R interface to the National Lakes Assessment
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
docs
man
vignettes
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
README.Rmd
README.md
cran-comments.md
nlaR.Rproj

README.md

nlaR

lifecycle CRAN status Travis-CI Build Status

The goal of nlaR is to provide an R interface to the National Lakes Assessment data. At this point it serves either the 2007 or 2012 data (see examples below).

Installation

You can install nlaR from Github with:

# install.packages("devtools")
devtools::install_github("jsta/nlaR")

Usage

Load package

library(nlaR)

Retrieve data from EPA Website

Turn on automated data storage at the location returned by rappdirs::user_data_dir()

nla_get(2012, use_rappdirs = TRUE)

Load data from local machine

dt <- nla_load(2012)

View NLA tables

names(dt)
#>  [1] "algaltoxins"    "atrazine"       "bentcond"       "bentmet"       
#>  [5] "benttaxa_wide"  "chla_wide"      "phytocnt"       "phytotaxa_wide"
#>  [9] "secchi"         "topsedhg"       "waterchem_wide" "wide_benthic"  
#> [13] "wide_phab"      "wide_phabmet"   "wide_profile"   "wide_siteinfo" 
#> [17] "zoopcond"       "zoopmets"       "zooptaxa_wide"
head(dt$phytocnt)
#>   PUBLICATION_DATE  UID SAMPLE_TYPE TAXA_ID        PARAMETER   RESULT
#> 1        2/12/2014 6160        PHYL    4075        BIOVOLUME 219.9113
#> 2        2/12/2014 6160        PHYL    4075          DENSITY       25
#> 3        2/12/2014 6160        PHYL    4075   INITIAL_VOLUME     1080
#> 4        2/12/2014 6160        PHYL    4095 SUBSAMPLE_VOLUME      200
#> 5        2/12/2014 6160        PHYL    4095   VOLUME_COUNTED       10
#> 6        2/12/2014 6160        PHYL    4095       TOTAL_AREA 283.5287

More Examples

See vignettes.

References

  • National Lakes Assessment EPA page

  • Water quality metadata

  • Stoddard, J.L., Van Sickle, J., Herlihy, A.T., Brahney, J., Paulsen, S., Peck, D.V., Mitchell, R. and Pollard, A.I., 2016. Continental-scale increase in lake and stream phosphorus: Are oligotrophic systems disappearing in the United States?. Environmental Science & Technology, 50(7), pp.3409-3415. 10.1021/acs.est.5b05950