# Long Term Water Quality Trend Analysis

## Documentation for package ‘baytrends’ version 2.0.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analysisOrganizeData | Analysis Organization & Data Preparation
baytrends | baytrends: Long Term Water Quality Trend Analysis
closeOut | Document Processing Time and Other Session Time
createResiduals | Calculate GAM residuals
dataCensored | Chesapeake Bay Program Monitoring Data, 1985-2016
detrended.flow | Create Seasonally Detrended Flow Data Set
detrended.salinity | Create Seasonally Detrended Salinty Data Set
gamDiff | Compute an estimate of difference based on GAM results
gamPlotDisp | Plot censored gam fits vs. time
gamPlotDispSeason | Plot censored gam fits vs. time
gamTest | Perform GAM analysis
gamTestSeason | Perform GAM analysis for Specified Season
impute | Impute Censored Values
imputeDF | Impute Censored Values in dataframes
layerAggregation | Aggregate data layers
layerLukup | Layer List
loadData | Load/Clean CSV and TXT Data File
loadExcel | Load/Clean Excel sheet
loadModels | Load Built-in GAM formulas
loadModelsResid | Load Built-in GAM formulas for calculating residuals
makeSurvDF | Convert dataframe to include survival (Surv) objects
nobs | Compute the Number of Non-Missing Observations
parameterList | Parameter List
sal | Salinity data
saveDF | Save R object to disk
selectData | Select data for analysis from a larger data frame
stationMasterList | Chesapeake Bay Program long-term tidal monitoring stations
unSurv | Converts Surv object into a 3-column matrix
unSurvDF | Converts Surv objects in a dataframe to "lo" and "hi" values
usgsGages | USGS Gages