Commit fedaa281 authored by Fisher, Jason C.'s avatar Fisher, Jason C.
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tidy README.md files

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The contents of this folder include an [R script](build-datasets.R) used to build datasets in the inldata package, and a subset of the data read during the build process. The R script retrieves and parses data sets from local and remote sources. Access to the internet is required to download data from the following remote sources:
- National Elevation Dataset ([NED](https://catalog.data.gov/dataset/usgs-national-elevation-dataset-ned)) data from the U.S. Geological Survey (USGS) rockyftp server at ftp://rockyftp.cr.usgs.gov.
- Spatial data from the 2019 [TIGER/Line Geodatabase](https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-geodatabase-file.html) (contains spatial extracts from the U.S. Census Bureau's MAF/TIGER database) at ftp://ftp2.census.gov/geo/tiger/TIGER2019.
- National Hydrography Dataset ([NHD](https://www.usgs.gov/core-science-systems/ngp/national-hydrography/national-hydrography-dataset)) data from the USGS NHD file geodatabase at https://s3.amazonaws.com/edap-nhdplus.
- National Elevation Dataset ([NED]) data from the U.S. Geological Survey (USGS) rockyftp server at <ftp://rockyftp.cr.usgs.gov>.
- Spatial data from the 2019 [TIGER/Line Geodatabase] (contains spatial extracts from the U.S. Census Bureau's MAF/TIGER database) at <ftp://ftp2.census.gov/geo/tiger/TIGER2019>.
- National Hydrography Dataset ([NHD]) data from the USGS NHD file geodatabase at <https://s3.amazonaws.com/edap-nhdplus>.
Each of the package datasets represents a snapshot of the data at a specified point in time. While geospatial datasets may very little over time (such as the boundary of the Idaho National Laboratory), other datasets continue grow as new data becomes available (such as the water-quality data collected from wells). Rebuilding the datasets using this R script does not ensure that the most recent data versions will be obtained. For example, water-quality data is manually accessed using a procedure described in the [./qwdata/README.md](data-raw/qwdata/README.md) file. And URL's of remote sources may change over time and require updating within the R script. The take-home message from running the R script is that remote sources need to be scrutinized and run times may vary substantially based on the speed of your internet connection and server delays. Lastly, any changes in the datasets need to be reflected in its help documentation by editing the appropriate R-source file located in the ../R folder.
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| +-- siteids.txt (site numbers)
+-- README.md
+-- background.tsv (background concentrations)
+-- benchmarks.csv (benchmark concentrations, see https://water.usgs.gov/water-resources/hbsl/)
+-- benchmarks.csv (benchmark concentrations, see <https://water.usgs.gov/water-resources/hbsl/>)
+-- build-datasets.R (script for building datasets)
+-- counting-error.tsv (radioactivity counting error)
+-- detection-limites.tsv (laboratory detection limits)
......@@ -52,7 +52,7 @@ Each of the package datasets represents a snapshot of the data at a specified po
## System Requirements
The R script requires that the `7z` executable is on your path. Install the [7-Zip](https://www.7-zip.org/) program if the executable is not found.
The R script requires that the `7z` executable is on your path. Install the [7-Zip] program if the executable is not found.
## Build Datasets
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setwd("~/inldata/data-raw")
source("build-datasets.R")
```
<!-- Embedded References -->
[NED]: https://catalog.data.gov/dataset/usgs-national-elevation-dataset-ned
[TIGER/Line Geodatabase]: https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-geodatabase-file.html
[NHD]: https://www.usgs.gov/core-science-systems/ngp/national-hydrography/national-hydrography-dataset
[7-Zip]: https://www.7-zip.org/
\ No newline at end of file
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The National Water Information System (NWIS) is a distributed database for the storage and retrieval of water data collected at sites in the United States (U.S. Geological Survey, 2019). The Water-Quality System (QWDATA) is a subsystem of NWIS that stores water-quality data. This document provides instructions for accessing data collected through activities at well sites in the in the U.S. Geological Survey (USGS) water-quality aquifer monitoring network, Idaho National Laboratory and vicinity, Idaho. Instructions may be entered interactively through a series of menus, or scripted and executed from the command line. Access to the QWDATA software is limited to U.S. Geological Survey employees&mdash;contact your database administrator or IT specialist for details.
QWDATA software is run remotely using a secure shell (SSH) client (such as [PuTTY](http://www.chiark.greenend.org.uk/~sgtatham/putty/)). Software input files are summarized in the following table:
QWDATA software is run remotely using a secure shell (SSH) client (such as [PuTTY]). Software input files are summarized in the following table:
| File name | Data description |
|:---------------------------------|:-----------------|
| [alphacodes.txt](alphacodes.txt) | List of alpha parameter codes used in QWDATA. These codes identify the fields (columns) to include in the output data table (such as date, time, and parameter value). See the QWDATA user's manual ([Dupr&eacute; and others, 2013](#references), appendix A, table 13, p. 227--231) for code descriptions. |
| [pcodes.txt](pcodes.txt) | List of USGS parameter codesto be tabled. These codes are used to identify the constituent and the units of measure. The codes are documented in the "[NWIS Parameter Code Dictionary](https://nwis.waterdata.usgs.gov/usa/nwis/pmcodes)". |
| [pcodes.txt](pcodes.txt) | List of USGS parameter codesto be tabled. These codes are used to identify the constituent and the units of measure. The codes are documented in the "[NWIS Parameter Code Dictionary]". |
| [siteids.txt](siteids.txt) | List of USGS site information to be tabled. Specified in a fixed-column format: (1-5) agency code; (6-20) left-justified site number. |
| [commands.txt](commands.txt) | List of QWDATA menu commands, see [Interactive](#interactive) instructions for command descriptions. This file is only applicable for the [Scripted](#scripted) instructions. |
......@@ -134,8 +134,13 @@ Exit the software by entering `99`.
## References
Dupr&eacute;, D.H, Scott, J.C., Clark, M.L., Canova, M.G, and Stoker, Y.E., 2013, User's manual for the National Water Information System of the U.S. Geological Survey: Water-Quality System, Version 5.0: U.S. Geological Survey Open-File Report 2013–1054, 730 p., http://pubs.usgs.gov/of/2013/1054. Supercedes Open-File Report 2006–1145.
Dupr&eacute;, D.H, Scott, J.C., Clark, M.L., Canova, M.G, and Stoker, Y.E., 2013, User's manual for the National Water Information System of the U.S. Geological Survey: Water-Quality System, Version 5.0: U.S. Geological Survey Open-File Report 2013–1054, 730 p., <https://pubs.usgs.gov/of/2013/1054/>. Supercedes Open-File Report 2006–1145.
U.S. Geological Survey, 2019, National Water Information System—Water-Quality System data retrieval program, accessed June 11, 2019.
U.S. Geological Survey, 2019, National Water Information System—web services, accessed June 11, 2019, at https://doi.org/10.5066/F7P55KJN.
U.S. Geological Survey, 2019, National Water Information System—web services, accessed June 11, 2019, at <https://doi.org/10.5066/F7P55KJN>.
<!-- Embedded References -->
[PuTTY]: https://www.chiark.greenend.org.uk/~sgtatham/putty/
[NWIS Parameter Code Dictionary]: https://nwis.waterdata.usgs.gov/usa/nwis/pmcodes
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