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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# National Eutrophication Survey
[](https://doi.org/10.5063/F1CZ35HF)
This respository contains a digitally transcribed copy ([nes_data.csv](https://github.com/ReproducibleQM/NES/raw/master/nes_data.csv)) of the National Eutrophication Survey (NES) dataset. The original data can be found in the `archival_pdfs` folder or by searching: https://www.epa.gov/nscep
## Locations
```{r eval=FALSE, echo=FALSE}
library(magick)
points <- image_read("06_images/points.jpeg")
image_write(image_trim(points),
"06_images/points_trim.jpeg")
```
## Data
<!-- Do not edit this table without first updating METADATA.md -->
| variable name | description |units|
|---------------|--------------------------|-----|
|pdf|pdf identifier (474 - 477)| integer|
|pagenum | page number of the pdf|integer|
|storet_code | identifier which links measurement to coordinate locations|character|
|state | state where the water body resides |character|
|name | name of the water body|character|
|county | county where the water body resides |character|
|lake_type | natural or impoundment |character|
|drainage_area | the total drainage area | square kilometers |
|surface_area | the area of the water surface|sq km|
|mean_depth | the volume of the water body divided by the surface area in square meters| meters|
|total_inflow | the mean of the inflows of all tributaries and the immediate drainage | cubic meters per second|
|retention_time | a mean value determined by dividing the lake volume, in cubic meters, by the mean annual outflow in cubic meters per unit cof time| years or days|
|retention_time_units | the units of time for each retention entry|years or days|
|alkalinity | alkalinity|milligrams per liter|
|conductivity | conductivity|microohms|
|secchi | secchi|meters|
|tp | total phosphorus| milligrams per liter|
|po4 | orthophosphate| milligrams per liter|
|tin | total inorganic nitrogen| milligrams per liter|
|tn | total nitrogen| milligrams per liter|
|p_pnt_source_muni | municipal point source phosphorus loading| kilograms per year|
|p_pnt_source_industrial | industrial point source phosphorus loading| kilograms per year|
|p_pnt_source_septic | septic point source phosphorus loading| kilograms per year|
|p_nonpnt_source | nonpoint source phosphorus loading| kilograms per year|
|p_total | total phosphorus loading| kilograms per year|
|n_pnt_source_muni | municipal point source nitrogen loading| kilograms per year|
|n_pnt_source_industrial | industrial point source nitrogen loading| kilograms per year|
|n_pnt_source_septic | septic point source nitrogen loading| kilograms per year|
|n_nonpnt_source | nonpoint source nitrogen loading| kilograms per year|
|n_total | total nitrogen loading| kilograms per year|
|p_total_out | total phosphorus outlet load| kilograms per year|
|p_percent_retention | percent phosphorus retention| percent|
|p_surface_area_loading | phosphorus surface area loading| grams per square meter per year|
|n_total_out | total nitrogen outlet load| kilograms per year|
|n_percent_retention | percent nitrogen retention|percent|
|n_surface_area_loading | nitrogen surface area loading| grams per square meter per year|
|lat | latitude|decimal degrees|
|long | longitude|decimal degrees|
## Workflow
1. Use the [nesR](https://github.com/jsta/nesR) package to generate the files in [/02_raw_data](/02_raw_data).
2. Hand check the files in [/02_raw_data/merged_data](/02_raw_data/merged_data) against the pdfs in [/01_archival_pdfs](/01_archival_pdfs).
3. Combine files with [05_analysis_scripts/PDF_Merge.R](05_analysis_scripts/PDF_Merge.R).
## Contributing
We've combed the data to try and find all the transciption errors but it's difficult to catch them all. If you find any errors please open an [issue](https://github.com/ReproducibleQM/NES/issues/) or submit a pull request against the files in [/03_qa_data](/03_qa_data).
## References
Stachelek, J., Ford, C., Kincaid, D., King, K., Miller, H. and Nagelkirk, R., 2018. The National Eutrophication Survey: lake characteristics and historical nutrient concentrations. Earth System Science Data, 10(1), pp.81-86. (https://doi.org/10.5194/essd-10-81-2018)
Stachelek, J. (2017). nesR: Scrape Data from National Eutrophication Survey archival PDFs. R package version 0.1. (https://github.com/jsta/nesR) (https://dx.doi.org/10.5281/zenodo.400258)
Stachelek, J. (2017). nesRdata: National Eutrophication Survey Data Package. R package version 0.1. https://github.com/jsta/nesRdata