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.
Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
devtools, fitdistrplus, imputeTS, knitr, nlme, pander,
readxl, rmarkdown, testthat
XML, dataRetrieval, digest, gdata, memoise, methods, plyr,
survival, zCompositions

devtools, fitdistrplus, imputeTS, knitr, nlme, pander,
readxl, rmarkdown, sessioninfo, testthat

devtools, fitdistrplus, grDevices, imputeTS, knitr, nlme,
pander, readxl, rmarkdown, sessioninfo, testthat

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>.
devtools, dplyr, fitdistrplus, grDevices, imputeTS, knitr,
nlme, pander, readxl, rmarkdown, sessioninfo, testthat
XML, dataRetrieval, digest, memoise, mgcv, plyr, survival
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