Package: baytrends
Type: Package
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized 
    Additive Modeling (GAM) approach. The model development includes selecting a 
    GAM structure to describe nonlinear seasonally-varying changes over time, 
    incorporation of hydrologic variability via either a river flow or salinity, 
    the use of an intervention to deal with method or laboratory changes 
    suspected to impact data values, and representation of left- and 
    interval-censored data. The approach has been applied to water quality data 
    in the Chesapeake Bay, a major estuary on the east coast of the United 
    States to provide insights to a range of management- and research-focused 
    questions.  Methodology described in Murphy (2019) 
    <doi:10.1016/j.envsoft.2019.03.027>.
Version: 2.0.14
Authors@R: c(
  person(given  = "Rebecca",
         family = "Murphy",
         role   = "aut",
         comment = c(ORCID = "0000-0003-3391-1823")),
  person(given  = "Elgin",
         family = "Perry",
         role   = "aut"),
  person(given  = "Jennifer",
         family = "Keisman",
         role   = "aut",
         comment = c(ORCID = "0000-0001-6808-9193")),
  person(given  = "Jon",
         family = "Harcum",
         role   = "aut",
         comment = c(ORCID = "0000-0001-5910-5243")),
  person(given  = c("Erik", "W"),
         family = "Leppo",
         role   = c("aut", "cre"),
         email  = "Erik.Leppo@tetratech.com",
         comment = c(ORCID = "0000-0001-8026-7474")))
Depends: R (>= 4.1.0)
License: GPL-3
LazyData: TRUE
RoxygenNote: 7.3.3
Encoding: UTF-8
Imports: dataRetrieval, digest, dplyr, fitdistrplus, grDevices,
        lubridate, knitr, memoise, mgcv, pander, plyr, readxl,
        sessioninfo, survival, tibble, tidyr
Suggests: devtools, imputeTS, markdown, nlme, rmarkdown, testthat
URL: https://github.com/tetratech/baytrends
BugReports: https://github.com/tetratech/baytrends/issues
VignetteBuilder: knitr
Collate: analysisOrganizeData.R appendDateFeatures.R baytrends.R
        checkRange.R chkParameter.R closeOut.R createResiduals.R data.R
        detrended.flow.R detrended.salinity.R expectMaxFunctions.r
        findFile.R flwAveragePred.R fmtPval.R gamDiff.R gamPlotCalc.r
        gamPlotDisp.R gamPlotDispSeason.R gamTables.R gamTest.r
        gamTestSeason.r getUSGSflow.R headers2.R imputeCensored.R
        initializeResults.r layerAggregation.R loadData.R loadExcel.R
        loadModels.R loadModelsResid.R makeSurvDF.R mergeFlow.R
        mergeSalinity.R reAttDF.R saveDF.R seasAdjflow2.R selectData.R
        smwrBase_baseDay.R smwrBase_baseDay2decimal.R
        smwrBase_dectime.R smwrBase_dectime2Date.R
        smwrBase_eventProcessing.R smwrBase_fillMissing.R
        smwrBase_na2miss.R supportFunctions.R unSurv.R gdata_nobs.R
        zzz.R
NeedsCompilation: no
Packaged: 2026-02-24 17:12:26 UTC; Erik.Leppo
Author: Rebecca Murphy [aut] (ORCID: <https://orcid.org/0000-0003-3391-1823>),
  Elgin Perry [aut],
  Jennifer Keisman [aut] (ORCID: <https://orcid.org/0000-0001-6808-9193>),
  Jon Harcum [aut] (ORCID: <https://orcid.org/0000-0001-5910-5243>),
  Erik W Leppo [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8026-7474>)
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Repository: CRAN
Date/Publication: 2026-02-24 18:10:02 UTC
Built: R 4.7.0; ; 2026-06-12 03:48:27 UTC; windows
