LAGOSNE
Interface to the Lake Multi-Scaled Geospatial and Temporal Database
Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database < https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.
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.
Installation
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)
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 returned by rappdirs::user_data_dir(). Data only needs to be downloaded one time per version per machine. The latest version of the LAGOSNE dataset is 1.087.1.
library(LAGOSNE)lagosne_get("1.087.1")
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.
dt <- lagosne_load(version = "1.087.1")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"
Preview a table
head(dt$county)#> county_state county_name county_ha_in_nwi county_ha county_zoneid#> 1 CT Fairfield County 167421.8 168044.3 County_1#> 2 IL Ford County 125912.3 125912.3 County_10#> 3 IL Stark County 74682.0 74682.0 County_100#> 4 IL Stephenson County 146269.3 146269.3 County_101#> 5 IL Tazewell County 170204.0 170204.0 County_102#> 6 IL Vermilion County 233543.6 233543.6 County_103#> county_pct_in_nwi county_lat conty_long#> 1 100 41.27225 -73.38940#> 2 100 40.59720 -88.22340#> 3 100 41.09336 -89.79749#> 4 100 42.35175 -89.66246#> 5 100 40.50731 -89.51343#> 6 100 40.18342 -87.73293
Read table metadata
help.search("datasets", package = "LAGOSNE")
| 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_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 |
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 LAGOS:::keyword_partial_key()). See here for a comprehensive tutorial on generic data.frame subsetting.
# specific variableshead(lagosne_select(table = "epi_nutr", vars = c("tp", "tn")))#> tp tn#> 1 30 NA#> 2 10 NA#> 3 5 NA#> 4 9 NA#> 5 5 NA#> 6 27 NAhead(lagosne_select(table = "iws.lulc", vars = c("iws_nlcd2011_pct_95")))#> iws_nlcd2011_pct_95#> 1 2.77#> 2 2.97#> 3 0.27#> 4 0.00#> 5 0.00#> 6 0.00# categorieshead(lagosne_select(table = "epi_nutr", categories = "waterquality"))#> chla colora colort dkn doc nh4 no2 no2no3 srp tdn tdp tkn tn toc ton tp#> 1 NA NA NA NA NA 20 NA 20 NA NA NA NA NA NA NA 30#> 2 NA NA NA NA NA 20 NA 20 NA NA NA NA NA NA NA 10#> 3 3.9 NA 15 NA NA NA NA NA NA NA NA NA NA NA NA 5#> 4 4.8 NA 15 NA NA NA NA NA NA NA NA NA NA NA NA 9#> 5 2.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5#> 6 6.6 15 NA NA NA NA NA NA NA NA NA NA NA NA NA 27#> secchi#> 1 NA#> 2 NA#> 3 6.5#> 4 5.8#> 5 6.1#> 6 2.4head(lagosne_select(table = "county.chag", categories = "hydrology"))#> county_baseflowindex_min county_baseflowindex_max#> 1 45 55#> 2 30 35#> 3 28 35#> 4 34 66#> 5 22 40#> 6 28 37#> county_baseflowindex_mean county_baseflowindex_std#> 1 48.3755 1.8683#> 2 32.6106 1.4480#> 3 31.5548 1.3772#> 4 53.1078 4.6081#> 5 32.4689 4.1342#> 6 34.4157 1.1100head(lagosne_select(table = "hu4.chag", categories = "deposition")[,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#> 3 15.5222 22.8936 19.6234#> 4 8.5831 31.3832 17.2809#> 5 15.6669 24.2653 19.0625#> 6 12.6550 26.8946 18.1940#> hu4_dep_no3_1985_std#> 1 0.3868#> 2 2.2330#> 3 1.3634#> 4 3.2954#> 5 1.5500#> 6 1.8389# mix of specific variables and categorieshead(lagosne_select(table = "epi_nutr", vars = "lagoslakeid", categories = c("waterquality")))#> lagoslakeid chla colora colort dkn doc nh4 no2 no2no3 srp tdn tdp tkn tn#> 1 2 NA NA NA NA NA 20 NA 20 NA NA NA NA NA#> 2 2 NA NA NA NA NA 20 NA 20 NA NA NA NA NA#> 3 2 3.9 NA 15 NA NA NA NA NA NA NA NA NA NA#> 4 2 4.8 NA 15 NA NA NA NA NA NA NA NA NA NA#> 5 2 2.1 NA NA NA NA NA NA NA NA NA NA NA NA#> 6 3 6.6 15 NA NA NA NA NA NA NA NA NA NA NA#> toc ton tp secchi#> 1 NA NA 30 NA#> 2 NA NA 10 NA#> 3 NA NA 5 6.5#> 4 NA NA 9 5.8#> 5 NA NA 5 6.1#> 6 NA NA 27 2.4
Published LAGOSNE subsets
# Oliver et al. 2015lagos_get_oliver_2015()
dt <- lagos_load_oliver_2015()head(dt)#> lagoslakeid nhdid hu4id lat_decimal long_decimal area zmaxobs#> 1 1 50524769 202 42.54739 -73.17425 114.95 2.7#> 2 2 123632625 108 42.18409 -73.04728 24.87 6.1#> 3 3 50524793 202 42.53081 -73.19155 75.41 1.8#> 4 4 135695054 109 42.45435 -71.14079 9.26 5.2#> 5 5 135693974 109 42.60405 -70.82267 14.00 3.4#> 6 6 122373608 110 42.14209 -72.11992 80.29 13.7#> zmaxpredict#> 1 10.6#> 2 7.1#> 3 8.6#> 4 3.7#> 5 5.4#> 6 10.1
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 1.054.1):
# install devtools if not found# install.packages("devtools")devtools::install_github("cont-limno/LAGOSNE", ref = "v1.054.1")
Data
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")
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, and SK Oliver. 2017. LAGOSNE: Interface to the Lake Multi-Scaled Geospatial and Temporal Database. https://github.com/cont-limno/LAGOSNE.
News
LAGOSNE 1.1.0
MINOR IMPROVEMENTS
- Streamline console output and avoid errors during non-interactive use (#59)
BUG FIXES
- Switch data source URLs to enable downloads with more restrictive firewalls (#60)
LAGOSNE 1.0.0
- Package name and functions changed to LAGOSNE
- Initial CRAN submission