STOICH-utilities

The STOICH-utilities R package provides user tools for working with STOICH database files. This package is designed to enable easier and more robust access to the data files from STOICH database releases.

Getting Started

The STOICH database R package "stoichUtilities" is a set of functions to aid with tasks like filtering, pairing water samples with organism samples and merging tables. Since it is an R package you will need to have R installed. It is recommended to install RStudio (https://www.rstudio.com/) to help manage packages and provide an integrated development environment (IDE).

Installation

There are 3 options for installing the stoichUtilities package. Installing a prebuilt package contains the vignette, while a standard "Install and Restart" won't contain the vignette. Instructions for building your own package from source to get the vignette are also included.

Option 1: Install via CRAN

The "stoichUtilities" has been submitted to CRAN and should be available soon to install via the R package manager.

install.packages("stoichUtilities")

Option 2: Install a PreBuilt Package

Download the stoichUtilities_x.x.x.xxxx.tar.gz file.

Select the menu option Tools -> Install Packages

A window should pop up. For Install from: choose Package Archive File and navigate to the location of the tar.gz file.

Click "Install"

Option 3: Install from Source

Download Source Files

There are 2 options to get the source files:

• From the GitHub project page click the green Code button and choose "Download Zip"
• Use GitHub Desktop or CLI programs to Clone the STOICH-Utilities repository (click the green Code button to copy the URL from the GitHub project page).

Simple Install: Open and Build the R Library

Navigate to the source code location and open stoichUtilities\stoichUtilities.Rproj in RStudio.

Build the documentation: ctrl + shift + D or with the menu Build -> Document

Install the library and restart the R session: ctrl + shift + B or with the menu Build -> Install and Restart

Build Package Method: Build and Install Package from Source

Navigate to the source code location and open stoichUtilities\stoichUtilities.Rproj in RStudio.

Select the menu option Build -> Build Source Package

To install the package, follow instructions for Installing a PreBuilt Package.

Installing Required Packages

The stoichUtilities uses several other packages. Install the required packages.

install.packages(“tidyverse”)
install.packages(“lubridate”)
install.packages(“sf”)
install.packages(“units”)

Using the R Library

Additional examples are available at Examples.pdf.

Load the Required Libraries.

# Tidyverse and other support libraries
library(tidyverse)
library(lubridate)
library(sf)
library(units)

# Load stoichUtilities
library(stoichUtilities)

Working with STOICH Data

# Create a variable to store the user's home directory
basePath <- path.expand("~")

# Load the STOICH data (assumed to be in a directory named "data" inside the home directory)
stoichData <- stoichUtilities::loadSTOICH(dataPath=file.path(basePath, "data"))

# Filter the STOICH data
stoichFiltered <- stoichUtilities::filterSTOICH(dataTables=stoichData, var="State", val="FL", condition="Equal")

# Match organism stoichiometry data with water chemsitry data for samples that weren't taken at the exact same time
stoichPaired <- stoichUtilities::locateDataPairsSTOICH(stoichData, timeDiff=2, timeUnits="weeks", distance=5, pairMethod="Min Time", ignoreExisting=TRUE)

# Join all the tables into one large wide table
stoichTable <- stoichUtilities::joinSTOICH(stoichPaired)

Documentation

You can access documentation for any function using the help command.

help(loadSTOICH)