... | @@ -5,16 +5,7 @@ Exploration and Graphics for RivEr Trends (`EGRET`): |
... | @@ -5,16 +5,7 @@ Exploration and Graphics for RivEr Trends (`EGRET`): |
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An R-package for the analysis of long-term changes in water quality and streamflow,
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An R-package for the analysis of long-term changes in water quality and streamflow,
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including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS)
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including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS)
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Overview of `EGRET`: The following are 4 major features of `EGRET`.
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Evaluating long-term changes in river conditions (water quality and discharge) is an important use of hydrologic data. To carry out such evaluations, the hydrologist needs tools to facilitate several key steps in the process: acquiring the data records from a variety of sources, structuring it in ways that facilitate the analysis, routines that will process the data to extract information about changes that may be happening, and graphical techniques that can display findings about change. A pair of tightly linked R packages, called `dataRetrieval` and `EGRET` (Exploration and Graphics for RivEr Trends), have been developed for carrying out each of these steps in an integrated manner. They are designed to accept easily data from three sources: U.S. Geological Survey hydrologic data, Water Quality Portal Data (currently including U.S. Environmental Protection Agency (EPA) STORET data, and USDA STEWARDS data), and user-supplied flat files. The `dataRetrieval` package not only serves as a "front end" to the `EGRET` package, it can also be used to easily download many types of hydrologic data and organize it in ways that facilitate many other hydrologic applications. The `EGRET` package has components oriented towards the description of long-term changes in streamflow statistics (high flow, average flow, and low flow) as well as changes in water quality. For the water-quality analysis, it uses Weighted Regressions on Time, Discharge and Season (WRTDS) to describe long-term trends in both concentration and flux. `EGRET` also creates a wide range of graphical presentations of the water-quality data and of the WRTDS results. This report serves as a user guide to these two R packages, providing detailed guidance on installation and use of the software, documentation of the analysis methods used, as well as guidance on some of the kinds of questions and approaches that the software can facilitate.
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1. It is designed to obtain its water quality sample data, streamflow data, and metadata directly from the USGS NWIS (U.S. Geological Survey National Water Information System), but it allows for user-supplied text files as inputs. The program is designed to ingest the data directly into R and structure them into file structures suited to the analysis.
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2. It has all of the existing WRTDS functionality - computing concentrations, fluxes, flow normalized versions of those, trends in those and graphics to show results and to explore the behavior of the data (by season, by flow class...). Many graph and table outputs are possible and all are clearly labeled and suitable for presentation or publication. It is designed for both batch and interactive processing. It is very much oriented to graphics and should be thought of as an exploratory tool. It is intended for use with data sets of about 200 or more samples, over a time period of about 20 or more years. Some testing with smaller data sets has been done, and no significant problems have been identified in cases with sample sizes slightly larger than 100 but extensive testing with smaller data sets has not taken place yet.
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3. It has additional statistics and graphics to help evaluate the possibility that flux estimates may be biased (it is known that in certain cases, regression-based methods can produce severely biased flux estimates). It can also accept results from other estimation methods like LOADEST and produce the same types of graphics and statistics for them (this part is not yet documented).
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4. It has a streamflow history component, not related to water quality, that is not a part of WRTDS, but uses some similar concepts and shares some of the basic software and data structures. This component, called flowHistory provides a variety of table and graphical outputs looking only at flow statistics (like annual mean, annual 7-day low flow, annual 1-day maximum, or seasonal versions of these) all based on time-series smoothing. It is designed to be used in long-term studies of streamflow change (associated with climate or land use or water use change) and works best for daily streamflow data sets of 50 years or longer. It is put together with the WRTDS method because it uses the same data retrieval infrastructure as WRTDS and the same data structure.
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Package Installation
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Package Installation
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