baytrends v1.1.0

Monthly downloads

by Erik Leppo View Source

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.

Readme

baytrends

The baytrends package was developed to enable users to evaluate long-term trends in the Chesapeake Bay 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. This approach, which is fully transferable to other systems, allows for Chesapeake Bay water quality data to be evaluated in a statistically rigorous, yet flexible way to provide insights to a range of management- and research-focused questions.

Functions in baytrends

Name	Description
as.qw	Water-quality Data Conversion
createResiduals	Calculate GAM residuals
as.lcens	Left-censored Data Conversion
c.lcens	Combine Values into a Vector
dataCensored	Chesapeake Bay Program Monitoring Data, 1985-2016
.ExpLNiCens	Expectation maximization function: Log-normal case, i censured
censorLevels	Describe Censoring
censoring	Describe Censoring
baseDay	Base Day
convert2qw	Water-Quality Data
convertFqw	Water-Quality Data
.ExpNlCens	Expectation maximization function: Normal case, left censured
.ExpNiCens	Expectation maximization function: Normal case, i censured
closeOut	Document Processing Time and Other Session Time
.H1	Print out 1st level header (shortened pandoc.header)
censpp	Probability Plotting Positions
colorPlot	Plot Data
.H2	Print out 2nd level header (shortened pandoc.header)
.ExpLNmCens	Expectation maximization function: Log-normal case, Cens
.gamPlotCalc	plots data and gam fit vs. time
.ExpLNlCens	Expectation maximization function: Log-normal case, left censured
.initializeResults	#### Initialize stat.gam.result and chng.gam.result
as.double.qw	Numeric Representations
.T	Print out table title (customization of pandoc.emphasis and pandoc.strong )
baseDay2decimal	Base Day
.chkParameter	Reduce dataframe and parameter list based on user selected parameterFilt
.V	Print out text (blended pandoc.emphasis, .verbatim, and .strong)
.fmtPval	Format pvalues
.gamANOVA	Prepare ANOVA table for GAM analysis
.simCensored	Fit normal or log normal distribution; simulation in censored data provided by Elgin Perry phi.left and phi.right are distribution function, e.g., pnorm(q=10,mean=10,sd=1) =0.5 phi.sim is a uniform random number between phi.left and phi.right sim is imputed value
.layerAggregation	Aggregate data layers
.findFile	Find Recent File Information
.mergeFlow	merge flow variable into analysis data frame and update iSpec with variable name
.ExpLNrCens	Expectation maximization function: Log-normal case, right censured
.F	Print out figure title (customization of pandoc.emphasis and pandoc.strong )
baytrends	baytrends: Long Term Water Quality Trend Analysis
datePretty	Pretty Axis
dectime	Decimal Time
detrended.salinity	Create Seasonally Detrended Salinty Data Set
.H3	Print out 3rd level header (shortened pandoc.header)
dlimit	Impute Detection Limits
as.mcens	Multiply-censored Data Conversion
mdlKMstats	Estimate Statistics
format.lcens	Encode in a Common Format
mdlMLE	Estimate Statistics
gamDiff	Compute an estimate of difference based on GAM results
.vTable	Print out character vector table in wrapped mode
isCharLike	Test whether an object can be treated in a particular way
layerLukup	Layer List
makeColNames	Column Names
dectime2Date	Date Conversion
detrended.flow	Create Seasonally Detrended Flow Data Set
.ExpNmCens	Expectation maximization function: Normal case
.ExpNrCens	Expectation maximization function: Normal case, right censured
getUSGSflow	Retrieve USGS daily flow data in a wide format
group2row	Restructure Data
.H5	Print out 5th level header (shortened pandoc.header)
mean.lcens	Arithmetic Mean
.H4	Print out 4th level header (shortened pandoc.header)
.P	Paragraph (customization of pandoc.p)
.gamCoeff	Prepare table of coefficients for GAM analysis
.gamDiffPORtbl	Compute and present report on percent different for log-transformed data
eventNum	Event Processing
.H	Print out header (shortened pandoc.header)
print.censReg	Print Results
median.lcens	Median Value
print.censStats	Print Results
fillMissing	Fill Missing Values
mcenKM	Estimate Statistics
.appendDateFeatures	Appends date features to data frame
.reAttDF	Re-attribute df based on previous df
.mergeSalinity	merge salinity into analysis data frame and update iSpec with variable name
lcens-class	Left-censored Data
loadModelsResid	Load Built-in GAM formulas for calculating residuals
loadModels	Load Built-in GAM formulas
importRDB	Import Files
length.lcens	Length of an Object
renderPretty	Label Axes
mdlROS	Estimate Statistics
mean.qw	Arithmetic Mean
importQW	Water-Quality Data
importNWISqw	Water-Quality Data
impute	Impute Censored Values
print.censMCT	Print Results
imputeLessThans	Impute Censored Values
parameterList	Parameter List
residuals.censReg	Extract Model Residuals
seasAdjflow	Create Daily Seasonally-adjusted Log Flow Residuals
is.na.lcens	Missing Values
.checkRange	Check Data Range -- function that checks for allowable values
print.censQuantile	Print Results
rmse	Root-Mean-Squared and Relative Differences
mcenMLE	Estimate Statistics
loadData	Load/Clean CSV and TXT Data File
sal	Salinity data
loadExcel	Load/Clean Excel sheet
setColor	Colors
setGD	Graphics Page
selectData	Select data for analysis from a larger data frame
mcenROS	Estimate Statistics
setPlot	Plot Parameters
month.USGS	Month Abbreviations
na2miss	Recode Data
print.summary.censReg	Print Results
setExplan	Explanation
vif	Variance Inflation Factors
str.lcens	Display Structure
strip.blanks	Remove Spaces
filterWgts	Create filter weights
xyPlot	Plot Data
print.lcens	Print Values
flwAveragePred	Flow Averaged Predictions
gamPlotDisp	Plot censored gam fits vs. time
qw.export	qw.export
pcodeNWISqw	Parameter Code Information
summary.censReg	Summarizing Linear Model Fits
gamTest	Perform GAM analysis
timePlot	Time-series Plots
qw2mcens	Conversion to class "mcens"
qwCoalesce	Replace missing values
lineWt	Line Weights
%cn%	Partial Value Matching
setMargin	Graph Margins
linearPretty	Pretty Axis
mcens-class	Mutliply-censored Data
mdlKM	Estimate Statistics
qw.import	qw.import
setMultiPlot	Plot Parameters
ratio	Compute Ratios
splitQual	Split Leading Qualifiers
stationMasterList	Chesapeake Bay Program long-term tidal monitoring stations
rbindQW	Combine Data by Rows
namePretty	Pretty Axis
numericData	Numeric Values
%~=%	Possible Equality
quantile.lcens	Sample Quantiles
qw-class	Water-quality Data
saveDF	Save R object to disk
usgsGages	USGS Gages
sdlFill	Estimate Statistics
show-censored	Show Methods for WSqw objects
readNWQLdl	Historical Reporting Limits
vcov.censReg	Variance-Covariance Matrix
refLine	Reference Line
[.lcens	Subset an Object
summary.lcens	Summarize Data
sort.lcens	Sorting Vectors
timePretty	Pretty Axis
transData	Transform Data
as.data.frame.lcens	Coerce to a Data Frame
addCaption	Add Caption
analysisOrganizeData	Analysis Organization & Data Preparation
appendDateFeatures	Append Date Features
as.character.lcens	Character Representations
View	Invoke a Data Viewer
add	Add Water-Quality Data
Arith-censored	Arithmetic Methods for lcens, mcens, and qw objects
Math-censored	Mathematical Transform Methods for lcens objects
No Results!

Vignettes of baytrends

Name
data/dataCensored_TEST.csv
baytrends_overview.pdf
create_Seasonally_Detrended_Flow_and_Salinity_Data_Sets.Rmd
statgam_and_chnggam_output_fields.pdf
vignette_qw.Rmd
No Results!

Last month downloads

Details

Type	Package
Date	2019-03-14
License	GPL-3
LazyData	TRUE
RoxygenNote	6.1.1
Encoding	UTF-8
URL	https://github.com/tetratech/baytrends
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

imports	dataRetrieval , digest , gdata , memoise , methods , plyr , survival , XML , zCompositions
suggests	devtools , fitdistrplus , imputeTS , knitr , nlme , pander , readxl , rmarkdown , sessioninfo , testthat
depends	lubridate , mgcv , R (>= 3.2.0)
Contributors	Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik Leppo