baytrends

Long Term Water Quality Trend Analysis

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.

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Description file content

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.
Author
Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Version
1.1.0
Date
2019-03-14
Maintainer
Erik Leppo
Depends
R (>= 3.2.0), lubridate, mgcv
License
GPL-3
LazyData
TRUE
RoxygenNote
6.1.1
Encoding
UTF-8
Suggests
devtools, fitdistrplus, imputeTS, knitr, nlme, pander, readxl, rmarkdown, sessioninfo, testthat
Imports
XML, dataRetrieval, digest, gdata, memoise, methods, plyr, survival, zCompositions
URL
VignetteBuilder
knitr
Collate
'a1_smwrQW_qw-class.R' 'a2_smwrQW_lcens-class.R' 'a3_smwrQW_mcens-class.R' 'analysisOrganizeData.R' 'appendDateFeatures.R' 'as.lcens.R' 'as.mcens.R' 'as.qw.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' 'gamTables.R' 'gamTest.r' 'getUSGSflow.R' 'headers2.R' 'imputeCensored.R' 'initializeResults.r' 'layerAggregation.R' 'loadData.R' 'loadExcel.R' 'loadModels.R' 'loadModelsResid.R' 'mergeFlow.R' 'mergeSalinity.R' 'qw.export.R' 'qw.import.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_group2row.R' 'smwrBase_importRDB.R' 'smwrBase_isLike.R' 'smwrBase_na2miss.R' 'smwrBase_z%cn%.R' 'smwrGraphs_addCaption.R' 'smwrGraphs_colorPlot.R' 'smwrGraphs_datePretty.R' 'smwrGraphs_lineWt.R' 'smwrGraphs_linearPretty.R' 'smwrGraphs_month.USGS.R' 'smwrGraphs_namePretty.R' 'smwrGraphs_numericData.R' 'smwrGraphs_refLine.R' 'smwrGraphs_renderPretty.R' 'smwrGraphs_setColor.R' 'smwrGraphs_setExplan.R' 'smwrGraphs_setGD.R' 'smwrGraphs_setMargin.R' 'smwrGraphs_setMultiPlot.R' 'smwrGraphs_setPage.R' 'smwrGraphs_setPlot.R' 'smwrGraphs_strip.blanks.R' 'smwrGraphs_timePlot.R' 'smwrGraphs_timePretty.R' 'smwrGraphs_transData.R' 'smwrGraphs_xyPlot.R' 'smwrQW_censoring.R' 'smwrQW_is.na.R' 'smwrQW_mcenKM.R' 'smwrQW_mcenMLE.R' 'smwrQW_mcenROS.R' 'smwrQW_mdlMLE.R' 'smwrQW_mdlROS.R' 'smwrQW_pcodeNWISqw.R' 'smwrQW_x_Arith-censored.R' 'smwrQW_x_Math-censored.R' 'smwrQW_x_View.r' 'smwrQW_x_add.R' 'smwrQW_x_as.character.R' 'smwrQW_x_as.data.frame.R' 'smwrQW_x_as.double.R' 'smwrQW_x_c.R' 'smwrQW_x_censorlevels.R' 'smwrQW_x_censpp.R' 'smwrQW_x_convert2qw.R' 'smwrQW_x_convertFqw.R' 'smwrQW_x_dlimit.R' 'smwrQW_x_format.R' 'smwrQW_x_importNWISqw.R' 'smwrQW_x_importQW.R' 'smwrQW_x_imputeLessThans.R' 'smwrQW_x_length.R' 'smwrQW_x_makeColNames.R' 'smwrQW_x_mdlKM.R' 'smwrQW_x_mdlKMstats.R' 'smwrQW_x_mean.qw.R' 'smwrQW_x_meanStats.R' 'smwrQW_x_medianStats.R' 'smwrQW_x_print.censMCT.R' 'smwrQW_x_print.censQuantile.R' 'smwrQW_x_print.censReg.R' 'smwrQW_x_print.censStats.R' 'smwrQW_x_print.summary.censReg.R' 'smwrQW_x_printData.R' 'smwrQW_x_quantile.R' 'smwrQW_x_qw2mcens.R' 'smwrQW_x_qwCoalesce.R' 'smwrQW_x_ratio.R' 'smwrQW_x_rbindQW.R' 'smwrQW_x_readNWQLdl.R' 'smwrQW_x_residuals.censReg.R' 'smwrQW_x_sdlFill.R' 'smwrQW_x_show-censored.R' 'smwrQW_x_sort.censored.R' 'smwrQW_x_splitQual.R' 'smwrQW_x_str.R' 'smwrQW_x_subset.R' 'smwrQW_x_summary.R' 'smwrQW_x_summary.censReg.R' 'smwrQW_x_vcov.censReg.R' 'smwrQW_x_z%eq%.R' 'smwrStats_rmse.R' 'smwrStats_vif.R' 'supportFunctions.R' 'zzz.R'
NeedsCompilation
no
Packaged
2019-03-14 17:50:56 UTC; Erik.Leppo
Repository
CRAN
Date/Publication
2019-03-14 18:23:27 UTC

install.packages('baytrends')

1.1.0

8 days ago

https://github.com/tetratech/baytrends

Erik Leppo

GPL-3

Depends on

R (>= 3.2.0), lubridate, mgcv

Imports

XML, dataRetrieval, digest, gdata, memoise, methods, plyr, survival, zCompositions

Suggests

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

Discussions