The LAGOSNE package provides an R interface to download LAGOS-NE data from remote databases, store this data locally, and perform a variety of filtering and subsetting operations.
# 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", update_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 returned by rappdirs::user_data_dir(). 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 1.087.1.
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).
#> [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" "secchi"
#> [37] "lagos_source_program" "locus"#> [1] "epi_nutr" "secchi"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 2101262lake_info(name = "Pine Lake", state = "Iowa")
# or using a lagoslakeid
# lake_info(lagoslakeid = 4389)#> lagoslakeid nhdid lagosname1 meandepth meandepthsource maxdepth
#> 2 4510 155845265 UPPER PINE LAKE 2.21 IA_CHEMISTRY 4.88
#> maxdepthsource legacyid gnis_name nhd_lat nhd_long lake_area_ha
#> 2 IA_CHEMISTRY 122 Pine Lake 42.37833 -93.05967 36.07355
#> lake_perim_meters nhd_fcode nhd_ftype iws_zoneid hu4_zoneid hu6_zoneid
#> 2 5671.001 39004 390 IWS_51040 HU4_57 HU6_78
#> hu8_zoneid hu12_zoneid edu_zoneid county_zoneid state_zoneid elevation_m
#> 2 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
#> 2 IA Iowa 42.07456 -93.49983 100 14573561
#> state_ha lakeconnection iws_ha
#> 2 14573561 DR_Stream 3593.379| Package | Topic | Title |
|---|---|---|
| LAGOSNE | chag | CHAG Datasets |
| LAGOSNE | classifications | LAGOSNE Spatial Classifications Metadata |
| LAGOSNE | conn | Connectivity Datasets |
| LAGOSNE | epi_nutr | Epilimnion Water Quality Data |
| LAGOSNE | lagoslakes | Lake Geospatial Metadata |
| LAGOSNE | lakes_limno | Metadata for Lakes with Water Quality |
| LAGOSNE | lg_extent | LAGOSNE extent |
| LAGOSNE | lg_subset | LAGOSNE subset |
| LAGOSNE | locus | Metadata for all lakes > 1ha |
| LAGOSNE | lulc | Land Use Land Cover (LULC) Data Frames |
| LAGOSNE | secchi | Secchi (Water Clarity) Data |
| LAGOSNE | source | LAGOSNE sources |
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 24.00 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
#> 1 62.00 40 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
#> ton tp secchi
#> 1 NA 24.00 2.10
#> 2 NA 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
#> 1 MA_DEP_CHEM 3201 62.00 40 NA NA NA NA NA NA NA
#> 2 IA_CHEMISTRY 4510 30.64 NA NA NA NA NA NA 1619.6 NA
#> tdn tdp tkn tn toc ton tp secchi eventida1087
#> 1 NA NA NA NA NA NA 24.00 2.10 70686
#> 2 NA NA NA 3521.7 NA NA 136.56 0.65 100949To 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 1.054.1):
# install devtools if not found
# install.packages("devtools")
devtools::install_github("cont-limno/LAGOSNE", ref = "v1.054.1")Until older datasets have been made available in a public repository, LAGOSNE users will need to use the lagosne_compile function (not lagosne_get) and supply the path to their local locus, limno and geo data folders. Replace the paths in the example below with the path to each respective folder on your system. Most people will have access to these folders through Dropbox. For example, the limno_folder would be assigned to something like: C:/Users/FWL/Dropbox/CSI_LAGOS-exports/LAGOS-NE-LIMNO-EXPORT
library(LAGOSNE)
lagosne_compile("1.054.1", format = "rds",
limno_folder = "~/Downloads/LAGOS-NE-LIMNO-EXPORT",
geo_folder = "~/Downloads/LAGOS-NE-GEO-EXPORT",
locus_folder = "~/Downloads/LAGOS-NE-LOCUS-EXPORT")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, and SK Oliver. 2017. LAGOSNE: Interface to the Lake Multi-Scaled Geospatial and Temporal Database. https://github.com/cont-limno/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. http://doi.org/ckpj
Soranno P, Cheruvelil K. 2017. LAGOS-NE-LIMNO v1.087.1: 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. http://doi.org/ckpk.
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. http://doi.org/ckpm