An R Package to synchronize fish and invertebrate datasets from federal sources in the United States • finsyncR

finsyncR (fish and invertebrate synchronizer in R) is a data management package that integrates and processes national-level aquatic biomonitoring datasets in the U.S., with a focus on fish and macroinvertebrates sampled in rivers and streams. The package streamlines the process of retrieving and harmonizing these data, improving access to cleaned data and making the application these data straightforward for researchers. The sources of data for this package are the United States Environmental Protection Agency’s (USEPA) National Aquatic Resource Surveys (NARS), namely the National River and Streams Assessment (NRSA), and United States Geological Survey’s (USGS) BioData.

Installation

You can install the released version of finsyncR from GitHub with:

library(devtools)

devtools::install_github("USEPA/finsyncR",
                         build_vignette = TRUE)

Example of function and output

This is a basic example which shows you how to use the getFishData() function to generate the fish dataset for both USGS and USEPA datasets. Users should be aware that the getFishData() and getInvertData() functions take a fair amount of time to run. While running, the functions print statements updating the user on the progress of the workflow.

library(finsyncR)

Fish <- getFishData(taxonLevel = "Species",
                    agency = c("USGS","EPA"))

head(Fish)[,c(1:5,36,90,400)]
#>   Agency      SampleID ProjectLabel    SiteNumber      StudyReachName
#> 1   USGS BDB-000025003     MMSD Eco USGS-04086600 04086600-A-MMSD Eco
#> 2   USGS BDB-000025011     MMSD Eco USGS-04087030 04087030-A-MMSD Eco
#> 3   USGS BDB-000025015     MMSD Eco USGS-04087070 04087070-A-MMSD Eco
#> 4   USGS BDB-000025019     MMSD Eco USGS-04087088 04087088-A-MMSD Eco
#> 5   USGS BDB-000025023     MMSD Eco USGS-04087119 04087119-A-MMSD Eco
#> 6   USGS BDB-000025034     MMSD Eco USGS-04087204 04087204-A-MMSD Eco
#>   Percina.caprodes Notropis.telescopus Notropis.amabilis
#> 1                0                   0                 0
#> 2                0                   0                 0
#> 3                0                   0                 0
#> 4                0                   0                 0
#> 5                0                   0                 0
#> 6                0                   0                 0

Possible uses of finsyncR

Potential uses of the finsyncR package and resulting data include studies of changes in fish and macroinvertebrate communities across space and time and the environmental causes and ecological consequences of those changes. The table below provides example code to generate macroinvertebrates and fish datasets given hypothetical research questions.

Research question	Output dataset requested	Macroinvertebrates	Fish
How does density/CPUE change through time across EPA and USGS samples?	Density/CPUE at sites for lowest taxonomic resolution, with shared taxa only, removing hybrid fish, and excluding boatable streams/rivers	`getInvertData(dataType = "density",` `taxonLevel = "Genus",` `taxonFix = "lump",` `agency = c("USGS","EPA"),` `lifestage = FALSE,` `rarefy = FALSE,` `sharedTaxa = TRUE,` `seed = 0,` `boatableStreams = FALSE)`	`getFishData(dataType = "density",` `taxonLevel = "Species",` `agency = c("USGS","EPA"),` `standardize = "CPUE",` `hybrids = FALSE,` `sharedTaxa = TRUE,` `boatableStreams = FALSE)`
How does the composition of families differ between EPA and USGS samples?	Occurrence at sites for Family resolution, with all taxa, rarefying macroinvertebrate counts to 300 individuals, and excluding boatable streams/rivers	`getInvertData(dataType = "occur",` `taxonLevel = "Family",` `taxonFix = "none",` `agency = c("USGS","EPA"),` `lifestage = FALSE,` `rarefy = TRUE,` `rarefyCount = 300,` `sharedTaxa = FALSE,` `seed = 1,` `boatableStreams = FALSE)`	`getFishData(dataType = "occur",` `taxonLevel = "Family",` `agency = c("USGS","EPA"),` `standardize = "none",` `sharedTaxa = FALSE,` `boatableStreams = FALSE)`
What are spatial occupancy patterns within the Upper-Midwest Ecoregion using the randomized sampling design of the EPA NARS?	Occurrence for lowest taxonomic resolution for only EPA samples, then filtered to the UWM Ecoregion	`getInvertData(dataType = "occur",` `taxonLevel = "Family",` `taxonFix = "none",` `agency = c("EPA"),` `rarefy = TRUE,` `rarefyCount = 500,` `sharedTaxa = FALSE,` `seed = 1,` `boatableStreams = TRUE) %>%` `filter(NARS_Ecoregion == "UMW")`	`getFishData(dataType = "occur",` `taxonLevel = "Family",` `agency = c("EPA"),` `standardize = "none",` `sharedTaxa = FALSE,` `boatableStreams = TRUE) %>%` `filter(NARS_Ecoregion == "UMW")`

Metadata

Metadata can be found in the “Metadata” vignette: vignette("Metadata", package = "finsyncR").

Using finsyncR

A compendium on the correct use of the finsyncR package and its output datasets can be found in the “Getting Started” vignette: vignette("GettingStarted", package = "finsyncR").

Contributing to finsyncR

For information on how to contribute to the finsyncR package, please see the contributing to finsyncR document.

Packages of interest

Other R packages of potential interest to finsyncR users include StreamCatTools and TADA. StreamCatTools is an R package for accessing StreamCat data via the StreamCat API and for working with site data in conjunction with StreamCat and NHDPlus. TADA is an R package can be used to compile and evaluate Water Quality Portal (WQP) data for samples collected from surface water monitoring sites on streams and lakes.

Open-Source Code Policy

Effective August 8, 2016, the OMB Mandate: M-16-21; Federal Source Code Policy: Achieving Efficiency, Transparency, and Innovation through Reusable and Open Source Software applies to new custom-developed code created or procured by EPA consistent with the scope and applicability requirements of Office of Management and Budget’s (OMB’s) Federal Source Code Policy. In general, it states that all new custom-developed code by Federal Agencies should be made available and reusable as open-source code.

The EPA specific implementation of OMB Mandate M-16-21 is addressed in the System Life Cycle Management Procedure. EPA has chosen to use GitHub as its version control system as well as its inventory of open-source code projects. EPA uses GitHub to inventory its custom-developed, open-source code and generate the necessary metadata file that is then posted to code.gov for broad reuse in compliance with OMB Mandate M-16-21.

If you have any questions or want to read more, check out the EPA Open Source Project Repo and EPA’s Interim Open Source Code Guidance.

License

All contributions to this project will be released under the CCO-1.0 license file dedication. By submitting a pull request or issue, you are agreeing to comply with this waiver of copyright interest.

Disclaimer

The approaches provided in this package concerning the way the BioData and NRSA data are treated are not necessarily the same as the approaches used in other USGS and EPA publications or national assessments. So, replicating analyses using the processed data in this package may not produce identical results. For instance, multimetric indices produced from NRSA data from finsyncR may not match multimetric indices in EPA national assessment reports.

The methods developed to join the EPA and USGS datasets described in this manuscript have not been designed with the intent of adding other fish and macroinvertebrate datasets. So, the appropriateness of these methods cannot be guaranteed for other datasets.

The United States Environmental Protection Agency (EPA) GitHub project code is provided on an “as is” basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.