Deprecation updates

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Auto format with air
+aab120c4a96c827c3a8ef3f9b9bbb8e882993a40

R/RMINC.R

@@ -1,8 +1,8 @@
 #' RMINC: R interface to the MINC universe
-#' 
+#'
 #' RMINC provides a means of accessing and performing statistical
 #' analyses on MINC volumes. With facilities to calculate voxel-wise
-#' statistics, perform FDR correction, rapidly visualize 
+#' statistics, perform FDR correction, rapidly visualize
 #' results, and much more.
 #' @import dplyr
 #' @import tidyr
@@ -24,7 +24,7 @@
 #'                   quantile qwilcox rnorm runif sd setNames
 #'                   simulate smooth.spline t.test terms var
 #'                   update vcov AIC BIC getCall aggregate optimize
-#' @importFrom utils download.file capture.output glob2rx read.csv read.table 
+#' @importFrom utils download.file capture.output glob2rx read.csv read.table
 #'                   untar write.table
 #' @importFrom grid plotViewport popViewport pushViewport
 #' @importFrom gridBase baseViewports
@@ -36,39 +36,39 @@
 #' @importFrom rjson fromJSON
 #' @importFrom purrr map map_df map2
 #' @importFrom rlang UQ quo
-#' @useDynLib RMINC, .registration = TRUE 
+#' @useDynLib RMINC, .registration = TRUE
 #' @docType package
 #' @name RMINC
 NULL
 
 #' Voxel Atlas Definitions
-#' 
+#'
 #' Voxel based analyses often require an atlas to differentiate
-#' voxels by structure membership. In conjunction with the atlas, 
+#' voxels by structure membership. In conjunction with the atlas,
 #' a set of atlas definitions allow you to calculate summaries by region
-#' for measures and statistics of interest. For example the \code{defs} 
+#' for measures and statistics of interest. For example the \code{defs}
 #' argument of \link{anatGetAll} is a character vector
 #' pointing to atlas definitions.
-#' 
+#'
 #' @details
 #' the basic format for voxel atlas definitions is a 3-column csv
 #' file. The file should be formatted like: \cr
 #' \tabular{lrr}{
 #' Structure \tab right.label \tab left.label \cr
 #' amygdala \tab 51 \tab 151 \cr
-#' anterior commisure: pars anterior \tab 115 \tab 215 
+#' anterior commisure: pars anterior \tab 115 \tab 215
 #' }
 #' The csv file may contain additional columns, but the
 #' three columns above must by present with names spelling/case
 #' sensitive. Additional columns may include a tissue.type
 #' column which is used in some functions.
-#' 
+#'
 #' @name voxel_atlas_defs
 NULL
 
 #' RMINC Masked Value
-#' 
-#' RMINC_MASKED_VALUE is an object with the S3 class "RMINC_MASKED_VALUE" with NA value 
+#'
+#' RMINC_MASKED_VALUE is an object with the S3 class "RMINC_MASKED_VALUE" with NA value
 #' used to differentiate whether an NA was generated by the user or by an RMINC masking
 #' procedure. The value, which will be written out with \link{mincWriteVolume}, can be changed
 #' to zero for example with \link{setRMINCMaskedValue}.
@@ -78,35 +78,36 @@ NULL
 
 ### Package initialization function, syncs environment vars and defines defaults
 .onLoad <-
-  function(libname, pkgname){
-    empty_to_null <- function(x){
+  function(libname, pkgname) {
+    empty_to_null <- function(x) {
       `if`(x == "", NULL, x)
     }
-    
+
     #Set default options taken from Hadley's r-packages book
     op <- options()
-    
+
     op.RMINC <- list(
-      RMINC_MASKED_VALUE = 
-        structure(0, class = "RMINC_MASKED_VALUE")
-    , RMINC_LABEL_DEFINITIONS =
-        empty_to_null(Sys.getenv("RMINC_LABEL_DEFINITIONS"))          
-    , RMINC_BATCH_CONF =
-        `if`(Sys.getenv("RMINC_BATCH_CONF") == ""
-           , system.file("parallel/pbs_batchtools.R", package = "RMINC")
-           , Sys.getenv("RMINC_BATCH_CONF"))
-    , RMINC_DATA_DIR =
-        empty_to_null(Sys.getenv("RMINC_DATA_DIR"))           
+      RMINC_MASKED_VALUE = structure(0, class = "RMINC_MASKED_VALUE"),
+      RMINC_LABEL_DEFINITIONS = empty_to_null(Sys.getenv(
+        "RMINC_LABEL_DEFINITIONS"
+      )),
+      RMINC_BATCH_CONF = `if`(
+        Sys.getenv("RMINC_BATCH_CONF") == "",
+        system.file("parallel/pbs_batchtools.R", package = "RMINC"),
+        Sys.getenv("RMINC_BATCH_CONF")
+      ),
+      RMINC_DATA_DIR = empty_to_null(Sys.getenv("RMINC_DATA_DIR"))
     )
-    
+
     toset <- !(names(op.RMINC) %in% names(op))
-    if(any(toset)) options(op.RMINC[toset])
-
+    if (any(toset)) {
+      options(op.RMINC[toset])
+    }
+
     invisible()
   }
 
 # Silence warning about magrittr/dplyr dot
 # a la https://github.com/smbache/magrittr/issues/29
 utils::globalVariables(".")
 utils::globalVariables(".data")
-