## ----setup, echo = FALSE, message=FALSE-------------------

library(knitr)

knitr::opts_chunk$set(echo = TRUE, 
                      warning = FALSE, 
                      message = FALSE, 
                      fig.width=7, fig.height=7)


## ----eval=FALSE-------------------------------------------
# nCores <- detectCores() - coreOut
# cl <- makeCluster(nCores)
# registerDoParallel(cl)
# repAnnual <- foreach(n = 1:nBoot,.packages=c('EGRETci')) %dopar% {
#    annualResults <- bootAnnual(eList,
#                                blockLength,
#                                startSeed = n)
# }
# stopCluster(cl)
# 

## ----setupData, eval=FALSE--------------------------------
# library(EGRET)
# library(EGRETci)
# eList <- Choptank_eList
# pairResults2 <- runPairs(eList, year1 = 1985, year2 = 2010,
#                          windowSide = 7, flowBreak = TRUE,
#                          Q1EndDate = "1995-05-31", wall = TRUE,
#                          sample1EndDate = "1995-05-31",
#                          QStartDate = "1979-10-01",
#                          QEndDate = "2010-09-30",
#                          paStart = 4, paLong = 5)
# 

## ----echo = FALSE-----------------------------------------
library(EGRET)
library(EGRETci)
eList <- Choptank_eList
pairResults2 <- readRDS("pairResults2.rds")

## ----echo=TRUE, eval=FALSE--------------------------------
# bootPairOut2 <- runPairsBoot(eList,
#                              pairResults2,
#                              nBoot = 10)

## ----eval=FALSE-------------------------------------------
# plotHistogramTrend(eList, eBoot, caseSetUp = NA,
#                    flux = TRUE, xMin = NA, xMax = NA,
#                    xStep = NA, printTitle = TRUE,
#                    cex.main = 1.1, cex.axis = 1.1,
#                    cex.lab = 1.1, col.fill = "grey", ...)

## ----echo = FALSE-----------------------------------------
bootPairOut2 <- readRDS("bootPairOut2.rds")

## ----echo = TRUE, eval=FALSE------------------------------
# bootPairOut2 <- runPairsBoot(eList, pairResults2, nBoot = 100)

## ---------------------------------------------------------
plotHistogramTrend(eList,bootPairOut2, caseSetUp = NA)
plotHistogramTrend(eList,bootPairOut2, caseSetUp = NA, flux = FALSE)

## ----eval=FALSE-------------------------------------------
# CIAnnualResults <- ciCalculations(eList,
#                                   startSeed = 494817,
#                                   verbose = TRUE, ...)

## ----setupSeries, eval=FALSE------------------------------
# eList <- Choptank_eList
# eListOut <- runSeries(eList, windowSide = 7, verbose = FALSE)
# CIAnnualResults <- ciCalculations(eListOut,
#                                   verbose = FALSE,
#                                   nBoot = 100,
#                                   blockLength = 200,
#                                   widthCI = 90)

## ----echo = FALSE-----------------------------------------
CIAnnualResults <- readRDS("CIAnnualResults.rds")
eListOut <- readRDS("eListOutSeries.rds")

## ----eval = FALSE-----------------------------------------
# CIAnnualResults <- ciCalculations(eListOut,
#                                   verbose = FALSE,
#                                   nBoot = 100,
#                                   blockLength = 200,
#                                   widthCI = 90)

## ---------------------------------------------------------
plotConcHistBoot(eListOut, CIAnnualResults)
plotFluxHistBoot(eListOut, CIAnnualResults)

## ----echo = TRUE, eval=FALSE------------------------------
# eList <- Choptank_eList
# groupResults <- runGroups(eList,
#                           group1firstYear = 1995, group1lastYear = 2004,
#                           group2firstYear = 2005, group2lastYear = 2010,
#                           windowSide = 7, wall = TRUE,
#                           sample1EndDate = "2004-10-30",
#                           paStart = 4, paLong = 2, verbose = FALSE)
# bootGroupsOut <- runGroupsBoot(eList, groupResults, nBoot = 100)
# 

## ----eval = TRUE, echo=FALSE------------------------------
groupResults <- readRDS("groupResults.rds")
bootGroupsOut <- readRDS("bootGroupsOut.rds")

## ----eval = FALSE-----------------------------------------
# plotHistogramTrend(eList, eBoot, flux = TRUE,
#                          xMin = NA, xMax = NA, xStep = NA,
#                          printTitle = TRUE, cex.main = 1.1,
#                          cex.axis = 1.1, cex.lab = 1.1,
#                          col.fill = "grey")

## ----eval = TRUE------------------------------------------
plotHistogramTrend(eList, bootGroupsOut, 
                   xMin = -30, xMax = 40, xStep = 10)

plotHistogramTrend(eList, bootGroupsOut, 
                   flux=FALSE, xMin = -10,
                   xMax = 50, xStep = 5)

