Skip to content

Latest commit

 

History

History
275 lines (225 loc) · 11.9 KB

README.md

File metadata and controls

275 lines (225 loc) · 11.9 KB
Raw

Project Status: Active - The project has reached a stable, usable state and is being actively developed. R-CMD-check CRAN_Status_Badge CRAN RStudio mirror downloads

NSF-1065786 NSF-1638679 NSF-1065649 NSF-1065818 NSF-1638554

LAGOSNE

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 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"          "lagos_source_program"
#> [37] "locus"

Locate tables containing a variable

query_lagos_names("secchi")
#> [1] "epi_nutr"

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  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 3593.379

Read 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         64904

Published 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