create_toxEval: Load and check toxEval data

In USGS-R/toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Load and check toxEval data

Description

This function is used to load a data file for analysis in the form of a single Excel file. The Excel file should include 3 mandatory sheets named "Data", "Chemicals", and "Sites". Additionally there are 2 optional sheets: "Exclude" and "Benchmarks". This function creates a data frame for each sheet, perform basic checks on the data to assure that required columns are included for each sheet

Usage

create_toxEval(excel_file_path, ...)

Arguments

excel_file_path	Path to Excel file that contains at least 3 sheets: Data, Chemicals, and Sites, and could optionally contain Exclude and Benchmarks.
...	data frames to override data within the original x list.

Details

Required columns in the Data sheet include "CAS", "SiteID", "Value", and "Sample Date". The "Value" column includes concentration measurements in units of \mug/L. "Sample Date" can be either a date or date/time or an integer. Additional columns may be included for user purposes, but will not be used in toxEval.

Required columns in the Chemical sheet include "CAS", "Class". "CAS" values in this sheet must exactly match corresponding "CAS" values in the Data sheet. The "Class" designation allows data to be grouped in a user-specified way. For example, in a data set of multiple pesticides, it may be valuable to explore differences and similarities to of insecticides, herbicides and fungicides. Additional columns may be included for user purposes, but will not be used in toxEval.

Required columns in the Sites sheet includes "SiteID", "Short Name", and for the Shiny application "dec_lat","dec_lon". Values in the "SiteID" column in this sheet exactly match corresponding values in the "SiteID" column in the Data sheet. Additional columns may be included for user purposes, but will not be used in toxEval.

When using the optional sheet Exclude, columns required include "CAS" and "endPoint". These are used to exclude particular chemicals (via CAS), ToxCast endpoints (via endPoint), or a unique chemical/endpoint combination. Additional columns may be included for user purposes, but will not be used in toxEval.

When using the optional sheet Benchmarks, columns required include "CAS", "endPoint","ACC_value" and "chnm". This sheet is used to over-ride the functions using endpoints from the ToxCast database, allowing the user to import endpoint information from other sources. It could also be useful for reproducing results in the future (for example, if after ToxCast updates, analysis with an older version of ToxCast may be reproduced by including the selected ToxCast endpoint database in this sheet. Additional columns may be included for user purposes, but will not be used in toxEval.

For more information, see the "Prepare Data" vignette: vignette("PrepareData", package = "toxEval").

All remaining toxEval functions use data from via the list that is returned from this function.

Value

The object returned from this function contains a list of between three and five data frames. The minimum data frames returned are chem_data (containing at least the columns: "CAS", "SiteID", "Value", "Sample Date"), chem_info (containing at least the columns: "CAS", "Class"), and chem_site (containing at least the columns: "SiteID", "Short Name". For the Shiny app, "dec_lat" and "dec_lon" are also required). The optional data frames are exclusions (containing at least the columns: "CAS" and "endPoint"), and benchmarks (containing at least the columns: "CAS", "endPoint", "ACC_value" and "chnm")

Examples

path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"
excel_file_path <- file.path(path_to_tox, file_name)
tox_list <- create_toxEval(excel_file_path)

USGS-R/toxEval documentation built on Feb. 9, 2024, 6:24 p.m.