renamed zip and enumerate

Author: Qile0317

NAMESPACE

@@ -11,7 +11,7 @@ export(createMutator)
 export(divide)
 export(enclose)
 export(encloseBr)
-export(enumerate)
+export(enumerateit)
 export(findMissingRdSections)
 export(fmrs)
 export(getAvgHex)
@@ -60,7 +60,7 @@ export(trySplit)
 export(val)
 export(val1)
 export(warningp)
-export(zip)
+export(zipit)
 exportPattern("^[[:alpha:]]+")
 importFrom(Rcpp,evalCpp)
 importFrom(magrittr,"%>%")

R/iteration.R

@@ -1,24 +1,27 @@
 #' Zip Multiple Vectors or Lists
 #'
 #' This function combines multiple vectors or lists element-wise into a list of lists.
+#' A slightly lighter weight alternative to `itertools::izip()`
 #'
 #' @param ... Vectors or lists to be combined.
 #' 
 #' @return A list of lists, where each inner list contains the elements from the corresponding positions in the input vectors or lists.
 #' @export
 #' @keywords iteration
+#' @seealso [enumerateit()]
 #' @examples
 #' # Zip two vectors
-#' zip(c(1, 2, 3), c("a", "b", "c"))
+#' zipit(c(1, 2, 3), c("a", "b", "c"))
 #' # Zip three vectors
-#' zip(c(1, 2), c("x", "y"), c(TRUE, FALSE))
-zip <- function(...) mapply(list, ..., SIMPLIFY = FALSE)
+#' zipit(c(1, 2), c("x", "y"), c(TRUE, FALSE))
+zipit <- function(...) mapply(list, ..., SIMPLIFY = FALSE)
 
 #' Enumerate Elements with Indices
 #'
 #' This function pairs elements of vectors or lists with their indices. The output
 #' is meant to be used in a for loop, and each element extracted with the 
-#' [ind()], [val()], or [val1()] functions.
+#' [ind()], [val()], or [val1()] functions. A slightly lighter weight alternative
+#' to `itertools::enumerate()`
 #'
 #' @param ... Vectors or lists to be enumerated.
 #' @param zero_indexed A logical indicating whether indexing should start from zero. Default is FALSE.
@@ -31,13 +34,13 @@ zip <- function(...) mapply(list, ..., SIMPLIFY = FALSE)
 #' 
 #' @examples
 #' # Enumerate a vector
-#' enumerate(c("a", "b", "c"))
+#' enumerateit(c("a", "b", "c"))
 #' # Enumerate a vector starting from zero
-#' enumerate(c("a", "b", "c"), zero_indexed = TRUE)
+#' enumerateit(c("a", "b", "c"), zero_indexed = TRUE)
 #' # Enumerate two vectors
-#' enumerate(c(1, 2), c("x", "y"))
-enumerate <- function(..., zero_indexed = FALSE) {
-    zip(seq_along(..1) - zero_indexed, ...)
+#' enumerateit(c(1, 2), c("x", "y"))
+enumerateit <- function(..., zero_indexed = FALSE) {
+    zipit(seq_along(..1) - zero_indexed, ...)
 }
 
 #' Get Index from Enumerated Element
@@ -49,6 +52,7 @@ enumerate <- function(..., zero_indexed = FALSE) {
 #' @return The index of the enumerated element.
 #' @export
 #' @keywords iteration
+#' @seealso [enumerateit()]
 #' @examples
 #' # Extract index from an enumerated element
 #' elem <- list(1, "a")
@@ -65,6 +69,7 @@ ind <- function(elem) elem[[1]]
 #' @return The value at the specified index in the enumerated element.
 #' @export
 #' @keywords iteration
+#' @seealso [enumerateit()]
 #' @examples
 #' # Extract value from an enumerated element by index
 #' elem <- list(1, "a", "b")
@@ -80,6 +85,7 @@ val <- function(elem, index) elem[[index + 1]]
 #' @return The first value in the enumerated element.
 #' @export
 #' @keywords iteration
+#' @seealso [enumerateit()]
 #' @examples
 #' # Extract the first value from an enumerated element
 #' elem <- list(1, "a", "b")

R/math.R

@@ -5,15 +5,15 @@
 #' @param num A numeric vector to be bounded.
 #' @param lowerbound The lower bound of the range.
 #' @param upperbound The upper bound of the range.
-#' 
+#'
 #' @return A numeric vector with elements bounded within the specified range.
 #' @export
 #' @keywords math
-#' 
+#'
 #' @examples
 #' bound(1, 0, 2)
 #' bound(1:10, -1, 5)
-#' 
+#'
 bound <- function(num, lowerbound, upperbound) {
     sapply(num, function(x) min(max(x, lowerbound), upperbound))
 }

R/packageLoading.R

@@ -34,7 +34,7 @@
 #' @export
 #' @keywords packageLoading
 #' 
-installAndLoad <- function(cran = NULL, bioc = NULL, gh = NULL) {
+installAndLoad <- function(cran = NULL, bioc = NULL, gh = NULL, lib = .libPaths()[1], verbose = FALSE) {
 
     if (is.null(cran) && is.null(bioc) && is.null(gh)) {
         message("no packages inputted")
@@ -44,44 +44,56 @@ installAndLoad <- function(cran = NULL, bioc = NULL, gh = NULL) {
     # Load required libraries for installation
     if (!is.null(bioc))
         if (!requireNamespace("BiocManager", quietly = TRUE))
-            utils::install.packages("BiocManager")
+            utils::install.packages("BiocManager", lib = lib)
 
     if (!is.null(gh))
         if (!requireNamespace("devtools", quietly = TRUE))
-            utils::install.packages("devtools")
+            utils::install.packages("devtools", lib = lib)
 
     # Helper function to install and load a package
-    install_and_load <- function(packagepath) {
+    install_and_load <- function(packagepath, source) {
 
         if (is.null(packagepath)) return()
 
-        # github packages must be prioritized
+        # github packages must be prioritized to account for naming conventions
         if (source == "GitHub") {
             package <- strsplit(packagepath, "/")[[1]][2]
-            devtools::install_github(
-                packagepath, force = FALSE, quiet = TRUE, dependencies = TRUE
-            )
-            library(package, character.only = TRUE)
-            return()
+
+        } else {
+            package <- packagepath
         }
-        
-        package <- packagepath
 
-        if (!require(package, character.only = TRUE, quietly = TRUE)) {
+        if (require(package, character.only = TRUE, quietly = TRUE)) return()
 
-            if (source == "CRAN") {
-                utils::install.packages(package, dependencies = TRUE)
-            } else if (source == "Bioconductor") {
-                BiocManager::install(package)
-            }
+        if (source == "CRAN") {
+            utils::install.packages(
+                package,
+                dependencies = TRUE,
+                lib = lib
+            )
+        } else if (source == "Bioconductor") {
+            BiocManager::install(
+                package,
+                lib = lib,
+                dependencies = TRUE
+            )
+        } else {
+            warning("* installing `", package, "` from a raw GitHub repository")
+            devtools::install_github(
+                packagepath,
+                force = FALSE,
+                quiet = TRUE,
+                dependencies = TRUE,
+                lib = lib
+            )
         }
 
         library(package, character.only = TRUE)
     }
 
-    for (el in zip(c("CRAN", "Bioconductor", "GitHub"), c(cran, bioc, gh))) {
-        for (pkg in el[[2]]) {
-            suppressPackageStartupMessages(install_and_load(pkg, el[[1]]))
-        }
+    for (el in zipi(list("CRAN", "Bioconductor", "GitHub"), list(cran, bioc, gh))) {
+        sapply(el[[2]], function(pkg) capture.output(suppressMessages((install_and_load(pkg, el[[1]])))))
     }
+
+    return()
 }