From c8f04fbc0eb3d0b40e0dfd08a0da1825b8d7ab47 Mon Sep 17 00:00:00 2001
From: Guangchuang Yu <guangchuangyu@gmail.com>
Date: Tue, 3 Dec 2024 17:37:41 +0800
Subject: [PATCH] c2()

---
 DESCRIPTION                    |  2 +-
 Makefile                       |  7 ++++---
 NAMESPACE                      |  7 +++++++
 NEWS.md                        |  4 ++++
 {inst/prototype => R}/concat.r | 35 +++++++++++++++++++++++++++-------
 man/c2.Rd                      | 25 ++++++++++++++++++++++++
 6 files changed, 69 insertions(+), 11 deletions(-)
 rename {inst/prototype => R}/concat.r (68%)
 create mode 100644 man/c2.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 6c07285..e056331 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: yulab.utils
 Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
-Version: 0.1.8
+Version: 0.1.8.001
 Authors@R: c(person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")))
 Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
 Imports:
diff --git a/Makefile b/Makefile
index 88a0529..b76a553 100644
--- a/Makefile
+++ b/Makefile
@@ -16,9 +16,10 @@ readme2:
 	Rscript -e 'rmarkdown::render("README.Rmd", "html_document")'
 
 build:
-	cd ..;\
-	R CMD build $(PKGSRC)
-
+	#cd ..;\
+	#R CMD build $(PKGSRC)
+	Rscript -e 'devtools::build()'
+	
 build2:
 	cd ..;\
 	R CMD build --no-build-vignettes $(PKGSRC)
diff --git a/NAMESPACE b/NAMESPACE
index 0d63f27..6e56028 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,10 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",chunked_array)
+S3method(as.vector,chunked_array)
+S3method(is.character,chunked_array)
+S3method(is.numeric,chunked_array)
+S3method(length,chunked_array)
+S3method(print,chunked_array)
 S3method(print,exec)
 export(Biocpkg)
 export(CRANpkg)
 export(Githubpkg)
 export(auto_set_regexpr_style)
+export(c2)
 export(check_pkg)
 export(combinations)
 export(exec)
diff --git a/NEWS.md b/NEWS.md
index fedf8dc..0985cc3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# yulab.utils 0.1.8.001
+
++ `c2()` to concate two vectors into a 'chunked_array' object (2024-12-03, Tue)
+
 # yulab.utils 0.1.8
 
 + add new citation (The Innovation 2024) (2024-11-07, Thu)
diff --git a/inst/prototype/concat.r b/R/concat.r
similarity index 68%
rename from inst/prototype/concat.r
rename to R/concat.r
index da33fc4..7bc8854 100644
--- a/inst/prototype/concat.r
+++ b/R/concat.r
@@ -1,4 +1,17 @@
+#' chunked array
+#' 
+#' concate two vector/chunked_array into a chunked_array object
+#' @title c2
+#' @param x a vector or chunked_array object
+#' @param y a vector or chunked_array object
+#' @return chunked_array object
+#' @author Guangchuang Yu
+#' @export
 c2 <- function(x, y) {
+    
+    if (length(x) == 0) return(y)
+    if (length(y) == 0) return(x)
+
     same_mode <- (is.numeric(x) && is.numeric(y)) ||
         (is.character(x) && is.character(y))
 
@@ -36,18 +49,21 @@ as_chunked_array <- function(x) {
 
 
 #' @method as.vector chunked_array
+#' @export
 as.vector.chunked_array <- function(x, mode = "any") {
     unlist(x$vector_list)
 }
 
 #' @method print chunked_array
-print.chunked_array <- function(x) {
+#' @export
+print.chunked_array <- function(x, ...) {
     n <- length(x)
     msg <- sprintf("chunked array with size of %d\n", n)
     cat(msg)
 }
 
 #' @method length chunked_array
+#' @export
 length.chunked_array <- function(x) {
     last_item(x$idx) + length(last_item(x$vector_list))
 }
@@ -59,22 +75,27 @@ last_item <- function(x) {
 }
 
 #' @method [ chunked_array
+#' @export
 `[.chunked_array` <- function(x, i, ...) {
-    array_idx <- vapply(i, \(ii) last_item(which(ii > x$idx)), numeric(1))
-
-    pos <- i - x$idx[array_idx]
-
-    output <- ifelse(is.numeric(x), numeric(1), character(1))
-    vapply(seq_along(i), \(j) x$vector_list[[array_idx[j]]][pos[j]], output)
+    # array_idx <- vapply(i, \(ii) last_item(which(ii > x$idx)), numeric(1))
+    # 
+    # pos <- i - x$idx[array_idx]
+    # 
+    # output <- ifelse(is.numeric(x), numeric(1), character(1))
+    # vapply(seq_along(i), \(j) x$vector_list[[array_idx[j]]][pos[j]], output)
+
+    as.vector(x)[i] # faster :)
 }
 
 
 #' @method is.numeric chunked_array
+#' @export
 is.numeric.chunked_array <- function(x) {
     is.numeric(x$vector_list[[1]])
 }
 
 #' @method is.character chunked_array
+#' @export
 is.character.chunked_array <- function(x) {
     is.character(x$vector_list[[1]])
 }
diff --git a/man/c2.Rd b/man/c2.Rd
new file mode 100644
index 0000000..3dc0ab5
--- /dev/null
+++ b/man/c2.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/concat.r
+\name{c2}
+\alias{c2}
+\title{c2}
+\usage{
+c2(x, y)
+}
+\arguments{
+\item{x}{a vector or chunked_array object}
+
+\item{y}{a vector or chunked_array object}
+}
+\value{
+chunked_array object
+}
+\description{
+chunked array
+}
+\details{
+concate two vector/chunked_array into a chunked_array object
+}
+\author{
+Guangchuang Yu
+}