knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-" )
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).
# 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)
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())
library(LAGOSNE)
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)
query_lagos_names("secchi")
query_lagos_names("secchi", dt = dt)
head(dt$state)
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) )
loadNamespace("printr")
help.search("datasets", package = "LAGOSNE")
unloadNamespace("printr")
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))
# 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())
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")
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.