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This package EGRETci implements a set of approaches to the analysis of uncertainty associated with WRTDS trend analysis as implemented in the EGRET package.
See: http://authors.elsevier.com/sd/article/S1364815215300220 for more details.
The EGRETci package is designed to carry out three specific types of tasks.
Evaluate a water quality trend over a specific span of years and
produce a variety of tabular results. This is done with a short workflow
involving the functions: trendSetUp and wBT.
The results come in three forms: 1) console output, which shows the
bootstrap replicate process as it is underway and the results when it
has finished, 2) a text file that shows the results of the bootstrap
analysis (a subset of what is included in the console output), and 3) a
set of outputs in a named list called eBoot. The contents of eBoot are
described below.
Plot histograms of values for the trend magnitudes, expressed in
percent change over the specified period, for flow-normalized
concentration and flow-normalized flux. This is done with the function
plotHistogramTrend. It depends on outputs contained in
eBoot. Note that there are a number of custom outputs similar to these
histograms that can be developed from the contents of eBoot (for
example, what is the likelihood that the flow normalized flux decreased
by more than 2000 kg/year over the trend period). Such analyses would
require a small amount of script writing by the user.
Plot confidence bands around the computed trends in
flow-normalized concentration and flow-normalized flux. This is done
using a function called ciCalculations and then, using the
output from that function running two functions that produce the
confidence band graphics for concentration and flux respectively
(plotConcHistBoot, and
plotFluxHistBoot).
citation(package = "EGRETci")
To cite EGRETci in publications, please use:
Hirsch, R.M., Archfield, S.A., De Cicco, L.A., "A bootstrap method for
estimating uncertainty of water quality trends", Environmental
Modelling & Software, Vol 73, Nov 2015, p 148-166. doi:
j.envsoft.2015.07.017
A BibTeX entry for LaTeX users is
@Article{,
author = {Robert M. Hirsch and Stacey A. Archfield and Laura A. {De Cicco}},
title = {A bootstrap method for estimating uncertainty of water quality trends},
journal = {Journal of Environmental Modelling and Software},
year = {2015},
}
Please consider reporting bugs and asking questions on the Issues page: https://github.com/USGS-R/EGRETci/issues
Follow @USGS_R on Twitter for updates on USGS R
packages:
Please email questions, comments, and feedback to: egret_comments@usgs.gov
Additionally, to subscribe to an email list concerning updates to these R packages, please send a request to egret_comments@usgs.gov.
We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the code of conduct for more information.
When using the WRTDS model (and corresponding confidence
intervals), it is important to be able to reproduce the results in the
future. The following version of R and package dependencies were used
most recently to pass the embedded tests within this package. There is
no guarantee of reproducible results using future versions of R or
updated versions of package dependencies; however, we will make diligent
efforts to test and update future modeling environments.
devtools::session_info()
Session info ----------------------------------------------------------------------
setting value
version R version 3.4.1 (2017-06-30)
system x86_64, mingw32
ui RStudio (1.0.143)
language (EN)
collate English_United States.1252
tz America/Chicago
date 2017-07-27
Packages --------------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
base * 3.4.1 2017-06-30 local
bindr 0.1 2016-11-13 CRAN (R 3.4.0)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)
binom 1.1-1 2014-01-02 CRAN (R 3.4.0)
codetools 0.2-15 2016-10-05 CRAN (R 3.4.1)
compiler 3.4.1 2017-06-30 local
curl 2.8.1 2017-07-21 CRAN (R 3.4.1)
dataRetrieval 2.7.2 2017-05-23 CRAN (R 3.4.1)
datasets * 3.4.1 2017-06-30 local
devtools 1.13.2 2017-06-02 CRAN (R 3.4.1)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
dotCall64 0.9-04 2016-10-07 CRAN (R 3.4.1)
dplyr 0.7.2 2017-07-20 CRAN (R 3.4.1)
EGRET 2.6.0 2017-07-27 CRAN (R 3.4.1)
EGRETci * 1.0.5 2017-07-24 CRAN (R 3.4.1)
fields 9.0 2017-06-06 CRAN (R 3.4.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.4.0)
glue 1.1.1 2017-06-21 CRAN (R 3.4.0)
graphics * 3.4.1 2017-06-30 local
grDevices * 3.4.1 2017-06-30 local
grid 3.4.1 2017-06-30 local
hms 0.3 2016-11-22 CRAN (R 3.4.0)
httr 1.2.1 2016-07-03 CRAN (R 3.3.1)
iterators 1.0.8 2015-10-13 CRAN (R 3.4.0)
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.1)
lubridate 1.6.0 2016-09-13 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
maps 3.2.0 2017-06-08 CRAN (R 3.4.0)
Matrix 1.2-10 2017-05-03 CRAN (R 3.4.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.1 2017-06-30 local
parallel 3.4.1 2017-06-30 local
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.1)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
readr 1.1.1 2017-05-16 CRAN (R 3.4.0)
reshape2 1.4.2 2016-10-22 CRAN (R 3.4.0)
rlang 0.1.1 2017-05-18 CRAN (R 3.4.1)
spam 2.1-1 2017-07-03 CRAN (R 3.4.1)
splines 3.4.1 2017-06-30 local
stats * 3.4.1 2017-06-30 local
stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
stringr 1.2.0 2017-02-18 CRAN (R 3.4.0)
survival 2.41-3 2017-04-04 CRAN (R 3.4.0)
tibble 1.3.3 2017-05-28 CRAN (R 3.4.0)
tools 3.4.1 2017-06-30 local
utils * 3.4.1 2017-06-30 local
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
xml2 1.1.1 2017-01-24 CRAN (R 3.4.0)
This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.