| analysisOrganizeData | Analysis Organization & Data Preparation |
| appendDateFeatures | Append Date Features |
| baseDay | Base Day |
| baseDay2decimal | Base Day |
| baytrends-package | 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 |
| dectime | Decimal Time |
| dectime2Date | Date Conversion |
| detrended.flow | Create Seasonally Detrended Flow Data Set |
| detrended.salinity | Create Seasonally Detrended Salinty Data Set |
| dot-appendDateFeatures | Appends date features to data frame |
| dot-checkRange | Check Data Range - function that checks for allowable values |
| dot-chkParameter | Reduce dataframe and parameter list based on user selected... |
| dot-ExpLNiCens | Expectation maximization function: Log-normal case, i... |
| dot-ExpLNlCens | Expectation maximization function: Log-normal case, left... |
| dot-ExpLNmCens | Expectation maximization function: Log-normal case, Cens |
| dot-ExpLNrCens | Expectation maximization function: Log-normal case, right... |
| dot-ExpNiCens | Expectation maximization function: Normal case, i censured |
| dot-ExpNlCens | Expectation maximization function: Normal case, left censured |
| dot-ExpNmCens | Expectation maximization function: Normal case |
| dot-ExpNrCens | Expectation maximization function: Normal case, right... |
| dot-F | Print out figure title (customization of pandoc.emphasis and... |
| dot-findFile | Find Recent File Information |
| dot-fmtPval | Format pvalues |
| dot-gamANOVA | Prepare ANOVA table for GAM analysis |
| dot-gamCoeff | Prepare table of coefficients for GAM analysis |
| dot-gamDiffPORtbl | Compute and present report on percent different for... |
| dot-gamPlotCalc | plots data and gam fit vs. time |
| dot-H | Print out header (shortened pandoc.header) |
| dot-H1 | Print out 1st level header (shortened pandoc.header) |
| dot-H2 | Print out 2nd level header (shortened pandoc.header) |
| dot-H3 | Print out 3rd level header (shortened pandoc.header) |
| dot-H4 | Print out 4th level header (shortened pandoc.header) |
| dot-H5 | Print out 5th level header (shortened pandoc.header) |
| dot-initializeResults | #### Initialize stat.gam.result and chng.gam.result |
| dot-mergeFlow | merge flow variable into analysis data frame and update iSpec... |
| dot-mergeSalinity | merge salinity into analysis data frame and update iSpec with... |
| dot-P | Paragraph (customization of pandoc.p) |
| dot-reAttDF | Re-attribute df based on previous df |
| dot-T | Print out table title (customization of pandoc.emphasis and... |
| dot-V | Print out text (blended pandoc.emphasis, .verbatim, and... |
| dot-vTable | Print out character vector table in wrapped mode |
| eventProcessing | Event Processing |
| fillMissing | Fill Missing Values |
| filterWgts | Create filter weights |
| flwAveragePred | Flow Averaged Predictions |
| 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 |
| getUSGSflow | Retrieve USGS daily flow data in a wide format |
| 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 |
| na2miss | Recode Data |
| nobs | Compute the Number of Non-Missing Observations |
| parameterList | Parameter List |
| sal | Salinity data |
| saveDF | Save R object to disk |
| seasAdjflow | Create Daily Seasonally-adjusted Log Flow Residuals |
| 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 |
