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 1.087.3.
library(LAGOSNE)
lagosne_get(dest_folder = lagos_path())Usage
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)#> [1] "county" "county.chag" "county.conn"
#> [4] "county.lulc" "edu" "edu.chag"
#> [7] "edu.conn" "edu.lulc" "hu4"
#> [10] "hu4.chag" "hu4.conn" "hu4.lulc"
#> [13] "hu8" "hu8.chag" "hu8.conn"
#> [16] "hu8.lulc" "hu12" "hu12.chag"
#> [19] "hu12.conn" "hu12.lulc" "iws"
#> [22] "iws.conn" "iws.lulc" "state"
#> [25] "state.chag" "state.conn" "state.lulc"
#> [28] "buffer100m" "buffer100m.lulc" "buffer500m"
#> [31] "buffer500m.conn" "buffer500m.lulc" "lakes.geo"
#> [34] "epi_nutr" "lakes_limno" "lagos_source_program"
#> [37] "locus"Preview a table
head(dt$state)
#> state state_name state_zoneid state_lat state_long state_pct_in_nwi
#> 1 IA Iowa State_13 42.07456 -93.49983 100
#> 2 MA Massachusetts State_2 42.25762 -71.81240 100
#> state_ha_in_nwi state_ha
#> 1 14573561 14573561
#> 2 2101262 2101262Preview a specific lake
lake_info(name = "Pine Lake", state = "Iowa")
# or using a lagoslakeid
# lake_info(lagoslakeid = 4389)#> lagoslakeid nhdid nhd_lat nhd_long lagosname1 meandepth
#> 1 4510 155845265 42.37833 -93.05967 UPPER PINE LAKE 2.21
#> meandepthsource maxdepth maxdepthsource legacyid gnis_name lake_area_ha
#> 1 IA_CHEMISTRY 4.88 IA_CHEMISTRY 122 Pine Lake 36.07355
#> lake_perim_meters nhd_fcode nhd_ftype iws_zoneid hu4_zoneid hu6_zoneid
#> 1 5671.001 39004 390 IWS_51040 HU4_57 HU6_78
#> hu8_zoneid hu12_zoneid edu_zoneid county_zoneid state_zoneid elevation_m
#> 1 HU8_400 HU12_3008 EDU_23 County_275 State_13 300.23
#> state state_name state_lat state_long state_pct_in_nwi state_ha_in_nwi
#> 1 IA Iowa 42.07456 -93.49983 100 14573561
#> state_ha lakeconnection iws_ha
#> 1 14573561 DR_Stream 3593.379Read table metadata
help.search("datasets", package = "LAGOSNE")| Package | Topic | Title |
|---|---|---|
| LAGOSNE | chag | Climate, Hydrology, Atmospheric, and Geologic (CHAG) Datasets |
| LAGOSNE | classifications | LAGOSNE Spatial Classifications Metadata |
| LAGOSNE | conn | Connectivity Datasets |
| LAGOSNE | epi_nutr | Epilimnion Water Quality Data |
| LAGOSNE | lagos_source_program | LAGOSNE sources |
| LAGOSNE | lagoslakes | Lake Geospatial Metadata |
| LAGOSNE | lakes_limno | Metadata for Lakes with Water Quality |
| LAGOSNE | locus | Metadata for all lakes > 1ha |
| LAGOSNE | lulc | Land Use Land Cover (LULC) Data Frames |
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))
#> tp tn
#> 1 29.00 NA
#> 2 136.56 3521.7
head(lagosne_select(table = "iws.lulc", vars = c("iws_nlcd2011_pct_95"), dt = dt))
#> iws_nlcd2011_pct_95
#> 1 0.04
# categories
head(lagosne_select(table = "locus", categories = "id", dt = dt))
#> lagoslakeid iws_zoneid hu4_zoneid hu6_zoneid hu8_zoneid hu12_zoneid
#> 1 3201 <NA> HU4_11 HU6_12 HU8_47 HU12_16312
#> 2 4510 IWS_51040 HU4_57 HU6_78 HU8_400 HU12_3008
#> edu_zoneid county_zoneid state_zoneid
#> 1 EDU_27 County_331 State_2
#> 2 EDU_23 County_275 State_13
head(lagosne_select(table = "epi_nutr", categories = "waterquality", dt = dt))
#> chla colora colort dkn doc nh4 no2 no2no3 srp tdn tdp tkn tn toc ton
#> 1 16.60 60 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 30.64 NA NA NA NA NA NA 1619.6 NA NA NA NA 3521.7 NA NA
#> tp secchi
#> 1 29.00 1.70
#> 2 136.56 0.65
head(lagosne_select(table = "hu4.chag", categories = "deposition", dt = dt)[,1:4])
#> hu4_dep_no3_1985_min hu4_dep_no3_1985_max hu4_dep_no3_1985_mean
#> 1 7.2171 10.0448 7.9366
#> 2 9.5538 21.1791 15.5290
#> hu4_dep_no3_1985_std
#> 1 0.3868
#> 2 2.2330
# mix of specific variables and categories
head(lagosne_select(table = "epi_nutr", vars = "programname",
categories = c("id", "waterquality"), dt = dt))
#> programname lagoslakeid chla colora colort dkn doc nh4 no2 no2no3 srp tdn
#> 1 MA_DEP 3201 16.60 60 NA NA NA NA NA NA NA NA
#> 2 IA_CHEM 4510 30.64 NA NA NA NA NA NA 1619.6 NA NA
#> tdp tkn tn toc ton tp secchi eventida10873
#> 1 NA NA NA NA NA 29.00 1.70 45773
#> 2 NA NA 3521.7 NA NA 136.56 0.65 64904Published 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