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., De Cicco, L.A., Archfield, S.A., Murphy, J.C., 2023,
#> Exploration and Graphics for RivEr Trends (EGRET) Uncertainty and
#> Confidence Intervals, version 2.0.5, doi:10.5066/P9CC9JEX
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> author = {Robert M. Hirsch and Laura A. {De Cicco} and Stacey A. Archfield and Jennifer C. Murphy},
#> title = {EGRETci},
#> publisher = {U.S. Geological Survey},
#> year = {2023},
#> url = {https://pubs.usgs.gov/tm/04/a10/},
#> }
Please consider reporting bugs and asking questions on the Issues page: https://github.com/DOI-USGS/EGRETci/issues
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.
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 (2022-10-31 ucrt)
#> os Windows 10 x64 (build 19044)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/Chicago
#> date 2023-03-06
#> pandoc 2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.2)
#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.2)
#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
#> htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.2)
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#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.2)
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#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
#> xfun 0.37 2023-01-31 [1] CRAN (R 4.2.2)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.2)
#>
#> [1] C:/Users/ldecicco/Documents/R/win-library/4.2
#> [2] C:/Program Files/R/R-4.2.2/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). 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. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.
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