nesR

Code to rescue (scrape) data from the National Eutrophication Survey archival PDF.

Installation

Prerequites

Until magick can handle local adaptive thresholding. This package requires you to be able to call the imagemagick convert command with system().

You can install nesR from github with:

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

Usage

Load package

library(nesR)

Get data

nes_file <- system.file("extdata/national-eutrophication-survey_477.PDF", 
                        package = "nesR")
res <- nes_get(nes_file, 89)
parse_nes(res)
#> Warning in read_ocr_dt(strsplit(nut_txt, " ")[[5]], section_name = "nuts"):
#> The following nuts positions may have bad OCR: 3
#>    state      name                county storet_code   lake_type
#> 1 NEVADA LAKE MEAD CLARK. NY; MOHAVE. Az        3201 IMPOUNDMENT
#>   drainage_area surface_area mean_depth total_inflow retention_time
#> 1      434601.8         <NA>       59.1       377.34            3.5
#>   alkalinity conductivity sechhi    tp   po4  tin   tn p_pnt_source_muni
#> 1        136          815    5.9 0.016 0.005 0.34 0.55            322055
#>   p_pnt_source_industrial p_pnt_source_septic p_nonpnt_source p_total
#> 1                    <NA>                <NA>              10 3370770
#>   n_pnt_source_muni n_pnt_source_industrial n_pnt_source_septic
#> 1              <NA>              6426644444                 375
#>   n_nonpnt_source  n_total p_total_out p_percent_retention
#> 1            <NA> 26880405      247325                  93
#>   p_surface_area_loading n_total_out n_percent_retention
#> 1                   6.23        <NA>                  55
#>   n_surface_area_loading
#> 1                   45.3

Build database

As written, building the NES database requires GNU Make and the ability to run R commands using the Rscript command-line utility (aka doesn't work on Windows).

make PDFSOURCE=474 all
make PDFSOURCE=475 all
make PDFSOURCE=476 all
make PDFSOURCE=477 all

References

Brett, M. T., and M. M. Benjamin. 2007. A review and reassessment of lake phosphorus retention and the nutrient loading concept. Freshwater Biology.

Reckhow, K. H. 1988. Empirical models for trophic state in southeastern US lakes and reservoirs.