CalSalMod

Table of Contents

• Introduction
• Installation
• Working Example
• Citing package

Introduction

This package contains equations to estimate salinity within the Caloosahatchee River Estuary consistent with the time-series model presented by Qiu and Wan (2013). The model is a simple 1-D model that takes into account measured freshwater inflow via the S-79 structure and un-gauged discharge from the Caloosahatchee tidal basin.

Currently this package just includes the simple salinity model, future versions will include forecasting ability and include an autoregressive term representing the system persistence and an exogenous term accounting for physical drivers.

Qiu C, Wan Y (2013) Time series modeling and prediction of 
salinity in the Caloosahatchee River Estuary. Water Resources 
Research 49:5804–5816. doi: 10.1002/wrcr.20415

Installation

Development version can be installed from this repo.

install.packages("devtools");# if you do not have it installed on your PC
devtools::install_github("SwampThingPaul/CalSalMod")

Working Example

Here is an example of the work flow using this package

#devtools::install_github("SwampThingPaul/AnalystHelper")
library(AnalystHelper)
library(zoo)
library(reshape2)

#devtools::install_github("SwampThingPaul/CalSalMod")
library(CalSalMod)

# Data from SFWMD
dates<-date.fun(c("2020-05-01","2021-04-30"))

# Rainfall and ET
RF.PET.DBKEY<-data.frame(SITE=c("S78W","S79_R"),DBKEY=c("UA637","16414"),param=c("ETPI","RF"))
wx.dat<-DBHYDRO_daily(dates[1],dates[2],RF.PET.DBKEY$DBKEY)
wx.dat<-merge(wx.dat,RF.PET.DBKEY,"DBKEY")

# Cross tab data
wx.dat.xtab<-dcast(wx.dat,Date~param,value.var="Data.Value",mean)
wx.dat.xtab$RF[wx.dat.xtab$RF<0]<-NA; # remove negative values (data issues)
wx.dat.xtab$ETPI[wx.dat.xtab$ETPI<0]<-NA; # remove negative values (data issues)

# 2 Day moving average rainfall
wx.dat.xtab$RF_2d<-with(wx.dat.xtab,c(NA,rollapply(RF,width=2,function(x)mean(x,na.rm=T))))
wx.dat.xtab$RF_2d[1]<-wx.dat.xtab$RF; # replaces first value with 0

wx.dat.xtab$Q.tidebasin<-with(wx.dat.xtab,cost_Q(RF_2d,ETPI))

# S79 Discharge
S79Q<-DBHYDRO_daily(dates[1],dates[2],"00865")

allQ.dat<-merge(wx.dat.xtab[,c("Date","Q.tidebasin")],S79Q[,c("Date","Data.Value")],"Date")
allQ.dat$Q.total<-rowSums(allQ.dat[,c("Q.tidebasin","Data.Value")],na.rm=T)

# Modelled salinity at Fort Myers
allQ.dat$mod.sal<-SalMod(Q.total=allQ.dat$Q.total,SITE="FtMyers")

# Measured Salinity
params<-data.frame(param=c("SPC","WT"),DBKEY=c(88289,88285))
sal.dat<-DBHYDRO_daily(dates[1],dates[2],params$DBKEY)
sal.dat<-merge(sal.dat,params,"DBKEY")

sal.dat.xtab<-dcast(sal.dat,Date~param,value.var="Data.Value",mean)
sal.dat.xtab$WT[sal.dat.xtab$WT<0]<-NA
sal.dat.xtab$sal<-with(sal.dat.xtab,SalinityCalc(SPC,WT))

Citing package

citation('CalSalMod')
#> 
#> To cite package 'CalSalMod' in publications use:
#> 
#>   Paul Julian (2021). CalSalMod: Caloosahatchee Estuary Salinity Model.
#>   R package version 0.1.0. https://github.com/SwampThingPaul/CalSalMod
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {CalSalMod: Caloosahatchee Estuary Salinity Model},
#>     author = {Paul Julian},
#>     year = {2021},
#>     note = {R package version 0.1.0},
#>     url = {https://github.com/SwampThingPaul/CalSalMod},
#>   }

At this time, this package is still under-development and not available on CRAN.

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