gamTestSeason: Perform GAM analysis for Specified Season

In leppott/baytrends: Long Term Water Quality Trend Analysis

Perform GAM analysis for Specified Season

Description

Perform GAM analysis for Specified Season. Relies on mgcv::gam to perform general additive model.

Usage

gamTestSeason(
  df,
  dep,
  stat,
  layer = NA,
  analySpec,
  gamTable = TRUE,
  gamPlot = 10,
  gamDiffModel = c(2),
  flow.detrended = NA,
  salinity.detrended = NA,
  gamSeasonPlot = c("7/1-9/30", "purple", "range")
)

Arguments

df	data frame
dep	dependent variable
stat	station
layer	layer
analySpec	analytical specifications
gamTable	gam table setting (set to FALSE to turn off table output)
gamPlot	gam plot setting (set to FALSE to turn off plotting)
gamDiffModel	GAM model(s) used for computing differences on sub-annual/multi-period basis
flow.detrended	data generated by detrended.flow. Default = NA.
salinity.detrended	data generated by detrended.flow. Default = NA.
gamSeasonPlot	Character vector for evaluating and displaying seasonal model (see details for further information).

Details

gamSeasonPlot is an additional argument (relative to the arguments used in the gamTest function) that is used to target a specific season for the focus of output and can be a 2- or 3-element vector. While the GAM is fit to all data as in the function gamTest, the output figure will only show the model corresponding to the gamSeasonPlot specifications. The first element of gamSeasonPlot can be a single date (e.g., ‘8/28’) or a date range (e.g., ‘7/1-9/30’). The second element specifies the color of the line to be plotted. If a date range is specified as the first element and an optional third element is provided as ‘range’, then the plot will show the season minimum and maximum as well as the mean; otherwise, only the mean is plotted. If the first element of gamSeasonPlot is a single date then observations within a +/- 15-day window of the date are plotted; otherwise, only observations within the date range are plotted. Estimates of difference are computed with baytrends::gamDiff by setting the argument doy.set to either the single date provided from gamSeasonPlot or the same doys used to compute the season mean. The option to specify seasons that "wrap" around end of year, i.e., 12/1-1/30, has not been implemented.

Value

Returns a list with results

See Also

gamTest

Examples

## Not run: 
# Specify parameter and station to analyze
dep        <- 'do'
stat       <- 'CB5.4'
layer      <- 'B'

# Prepare data and set up specifications for analysis
dfr <- analysisOrganizeData (dataCensored)
df        <- dfr[[1]]
analySpec <- dfr[[2]]

# Apply gamTest 
gamResult <- gamTest(df, dep, stat, layer, analySpec=analySpec)
gamPlotDisp(gamResult = gamResult, analySpec = analySpec,
            fullModel = 2, seasAvgModel = 2, seasonalModel = 2,
            diffType = "regular", obserPlot = TRUE, interventionPlot = TRUE,
            seasAvgPlot = TRUE, seasAvgConfIntPlot = FALSE,
            seasAvgSigPlot = FALSE, fullModelPlot = TRUE, seasModelPlot = TRUE,
            BaseCurrentMeanPlot = FALSE, adjustedPlot = FALSE)

# Apply gamTestSeason
gamResult2 <- gamTestSeason(df, dep, stat, layer, analySpec=analySpec,
                            gamSeasonPlot = c("7/15-8/15", "purple", "range"))
gamPlotDispSeason(gamResult = gamResult2, analySpec = analySpec,
                  fullModel = 2, seasAvgModel = 2, seasonalModel = 2,
                  diffType = "regular", obserPlot = TRUE, interventionPlot = TRUE,
                  seasAvgPlot = TRUE, seasAvgConfIntPlot = FALSE,
                  seasAvgSigPlot = FALSE, fullModelPlot = FALSE, seasModelPlot = FALSE,
                  BaseCurrentMeanPlot = TRUE, adjustedPlot = FALSE, gamSeasonFocus = TRUE)

## End(Not run)     

leppott/baytrends documentation built on Nov. 2, 2024, 6:42 p.m.