::badge("deprecated")` \code{doplot} is no longer supported and has been renamed \code{plot_gate}.
 #' @param verbose `r lifecycle::badge("deprecated")` \code{verbose} is no longer supported; this function will not display verbose output from internal \code{\link[sparr]{risk}} function.
 #'
-#' @details This function estimates a ratio of relative risk surfaces and computes the asymptotic p-value surface for a single gate with two conditions using three successive \code{\link[sparr]{risk}} functions. A relative risk surface is estimated for Condition A at each level of Condition B and then a ratio of the two relative risk surfaces is computed. 
+#' @details This function estimates a ratio of relative risk surfaces and computes the asymptotic p-value surface for a single gate with two conditions using three successive \code{\link[sparr]{risk}} functions. A relative risk surface is estimated for Condition A at each level of Condition B, and then a ratio of the two relative risk surfaces is computed. 
 #' 
 #' \deqn{RR_{Condition B1} = \frac{Condition A2 of B1}{Condition A1 of B1}}
 #' \deqn{RR_{Condition B2} = \frac{Condition A2 of B2}{Condition A1 of B2}}
@@ -31,7 +31,7 @@
 #' 
 #' Provides functionality for a correction for multiple testing. If \code{p_correct = "FDR"}, calculates a False Discovery Rate by Benjamini and Hochberg. If \code{p_correct = "uncorrelated Sidak"}, calculates an independent Sidak correction. If \code{p_correct = "uncorrelated Bonferroni"}, calculates an independent Bonferroni correction. If \code{p_correct = "correlated Sidak"} or if \code{p_correct = "correlated Bonferroni"}, then the corrections take into account the into account the spatial correlation of the surface. (NOTE: If \code{p_correct = "correlated Sidak"} or if \code{p_correct = "correlated Bonferroni"}, it may take a considerable amount of computation resources and time to calculate). If \code{p_correct = "Adler and Hasofer"} or if \code{p_correct = "Friston"}, then calculates a correction based on Random Field Theory. If \code{p_correct = "none"} (the default), then the function does not account for multiple testing and uses the uncorrected \code{alpha} level. See the internal \code{pval_correct} function documentation for more details.
 #' 
-#' The two condition variables (Condition A and Condition B) within \code{dat} must be of class 'factor' with two levels. The first level in each variable is considered the numerator (i.e., "case") value and the second level is considered the denominator (i.e., "control") value. The levels can also be specified using the \code{c1n} and \code{c2n} parameters.
+#' The two condition variables (Condition A and Condition B) within \code{dat} must be of class 'factor' with two levels. The first level in each variable is considered the numerator (i.e., "case") value, and the second level is considered the denominator (i.e., "control") value. The levels can also be specified using the \code{c1n} and \code{c2n} parameters.
 #'
 #' @return An object of class 'list' where each element is a object of class 'rrs' created by the \code{\link[sparr]{risk}} function with two additional components:
 #' 
@@ -108,7 +108,7 @@ lotrrs <- function(dat,
   }
 
   ## win
-  if (!is.null(win) & class(win) != "owin") { stop("'win' must be class 'owin'") }
+  if (!is.null(win) & !inherits(win, "owin")) { stop("'win' must be class 'owin'") }
   if (is.null(win)) {
     dat <- as.data.frame(dat)
     dat <- dat[!is.na(dat[ , 4]) & !is.na(dat[ , 5]) , ]

R/lrr_plot.R

@@ -33,7 +33,7 @@ lrr_plot <- function(input,
                      digits = 1) {
 
   # Inputs
-  if (class(input) != "im") {
+  if (!inherits(input, "im")) {
     stop("The 'input' argument must be an object of class 'im'")
   }
 

R/package.R

@@ -2,7 +2,7 @@
 #'
 #' Estimates statistically significant fluorescent marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of fluorescent markers to examine features of cells that may be different between groups.
 #'
-#' @details For a two-group comparison, the 'gateR' package uses the spatial relative risk function that is estimated using the {sparr} package. Details about the {sparr} package methods can be found in the tutorial: Davies et al. (2018) \doi{10.1002/sim.7577}. Details about kernel density estimation can be found in J. F. Bithell (1990) \doi{10.1002/sim.4780090616}. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) \doi{10.1002/sim.4780101112}.
+#' @details For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the \code{\link{sparr}} package. Details about the \code{\link{sparr}} package methods can be found in the tutorial: Davies et al. (2018) \doi{10.1002/sim.7577}. Details about kernel density estimation can be found in J. F. Bithell (1990) \doi{10.1002/sim.4780090616}. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) \doi{10.1002/sim.4780101112}.
 #' 
 #' This package provides a function to perform a gating strategy for flow cytometry data. The 'gateR' package also provides basic visualization for each gate.
 #' 
@@ -12,9 +12,9 @@
 #' 
 #' \code{\link{gating}} Extracts cells within statistically significant combinations of fluorescent markers, successively, for a set of markers. Statistically significant combinations are identified using two-tailed p-values of a relative risk surface assuming asymptotic normality. This function is currently available for two-level comparisons of a single condition (e.g., case/control) or two conditions (e.g., case/control at time 1 and time 2). Provides functionality for basic visualization and multiple testing correction.
 #' 
-#' \code{\link{rrs}} Estimates a relative risk surface and computes the asymptotic p-value surface for a single gate with a single condition. Includes features for basic visualization. This function is used internally within the \code{\link{gating}} function to extract the points within the significant areas.  This function can also be used as a standalone function.
+#' \code{\link{rrs}} Estimates a relative risk surface and computes the asymptotic p-value surface for a single gate with a single condition, including features for basic visualization. This function is used internally within the \code{\link{gating}} function to extract the points within the significant areas. This function can also be used as a standalone function.
 #' 
-#' \code{\link{lotrrs}} Estimates a ratio of relative risk surfaces and computes the asymptotic p-value surface for a single gate with two conditions. Includes features for basic visualization. This function is used internally within the \code{\link{gating}} function to extract the points within the significant areas. This function can also be used as a standalone function.
+#' \code{\link{lotrrs}} Estimates a ratio of relative risk surfaces and computes the asymptotic p-value surface for a single gate with two conditions, including features for basic visualization. This function is used internally within the \code{\link{gating}} function to extract the points within the significant areas. This function can also be used as a standalone function.
 #' 
 #' \bold{Flow Cytometry Data}
 #'