## ----setup, include=FALSE---------------------------------
library(rmarkdown)
options(continue=" ")
options(width=60)
library(knitr)
library(EGRET)
library(EGRETci)
## ----eval=FALSE, echo=TRUE--------------------------------
# library(EGRET)
# library(EGRETci)
# eList <- Choptank_eList
#
# #Interactive function to set up trend analysis:
# caseSetUp <- trendSetUp(eList)
# eBoot <- wBT(eList,caseSetUp,
# fileName = "outputText.txt")
#
# #Interactive save output function:
# saveEGRETci(eList, eBoot, caseSetUp)
#
#
## ----eval=FALSE-------------------------------------------
# library(EGRET)
# library(EGRETci)
# eList <- Choptank_eList
# eList <- setPA(eList, paStart = 12, paLong = 4)
# eList$INFO$windowY <- 10
# eList$INFO$minNumObs <- 50
# caseSetUp <- trendSetUp(eList,
# year1=1990,
# year2=2012,
# nBoot = 50,
# bootBreak = 39,
# blockLength = 200)
# eBoot <- wBT(eList, caseSetUp, fileName ="outputText.txt")
# saveEGRETci(eList, eBoot, caseSetUp, fileName = "output")
## ----, fig.height=6, fig.width=6--------------------------
library(EGRET)
library(EGRETci)
# Example data included in package:
eList <- Choptank_eList # Example data from EGRET package
eBoot <- Choptank_eBoot
caseSetUp <- Choptank_caseSetUp
#Concentration:
plotHistogramTrend(eList, eBoot, caseSetUp,
flux=FALSE, xSeq = seq(-20,60,5))
#Flux
plotHistogramTrend(eList, eBoot, caseSetUp,
flux=TRUE, xSeq = seq(-20,60,5))
## ----, histExampleCombo, fig.width=7, fig.height=4--------
par(mfrow=c(1,2))
plotHistogramTrend(eList, eBoot, caseSetUp, flux=FALSE,
printTitle=FALSE, ylim=c(0,0.07), xSeq=seq(-10,70,10))
plotHistogramTrend(eList, eBoot, caseSetUp, flux=TRUE,
printTitle=FALSE, ylim=c(0,0.07), xSeq=seq(-10,70,10))
# To return to figures printing in 1 row, 1 columns:
par(mfrow=c(1,1))
## ----, eval=FALSE-----------------------------------------
# library(EGRET)
# library(EGRETci)
#
# eList <- Choptank_eList
#
# CIAnnualResults <- ciCalculations(eList)
#
# save(eList,CIAnnualResults, file="CIAnnualResults.RData")
## ----eval=FALSE-------------------------------------------
# CIAnnualResults <- ciCalculations(eList, nBoot = 100, blockLength = 200, widthCI = 90)
## ----, eval=FALSE-----------------------------------------
# library(foreach)
# library(doParallel)
# library(iterators)
# library(EGRET)
# library(EGRETci)
#
# eList <- Choptank_eList
# eList <- modelEstimation(eList)
#
# nBoot <- 100
# blockLength <- 200
# coreOut <- 1 #Number of cores to leave out of processing tasks
#
# widthCI <- 90
# ciLower <- (50-(widthCI/2))/100
# ciUpper <- (50+(widthCI/2))/100
# probs <- c(ciLower,ciUpper)
#
# nCores <- detectCores() - coreOut
# cl <- makeCluster(nCores)
# registerDoParallel(cl)
# repAnnual <- foreach(n = 1:nBoot,.packages=c('EGRETci')) %dopar% {
# annualResults <- bootAnnual(eList, blockLength)
# }
# stopCluster(cl)
#
# # save(repAnnualResults, file="repAnnual.RData")
#
# CIAnnualResults <- ciBands(eList, repAnnual, probs)
# save(eList,CIAnnualResults, file="CIAnnualResults.RData")
#
## ----, fig.height=5, fig.width=7--------------------------
eList <- Choptank_eList
CIAnnualResults <- Choptank_CIAnnualResults
plotConcHistBoot(eList, CIAnnualResults)
plotFluxHistBoot(eList, CIAnnualResults)
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