In cont-limno/LAGOS: Interface to the Lake Multi-Scaled Geospatial and Temporal Database

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LAGOSNE

The LAGOSNE package provides an R interface to download LAGOS-NE data, store this data locally, and perform a variety of filtering and subsetting operations.

LAGOS-NE contains data for 51,101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2,600-12,000 lakes depending on the variable (see Soranno et al. 2017 below).

Installation

# install stable version from CRAN
install.packages("LAGOSNE")

# install development version from Github
# install devtools if not found - install.packages("devtools")
# devtools::install_github("cont-limno/LAGOSNE", dependencies = TRUE)

Data

The lagosne_get function downloads the LAGOSNE files corresponding to the specified version from the EDI data repository. Files are stored in a temporary directory before being "compiled" to an R data format in the location specified by the dest_folder argument. Recommended setting is lagos_path(). Data only needs to be downloaded one time per version per machine. Each LAGOSNE module has a unique version number. However, only the limno module has been dynamically updated. Therefore the LAGOSNE R package uses the limno module version number to check-out specific datasets. The latest version of the LAGOSNE dataset is r LAGOSNE::lagosne_version().

library(LAGOSNE)
lagosne_get(dest_folder = lagos_path())

Usage

Load Package

library(LAGOSNE)

Load data

The lagosne_load function returns a named list of data.frame objects. Use the names() function to see a list of available data frames names(dt).

dt <- lagosne_load()
names(dt)

dt <- readRDS(system.file("lagos_test_subset.rds", package = "LAGOSNE"))
names(dt)

Locate tables containing a variable

query_lagos_names("secchi")

query_lagos_names("secchi", dt = dt)

Preview a table

head(dt$state)

Preview a specific lake

lake_info(name = "Pine Lake", state = "Iowa")
# or using a lagoslakeid
# lake_info(lagoslakeid = 4389)

suppressWarnings(
  lake_info(name = "Pine Lake", state = "Iowa", dt = dt)
  )

Read table metadata

loadNamespace("printr")

help.search("datasets", package = "LAGOSNE")

unloadNamespace("printr")

Select data

lagosne_select is a convenience function whose primary purpose is to provide users with the ability to select subsets of LAGOS tables that correspond to specific keywords (see LAGOSNE:::keyword_partial_key() and LAGOSNE:::keyword_full_key()). See here for a comprehensive tutorial on generic data.frame subsetting.

# specific variables
head(lagosne_select(table = "epi_nutr", vars = c("tp", "tn"), dt = dt))
head(lagosne_select(table = "iws.lulc", vars = c("iws_nlcd2011_pct_95"), dt = dt))

# categories
head(lagosne_select(table = "locus", categories = "id", dt = dt))
head(lagosne_select(table = "epi_nutr", categories = "waterquality", dt = dt))
head(lagosne_select(table = "hu4.chag", categories = "deposition", dt = dt)[,1:4])

# mix of specific variables and categories
head(lagosne_select(table = "epi_nutr", vars = "programname", 
                    categories = c("id", "waterquality"), dt = dt))

Published LAGOSNE subsets

# Oliver et al. 2015
lagos_get_oliver_2015()
head(lagos_load_oliver_2015())

# Collins et al. 2017
lagos_get_collins_2017()
head(lagos_load_collins_2017())

Legacy Versions

R Package

To install versions of LAGOSNE compatible with older versions of LAGOS-NE run the following command where ref is set to the desired version (in the example, it is version 1.087.1):

# install devtools if not found
# install.packages("devtools")
devtools::install_github("cont-limno/LAGOSNE", ref = "v1.087.1")

References

Oliver, SK, PA Soranno, CE Fergus, T Wagner, K Webster, CE Scott, LA Winslow, J Downing, and EH Stanley. 2015. “LAGOS - Predicted and Observed Maximum Depth Values for Lakes in a 17-State Region of the U.S.” https://dx.doi.org/10.6073/pasta/edc06bbae6db80e801b6e52253f2ea09.

Soranno, P.A., Bacon, L.C., Beauchene, M., Bednar, K.E., Bissell, E.G., Boudreau, C.K., Boyer, M.G., Bremigan, M.T., Carpenter, S.R., Carr, J.W. Cheruvelil, K.S., and ... , 2017. LAGOS-NE: A multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes. GigaScience, https://doi.org/10.1093/gigascience/gix101

Soranno, PA, EG Bissell, KS Cheruvelil, ST Christel, SM Collins, CE Fergus, CT Filstrup, et al. 2015. “Building a Multi-Scaled Geospatial Temporal Ecology Database from Disparate Data Sources: Fostering Open Science and Data Reuse.” Gigascience 4 (1). https://dx.doi.org/10.1186/s13742-015-0067-4.

Stachelek J., Oliver S. 2017. LAGOSNE: Interface to the Lake Multi-scaled Geospatial and Temporal Database. R package version 1.1.0. https://cran.r-project.org/package=LAGOSNE

Soranno P, Cheruvelil K. 2017. LAGOS-NE-LOCUS v1.01: a module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925–2013. Environmental Data Initiative. https://doi.org/10.6073/PASTA/0C23A789232AB4F92107E26F70A7D8EF

Soranno P, Cheruvelil K. 2019. LAGOS-NE-LIMNO v1.087.3: a module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925–2013. Environmental Data Initiative. https://doi.org/10.6073/PASTA/08C6F9311929F4874B01BCC64EB3B2D7.

Soranno P, Cheruvelil K. 2017. LAGOS-NE-GEO v1.05: a module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925–2013. Environmental Data Initiative. https://doi.org/10.6073/PASTA/16F4BDAA9607C845C0B261A580730A7A

cont-limno/LAGOS documentation built on July 8, 2023, 2:34 a.m.