Document update; ready for CRAN

Author: dipterix

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: filearray
 Type: Package
 Title: File-Backed Array for Out-of-Memory Computation
-Version: 0.1.6.9001
+Version: 0.1.7
 Language: en-US
 Encoding: UTF-8
 License: LGPL-3

NEWS.md

@@ -1,3 +1,13 @@
+# filearray 0.1.7
+
+* Removed non-API R C interface
+* Allows `subsetAssign` to assign when value length is 1 (thanks `@talegari` issue `#9`)
+* Allows more flexible `fwhich` function with functional `val` input and options to include corresponding values as part of return (thanks `@talegari` issue `#10`)
+* Fixed `mapreduce` bug when partition length is way larger than the buffer size, causing buffer to stop updating
+* Fixed other `C++` issues, such as unused buffer allocation in subset-assign, and `min_` offset in `sub_vec_range`. These issues are not considered bugs since they don't affect the results, but the performance is slightly increased after fix.
+* Replaced `dipsaus` with more updated `ravetools` in the vignette performance profiling
+* Updated examples to get rid of warning messages and out-dated arguments.
+
 # filearray 0.1.6
 
 * Removed `c++11` from system requirement and `Makevars`

R/load.R

@@ -58,7 +58,7 @@
 #' @examples 
 #' 
 #' 
-#' # Prepare 
+#' # Prepare
 #' library(filearray)
 #' filebase <- tempfile()
 #' if(file.exists(filebase)){ unlink(filebase, TRUE) }
@@ -88,15 +88,15 @@
 #' # check-load, and create a new array if fail
 #' x <- filearray_load_or_create(
 #'     filebase = filebase, dimension = c(200, 30, 8),
-#'     verbose = TRUE, signature = "henry"
+#'     verbose = FALSE, signature = "henry"
 #' )
 #' x$get_header("signature")
 #' 
 #' # check-load with initialization
 #' x <- filearray_load_or_create(
-#'     filebase = filebase, 
+#'     filebase = filebase,
 #'     dimension = c(3, 4, 5),
-#'     verbose = TRUE, mode = "readonly",
+#'     verbose = FALSE, mode = "readonly",
 #'     on_missing = function(array) {
 #'         array[] <- seq_len(60)
 #'     }

R/method-map.R

@@ -62,10 +62,11 @@
 #' output$delete()
 #' 
 #' # Calculate the maximum of x1/x2 for every 100 elements
+#' # total 60 batches/loops (`.buffer_count`)
 #' output <- filearray_create(tempfile(), dimension = c(20,3))
 #' fmap(list(x1, x2), function(input){
 #'     max(input[[1]] / input[[2]])
-#' }, output, .input_size = 100, .output_size = 1)
+#' }, .y = output, .buffer_count = 60)
 #' 
 #' # check
 #' range(output[] - apply(x1[] / x2[], c(2,3), max))
@@ -81,48 +82,46 @@
 #'         Time = 1:301,
 #'         Location = 1:4
 #'     )
-#'     
+#' 
 #'     for(i in 1:4){
 #'         x[,,,i] <- runif(8638700)
 #'     }
 #'     # Step 1:
 #'     # for each location, trial, and marker, calibrate (baseline)
 #'     # according to first 50 time-points
-#'     
+#' 
 #'     output <- filearray_create(tempfile(), dimension = dim(x))
-#'     
+#' 
 #'     # baseline-percentage change
 #'     fmap(
-#'         list(x), 
+#'         list(x),
 #'         function(input){
 #'             # get locational data
 #'             location_data <- input[[1]]
 #'             dim(location_data) <- c(287, 100, 301)
-#'             
-#'             # collapse over first 50 time points for 
+#' 
+#'             # collapse over first 50 time points for
 #'             # each trial, and marker
 #'             baseline <- apply(location_data[,,1:50], c(1,2), mean)
-#'             
+#' 
 #'             # calibrate
-#'             calibrated <- sweep(location_data, c(1,2), baseline, 
+#'             calibrated <- sweep(location_data, c(1,2), baseline,
 #'                                 FUN = function(data, bl){
 #'                                     (data / bl - 1) * 100
 #'                                 })
 #'             return(calibrated)
-#'         }, 
-#'         
+#'         },
+#' 
 #'         .y = output,
-#'         
+#' 
 #'         # input dimension is 287 x 100 x 301 for each location
-#'         .input_size = 8638700,
-#'         
-#'         # output dimension is 287 x 100 x 301
-#'         .output_size = 8638700
+#'         # hence 4 loops in total
+#'         .buffer_count = 4
 #'     )
-#'     
+#' 
 #'     # cleanup
 #'     x$delete()
-#'     
+#' 
 #' }
 #' 
 #' # cleanup

R/methods.R

@@ -182,7 +182,7 @@ subset.FileArray <- function(x, ..., drop = FALSE, .env = parent.frame()){
 #' @param x any R vector, matrix, array or file-array
 #' @param val values to find, or a function taking one argument (a slice of 
 #' data vector) and returns either logical vector with the same length as the 
-#' slice or undex of the slice; see 'Examples'
+#' slice or index of the slice; see 'Examples'
 #' @param arr.ind logical; should array indices be 
 #' returned when \code{x} is an array?
 #' @param ret.values whether to return the values of corresponding indices as