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.

# 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)

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. 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.

library(LAGOSNE)
lagosne_get()

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)

#>  [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"

Locate tables containing a variable

query_lagos_names("secchi")

#> [1] "epi_nutr" "secchi"

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  2101262

Preview a specific lake

lake_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

Read table metadata

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

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  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       100949

Published LAGOSNE subsets

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

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.

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