added package loader and update docs

DESCRIPTION

@@ -5,7 +5,7 @@ Version: 0.1.0
 Date: 2024-05-23
 Authors@R: c(person("Qile", "Yang", email = "[email protected]", role = c("cre","aut","cph")))
 Maintainer: Qile Yang <[email protected]>
-Description: A wide variety of tools for general data analysis, wrangling, package development. All functions have vectorized implementations whenever possible.
+Description: A wide variety of tools for general data analysis, wrangling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible.
 BugReports: https://github.com/Qile0317/FastUtils/issues/
 License: MIT + file LICENSE
 Encoding: UTF-8

NAMESPACE

@@ -27,6 +27,7 @@ export(initEmptyTable)
 export(initList)
 export(initTestthat)
 export(initV)
+export(installAndLoad)
 export(isBound)
 export(isCamelCase)
 export(isEven)

R/packageLoading.R

@@ -0,0 +1,87 @@
+#' Install and Load Packages from Various Sources
+#'
+#' This function is designed to facilitate the installation and loading of R packages 
+#' from CRAN, Bioconductor, or GitHub. It checks if packages are installed; if not, it installs them,
+#' and then loads them into the R session. Most importantly, it can handle an arbitrary number
+#' of packages at once and install all possible dependencies 
+#'
+#' @param cran A character vector of CRAN package names to install and load.
+#' @param bioc A character vector of Bioconductor package names to install and load.
+#' @param gh A character vector of GitHub repositories in the format "username/repo" to install and load.
+#' 
+#' @details
+#' The function first checks if necessary namespaces (`BiocManager` for Bioconductor packages and 
+#' `devtools` for GitHub packages) are installed, and installs them if they are not present.
+#' It then proceeds to install and load packages from the specified sources. For GitHub packages, 
+#' installation is done using `devtools::install_github()`.
+#'
+#' @examples
+#' \dontrun{
+#' # Install and load a CRAN package
+#' installAndLoad(cran = c("ggplot2"))
+#'
+#' # Install and load a Bioconductor package
+#' installAndLoad(bioc = c("GenomicFeatures"))
+#'
+#' # Install and load a package from GitHub
+#' installAndLoad(gh = c("hadley/lubridate"))
+#'
+#' # Install and load packages from mixed sources
+#' installAndLoad(cran = c("dplyr"), bioc = c("BiocGenerics"), gh = c("r-lib/testthat"))
+#' }
+#' 
+#' @return None, function is used for side effects (installation and loading of packages).
+#' @export
+#' @keywords packageLoading
+#' 
+installAndLoad <- function(cran = NULL, bioc = NULL, gh = NULL) {
+
+    if (is.null(cran) && is.null(bioc) && is.null(gh)) {
+        message("no packages inputted")
+        return()
+    }
+
+    # Load required libraries for installation
+    if (!is.null(bioc))
+        if (!requireNamespace("BiocManager", quietly = TRUE))
+            install.packages("BiocManager")
+
+    if (!is.null(gh))
+        if (!requireNamespace("devtools", quietly = TRUE))
+            install.packages("devtools")
+
+    # Helper function to install and load a package
+    install_and_load <- function(packagepath) {
+
+        if (is.null(packagepath)) return()
+
+        # github packages must be prioritized
+        if (source == "GitHub") {
+            package <- strsplit(packagepath, "/")[[1]][2]
+            devtools::install_github(
+                packagepath, force = FALSE, quiet = TRUE, dependencies = TRUE
+            )
+            library(package, character.only = TRUE)
+            return()
+        }
+
+        package <- packagepath
+
+        if (!require(package, character.only = TRUE, quietly = TRUE)) {
+
+            if (source == "CRAN") {
+                install.packages(package, dependencies = TRUE)
+            } else if (source == "Bioconductor") {
+                BiocManager::install(package)
+            }
+        }
+
+        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, repo, el[[1]]))
+        }
+    }
+}

README.md

@@ -6,7 +6,7 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/Qile0317/FastUtils/blob/main/LICENSE.md)
 <!-- badges: end -->
 
-R package for fast, readable utility functions for general use. All functions have vectorized implementations whenever possible.
+R package with a wide variety of fast, readable functions for general data analysis, wrangling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible.
 
 ## Installation
 
@@ -23,21 +23,21 @@ library(devtools)
 devtools::install_github("Qile0317/FastUtils")
 ```
 
-## Usage
+## Usage and Documentation
 
 ```R
 library(FastUtils)
 ```
 
-There is a large collection of utility functions to use. Browse the reference manual with ```help(package = "FastUtils")``` to see all functions.
+There is a large collection of utility functions to use. Browse the reference manual with ```help(package = "FastUtils")``` to see all functions. Alternatively, check the reference manual online here: <https://qile0317.github.io/FastUtils/reference/index.html>.
 
 ### Package Conventions
 
 Almost all exported functions and parameters are named with `camelCase`, with the exception of those that try to modify or add on to existing functions from other packages with established ecosystems such as `testthat`.
 
 ## Contributing
 
-Github pull requests from forked branches are more than welcome as it is mostly a solo-project at the moment. For major changes, please open an issue first to discuss what you would like to change. Please also make sure to update tests as appropriate.
+Github pull requests from forked branches are more than welcome as it is mostly a solo-project at the moment. For major changes, please open an issue first to discuss what you would like to change. Please also make sure to update tests as appropriate. See `CONTRIBUTING.md` for more information.
 
 ## Contact