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To subscribe to an email list concerning updates to these R packages, please send a request to egret_comments@usgs.gov.
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Download and Package Installation
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Package Installation
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---------------------------------
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### Downloads:
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* The latest version of EGRET can be downloaded with this link:
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[EGRET_1.2.3](https://github.com/USGS-R/EGRET/raw/packageBuilds/EGRET_1.2.3.tar.gz)
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* The latest version of dataRetrieval can be downloaded with this link:
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[dataRetrieval_1.2.1](https://github.com/USGS-R/EGRET/raw/packageBuilds/dataRetrieval_1.2.1.tar.gz)
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* [EGRET User Guide](https://github.com/USGS-CIDA/WRTDS/raw/master/EGRET manual_4.doc) (Word Document)
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* [WRTDS NWQMC course slides](https://github.com/USGS-CIDA/WRTDS/raw/master/Documentation/WRTDS NWQMC course.pdf) (pdf)
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* [EGRET flowHistory presentation](https://github.com/USGS-CIDA/WRTDS/raw/master/Documentation/EGRET flowHistory presentation.pdf) (pdf)
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### Installation:
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While the EGRET and dataRetreival packages are in development (and not on CRAN), the following packages must first be manually installed:
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* zoo
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* survival
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* plyr
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* fields
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* spam - (spam is actually a legitimate package - SPArse Matrix)
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* spam - (spam is a legitimate package: SPArse Matrix)
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Once EGRET is sent to the CRAN repository, these packages will be automatically imported. Packages only need to be installed once.
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To install the EGRET package:
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Include the full path to EGRET_1.2.3.tar.gz to install the package (here is a Windows example, note the direction of the slashes -> /, this is backwards from how Windows typically defines a path ):
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install.packages("zoo")
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install.packages("survival")
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install.packages("plyr")
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install.packages("fields")
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install.packages("spam")
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install.packages("C:/RPackages/Statistics/EGRET_1.2.3.tar.gz", repos=NULL, type="source")
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A Mac example:
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install.packages("/Users/userA/RPackages/Statistic/EGRET_1.2.3.tar.gz", repos=NULL, type="source")
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The EGRET package requires the methods, zoo, survival, and fields packages, all available from CRAN.
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Similarly, to install the dataRetrieval package, use the following commands:
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install.packages("zoo")
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install.packages("C:/RPackages/Statistics/dataRetrieval_1.2.0.tar.gz", repos=NULL, type="source")
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The dataRetrieval package requires the zoo package available from CRAN.
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install.packages("zoo","survival","methods","fields","spam")
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install.packages("dataRetrieval", repos="http://usgs-r.github.com/EGRET/", type="source")
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install.packages("EGRET", repos="http://usgs-r.github.com/EGRET/", type="source")
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### Note on updating versions:
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Some users have found it necessary to delete the package folders before installing newer versions of either dataRetrieval or EGRET. If you are experiencing an issue after updating a package, trying deleting the package folder, the default location for Windows is something like this:
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/Users/ldecicco/Library/R/2.15/library/dataRetrieval
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Then, re-install the package using the directions above. Moving to CRAN should solve this problem.
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Stable releases are archived on the packageBuild branch of this repository:
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[EGRET_1.2.3](https://github.com/USGS-R/EGRET/raw/packageBuilds/EGRET_1.2.3.tar.gz)
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[dataRetrieval_1.2.1](https://github.com/USGS-R/dataRetrieval/raw/packageBuilds/dataRetrieval_1.2.1.tar.gz)
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Background Information
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----------------------
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... | ... | @@ -100,7 +73,13 @@ The second is an application to nitrate data for 8 monitoring sites on the Missi |
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[Mississippi River](http://pubs.acs.org/doi/abs/10.1021/es201221s)
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The manual available here assumes that the user understands the concepts underlying WRTDS. Thus, reading at least the first of these papers is necessary to understanding the manual.
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The manual assumes that the user understands the concepts underlying WRTDS. Thus, reading at least the first of these papers is necessary to understanding the manual.
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* [EGRET User Guide](https://github.com/USGS-R/EGRET/raw/Documentation/EGRET%2Bmanual_4.doc) (Word Document)
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* [WRTDS NWQMC course slides](https://github.com/USGS-R/EGRET/raw/Documentation/WRTDS+NWQMC+course.pdf) (pdf)
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* [EGRET flowHistory presentation](https://github.com/USGS-R/EGRET/raw/Documentation/EGRET+flowHistory+presentation.pdf) (pdf)
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Version updates
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####EGRET
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* Version 1.2.3 February 21, 2013
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* New estDailyFromSurfaces function utilizing "fields" package, written by Jeffrey Chanat. Greatly increases the speed of computations of the daily results. Two additional R packages are needed: fields and spam
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* Improved documentation, especially example functions.
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* runSurvReg modified to include the option of a very wide seasonal window (windowS), which has the effect of eliminating the influence of the seasonal weights.
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* Progress indicators modified to be more informative.
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* Fixed a calculation bug in function plotLogFluxPred.
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* Version 1.2.1 June 8, 2012
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* Differs only from 1.1.3 in two respects. It adds four new functions to the flowHistory capability and makes one bug fix to WRTDS. The four new flow History functions are: plot15 (makes an array of 15 plots for a given site - a matrix of 3 flow statistics (7-day min, mean, and 1-day max) versus 5 periods of analysis (annual, fall, winter, spring, and summer), plotSDLogQ (makes a plot of the running standard deviation of the Log Discharge versus time), plotFour (makes a set of four graphs: 1-day max, mean, 7-day min, and running standard deviation of the logs), and plotQTimeDaily (a way to plot discharge versus time, setup particularly to show flows above some threshold discharge). The bug fix in WRTDS made no changes to calculations, it just prevents a crash in a situation where the user has shortened the length of the daily record.
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