## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----initialize,echo=TRUE-----------------------------------------------------
library(baytrends)
## ----usgsgages, echo=FALSE, results='asis'------------------------------------
.T("Chesapeake Bay River Input Monitoring Stations",1,'e')
knitr::kable(usgsGages)
## ----flow, eval=FALSE, results='asis', fig.height=6.5, fig.width=6.5----------
# library(baytrends)
# # Define Function Inputs
# usgsGageID <- usgsGages$usgsGageID # all RIM stations
# siteName <- usgsGages$siteName # all RIM stations
# yearStart <- 1983
# yearEnd <- 2017
# dvAvgWinSel <- c(1, 5, 10, 15, 20, 30, 40, 50, 60, 90, 120, 150, 180, 210)
# dvAvgWgtSel <- "uniform"
# dvAvgSidesSel <- 1
# lowess.f <- 0.2
#
# # Run detrended.flow function
# flow.detrended <- detrended.flow(usgsGageID, siteName, yearStart, yearEnd
# , dvAvgWinSel, dvAvgWgtSel, dvAvgSidesSel
# , lowess.f)
#
# # Save list to data file separate use
# save(flow.detrended, file='mySeasonallyDetrendedFlow.rda')
## ----flow1, eval=TRUE, echo=FALSE, results='asis', fig.height=4.5, fig.width=6.5----
# Define Function Inputs
usgsGageID <- c("01578310")
siteName <- c("Susquehanna River at Conowingo, MD")
yearStart <- 2003 #1983
yearEnd <- 2017
dvAvgWinSel <- c(1, 10)
dvAvgWgtSel <- "uniform"
dvAvgSidesSel <- 1
lowess.f <- 0.2
# Run detrended.flow function
flow.detrended <- detrended.flow(usgsGageID, siteName, yearStart, yearEnd
, dvAvgWinSel, dvAvgWgtSel, dvAvgSidesSel
, lowess.f)
## ----salinity0, echo=FALSE, results='asis'------------------------------------
.T("Example Salinity Data",2,'e')
knitr::kable(head(sal[sal$layer %in% c('S', 'B') , ]),row.names = FALSE)
.T("Data Structure Associated with sal",3,'e')
## ----salinity1, echo=FALSE, results='markup'----------------------------------
str(sal)
## ----salinity2, eval=FALSE, results='asis', fig.height=6.5, fig.width=6.5-----
#
# # Define Function Inputs
# df.sal <- sal
# dvAvgWinSel <- 30
# lowess.f <- 0.2
# minObs <- 40
# minObs.sd <- 10
#
# # Run Function
# salinity.detrended <- detrended.salinity(df.sal, dvAvgWinSel,
# lowess.f, minObs, minObs.sd)
#
# # Save list to data file separate use
# save(salinity.detrended, file='mySeasonallyDetrendedSalinity.rda')
## ----salinity3, eval=TRUE, echo=FALSE, results='asis', fig.height=4.5, fig.width=6.5----
# Define Function Inputs
df.sal <- sal[sal$station=="CB5.4", ]
dvAvgWinSel <- 30
lowess.f <- 0.2
minObs <- 40
minObs.sd <- 10
# Run Function
salinity.detrended <- detrended.salinity(df.sal, dvAvgWinSel, lowess.f, minObs, minObs.sd)
## ----gamTrendExample, eval=TRUE, results='asis', fig.height=3.5, fig.width=6.5----
dfr <- analysisOrganizeData(dataCensored, reports = NA)
df <- dfr[["df"]]
analySpec <- dfr[["analySpec"]]
# down select analyzed GAM
analySpec$gamModels <- analySpec$gamModels[5]
stat = 'CB5.4'; dep = 'tn'; layer = 'S';
gamResult <- gamTest(df = df, dep = dep, stat = stat, layer = layer
, analySpec = analySpec
, salinity.detrended = salinity.detrended)
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